| ▼ src | |
| ► protocols | |
| ► abinitio | |
| ► abscript | |
| AbscriptLoopCloserCM.cc | |
| AbscriptLoopCloserCM.fwd.hh | Definition of the AbscriptLoopCloserCM class |
| AbscriptLoopCloserCM.hh | |
| AbscriptLoopCloserCMCreator.hh | |
| AbscriptMover.cc | |
| AbscriptMover.fwd.hh | Definition of the AbscriptMover class |
| AbscriptMover.hh | |
| AbscriptMoverCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| AbscriptStageMover.cc | |
| AbscriptStageMover.fwd.hh | Definition of the AbscriptStageMover class |
| AbscriptStageMover.hh | |
| ConstraintPreparer.cc | |
| ConstraintPreparer.fwd.hh | Definition of the ConstraintPreparer class |
| ConstraintPreparer.hh | |
| ConstraintPreparerCreator.hh | This class will create instances of Mover ConstraintPreparer for the MoverFactory |
| FragmentCM.cc | |
| FragmentCM.fwd.hh | Definition of the FragmentCM class |
| FragmentCM.hh | |
| FragmentCMCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| FragmentJumpCM.cc | |
| FragmentJumpCM.fwd.hh | Definition of the FragmentJumpCM class |
| FragmentJumpCM.hh | |
| FragmentJumpCMCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| JumpSampleData.cc | |
| JumpSampleData.fwd.hh | Definition of the JumpSampleData class |
| JumpSampleData.hh | |
| JumpSampleDataCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| RigidChunkCM.cc | |
| RigidChunkCM.fwd.hh | Definition of the RigidChunkCMCM class |
| RigidChunkCM.hh | |
| RigidChunkCMCreator.hh | This class will create instances of Mover RigidChunk for the MoverFactory |
| StageID.hh | |
| StagePreparer.cc | |
| StagePreparer.fwd.hh | Definition of the StagePreparer class |
| StagePreparer.hh | |
| StructPerturberCM.cc | |
| StructPerturberCM.fwd.hh | Definition of the StructPerturberCMCM class |
| StructPerturberCM.hh | |
| StructPerturberCMCreator.hh | This class will create instances of Mover StructPerturber for the MoverFactory |
| AbrelaxApplication.cc | |
| AbrelaxApplication.hh | Application-level code for Abrelax, fold_cst and JumpingFoldCst protocols |
| AbrelaxMover.cc | |
| AbrelaxMover.fwd.hh | |
| AbrelaxMover.hh | This class will be handled to a SampleProtocol as a control instance |
| AllResiduesChanged.hh | |
| BrokerMain.cc | |
| BrokerMain.hh | |
| ClassicAbinitio.cc | Ab-initio fragment assembly protocol for proteins |
| ClassicAbinitio.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ClassicAbinitio.hh | Header file for ClassicAbinitio protocol |
| ConstraintFragmentSampler.cc | Ab-initio fragment assembly protocol for proteins |
| ConstraintFragmentSampler.hh | Header file for ConstraintFragmentSampler protocol |
| DomainAssembly.cc | |
| DomainAssembly.hh | |
| DomainAssemblyCreator.hh | Declaration of the MoverCreator class for the DomainAssembly |
| DoubleLayerKinematicAbinitio.cc | This class will be handled to a SampleProtocol as a control instance |
| DoubleLayerKinematicAbinitio.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| DoubleLayerKinematicAbinitio.hh | This class will be handled to a SampleProtocol as a control instance |
| FoldConstraints.cc | Ab-initio fragment assembly protocol for proteins under the influence of contraints (e.g., NOE) |
| FoldConstraints.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FoldConstraints.hh | |
| FragmentSampler.cc | Ab-initio fragment assembly protocol for proteins |
| FragmentSampler.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FragmentSampler.hh | Header file for FragmentSampler protocol |
| HedgeArchive.cc | Iterative protocol starting with ab initio and getting progressively more concerned with full-atom relaxed structures |
| HedgeArchive.fwd.hh | |
| HedgeArchive.hh | |
| IterativeAbrelax.cc | Iterative protocol starting with abinitio and getting progressively more concerned with full-atom relaxed structures |
| IterativeAbrelax.hh | This class will be handled to a SampleProtocol as a control instance |
| IterativeBase.cc | Iterative protocol starting with abinitio and getting progressively more concerned with full-atom relaxed structures |
| IterativeBase.hh | |
| IterativeCentroid.cc | Iterative protocol starting with abinitio and getting progressively more concerned with full-atom relaxed structures |
| IterativeCentroid.hh | This class will be handled to a SampleProtocol as a control instance |
| IterativeFullatom.cc | Iterative protocol starting with abinitio and getting progressively more concerned with full-atom relaxed structures |
| IterativeFullatom.hh | This class will be handled to a SampleProtocol as a control instance |
| KinematicAbinitio.cc | Ab-initio fragment assembly protocol for proteins under the influence of contraints (e.g., NOE) |
| KinematicAbinitio.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| KinematicAbinitio.hh | Abinitio - Type sampling controlled by KinematicControl object |
| KinematicControl.cc | |
| KinematicControl.fwd.hh | |
| KinematicControl.hh | This class will be handled to a SampleProtocol as a control instance |
| KinematicTaskControl.cc | This class will be handled to a SampleProtocol as a control instance |
| KinematicTaskControl.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| KinematicTaskControl.hh | This class will be handled to a SampleProtocol as a control instance |
| LoopJumpFoldCst.cc | This class will be handled to a SampleProtocol as a control instance |
| LoopJumpFoldCst.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| LoopJumpFoldCst.hh | This class will be handled to a SampleProtocol as a control instance |
| MembraneAbinitio.cc | Ab-initio fragment assembly protocol for membrane proteins |
| MembraneAbinitio.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| MembraneAbinitio.hh | Header file for MembraneAbinitio protocol |
| PairingStatistics.cc | |
| PairingStatistics.fwd.hh | |
| PairingStatistics.hh | |
| Protocol.cc | |
| Protocol.fwd.hh | |
| Protocol.hh | Initialization protocols for relax |
| ResolutionSwitcher.cc | This class will be handled to a SampleProtocol as a control instance |
| ResolutionSwitcher.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ResolutionSwitcher.hh | Initialization protocols for relax |
| StrandConstraints.cc | |
| StrandConstraints.hh | |
| Template.cc | |
| Template.fwd.hh | |
| Template.hh | |
| TemplateJumpSetup.cc | |
| TemplateJumpSetup.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| TemplateJumpSetup.hh | |
| Templates.cc | |
| Templates.fwd.hh | |
| Templates.hh | |
| vs_test.cc | |
| vs_test.hh | |
| ► analysis | |
| InterfaceAnalyzerMover.cc | InterfaceAnalyzerMover implementation - class for in-depth interface quality analysis |
| InterfaceAnalyzerMover.fwd.hh | Fwd declaration for InterfaceAnalyzer: intense analysis of interface quality |
| InterfaceAnalyzerMover.hh | InterfaceAnalyzerMover examines interface structures and packages extra scores into a Job object |
| InterfaceAnalyzerMoverCreator.hh | This class will create instances of Mover InterfaceAnalyzerMover for the MoverFactory |
| LoopAnalyzerMover.cc | LoopAnalyzerMover implementation - class for in-depth loop structure quality analysis |
| LoopAnalyzerMover.fwd.hh | Fwd declaration for LoopAnalyzer: intense analysis of loop quality |
| LoopAnalyzerMover.hh | LoopAnalyzerMover examines loop structures and packages extra scores into a Job object |
| PackStatMover.cc | |
| PackStatMover.fwd.hh | Created on: Jan 25, 2012 |
| PackStatMover.hh | |
| PeptideDeriverFilter.cc | A filter that, for each dimer in a pose, outputs the peptide which contributes most to the interface |
| PeptideDeriverFilter.fwd.hh | A filter that, for each dimer in a pose, outputs the peptide which contributes most to the interface |
| PeptideDeriverFilter.hh | A filter that, for each dimer in a pose, outputs the peptide which contributes most to the interface |
| PeptideDeriverFilterCreator.cc | Creator class for PeptideDeriverFilterCreator |
| PeptideDeriverFilterCreator.fwd.hh | Creator class for PeptideDeriverFilterCreator |
| PeptideDeriverFilterCreator.hh | Creator class for PeptideDeriverFilterCreator |
| ► anchored_design | |
| Anchor.cc | Anchor methods implemented |
| Anchor.fwd.hh | Anchor classes forward declarations header |
| Anchor.hh | Header for Anchor |
| AnchorMovers.cc | Anchored design movers (protocol-level, perturb, refine) |
| AnchorMovers.fwd.hh | Anchor Movers forward declarations header |
| AnchorMovers.hh | Protocol-level outermost movers for anchored design; wraps a set of other moves |
| AnchorMoversData.cc | AnchorMoversData methods implemented |
| AnchorMoversData.fwd.hh | Anchor classes forward declarations header |
| AnchorMoversData.hh | Header for AnchorMoversData |
| ► antibody | |
| ► clusters | |
| CDRCluster.cc | Simple class to hold and access CDRCluster information of a region in a pose |
| CDRCluster.fwd.hh | |
| CDRCluster.hh | Simple class to hold and access CDRcluster info at a region in the pose. Construct in CDRClusterSet |
| CDRClusterEnum.hh | Enumerators for antibody clusters |
| CDRClusterEnumManager.cc | |
| CDRClusterEnumManager.fwd.hh | |
| CDRClusterEnumManager.hh | Functions for CDRClusterEnums |
| CDRClusterFeatures.cc | |
| CDRClusterFeatures.fwd.hh | |
| CDRClusterFeatures.hh | FeaturesReporter for North/Dunbrack Cannonical CDRClusters |
| CDRClusterFeaturesCreator.cc | |
| CDRClusterFeaturesCreator.hh | |
| CDRClusterMatcher.cc | Simple class for identifying CDR cluster in an antibody |
| CDRClusterMatcher.fwd.hh | |
| CDRClusterMatcher.hh | Simple class for identifying CDR clusters of an antibody |
| CDRClusterSet.cc | |
| CDRClusterSet.fwd.hh | |
| CDRClusterSet.hh | Functions for CDRClusterEnums |
| util.cc | |
| util.hh | |
| ► constraints | |
| ParatopeEpitopeSiteConstraintMover.cc | |
| ParatopeEpitopeSiteConstraintMover.fwd.hh | |
| ParatopeEpitopeSiteConstraintMover.hh | Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope |
| ParatopeSiteConstraintMover.cc | |
| ParatopeSiteConstraintMover.fwd.hh | |
| ParatopeSiteConstraintMover.hh | Adds and removes ambiguos site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs |
| util.cc | |
| util.hh | |
| ► database | |
| AntibodyDatabaseManager.cc | Handles all loading of CDR, Framework, and cluster/dmap info from external database file |
| AntibodyDatabaseManager.fwd.hh | Handles all loading of CDR, Framework, and cluster/dmap info from database file |
| AntibodyDatabaseManager.hh | Handles all loading of CDR, Framework, and cluster/dmap info from external database file |
| CDRSetOptions.cc | Create and hold AntibodyCDRSetInstructions for the graft design step |
| CDRSetOptions.fwd.hh | |
| CDRSetOptions.hh | Create and hold AntibodyCDRSetInstructions for the graft design step |
| CDRSetOptionsParser.cc | |
| CDRSetOptionsParser.fwd.hh | |
| CDRSetOptionsParser.hh | |
| ► design | |
| AntibodyDesignEnum.hh | Antibody Design enumerators |
| AntibodyDesignModeler.cc | Handles modeling of the antibody. Before and after design |
| AntibodyDesignModeler.fwd.hh | |
| AntibodyDesignModeler.hh | Handles modeling of the antibody. Before, after, and during design |
| AntibodyDesignMover.cc | Handles the Antibody Design Protocol |
| AntibodyDesignMover.fwd.hh | Handles all loading of CDR, Framework, and cluster/dmap info from database file |
| AntibodyDesignMover.hh | Handles the Antibody Design Protocol |
| AntibodyDesignMoverGenerator.cc | Handles modeling of the antibody. Before and after design |
| AntibodyDesignMoverGenerator.fwd.hh | |
| AntibodyDesignMoverGenerator.hh | Handles modeling of the antibody. Before, after, and during design |
| AntibodyGraftDesignMover.cc | Class that initially designs antibodies through grafting using an AntibodyDatabase + North_AHO numbering scheme |
| AntibodyGraftDesignMover.fwd.hh | |
| AntibodyGraftDesignMover.hh | Class that initially designs antibodies through grafting using an AntibodyDatabase + North_AHO numbering scheme |
| AntibodySeqDesignMover.cc | |
| AntibodySeqDesignMover.fwd.hh | |
| AntibodySeqDesignMover.hh | Mover class that designs cdrs using a number of different strategies |
| AntibodySeqDesignTFCreator.cc | Class for generating TaskFactories and TaskOperations for antibody design from a set of options |
| AntibodySeqDesignTFCreator.fwd.hh | |
| AntibodySeqDesignTFCreator.hh | Class for creating a TaskFactory from SeqDesignOptions for use in various protocols |
| CDRGraftDesignOptions.cc | |
| CDRGraftDesignOptions.fwd.hh | |
| CDRGraftDesignOptions.hh | GraftDesign options class and parser |
| CDRSeqDesignOptions.cc | |
| CDRSeqDesignOptions.fwd.hh | |
| CDRSeqDesignOptions.hh | Option control for Sequence Design of a single CDR |
| ConservativeDesignOperation.cc | TaskOperation to allow only conservative mutations at designable residues |
| ConservativeDesignOperation.fwd.hh | |
| ConservativeDesignOperation.hh | TaskOperation to allow only conservative mutations at designable residues |
| ConservativeDesignOperationCreator.hh | |
| ResidueProbDesignOperation.cc | |
| ResidueProbDesignOperation.fwd.hh | |
| ResidueProbDesignOperation.hh | Uses a probability distribution to sample allowed residues at a position, adding those types to the packer - only if they are designable |
| ResidueProbDesignOperationCreator.hh | |
| util.cc | |
| util.hh | Utility functions for antibody design namespace |
| ► snugdock | |
| SnugDock.cc | Dock and antigen to an antibody while optimizing the rigid body orientation of the VH and VL chains and performing CDR loop minimization |
| SnugDock.fwd.hh | Forward declaration |
| SnugDock.hh | Dock and antigen to an antibody while optimizing the rigid body orientation of the VH and VL chains and performing CDR loop minimization |
| SnugDockProtocol.cc | Dock and antigen to an antibody while optimizing the rigid body orientation of the VH and VL chains and performing CDR loop minimization |
| SnugDockProtocol.fwd.hh | Forward declaration |
| SnugDockProtocol.hh | Dock and antigen to an antibody while optimizing the rigid body orientation of the VH and VL chains and performing CDR loop minimization |
| Ab_TemplateInfo.cc | Grafts a cdr onto the template of an antibody framework |
| Ab_TemplateInfo.fwd.hh | Grafts a cdr onto the template of an antibody framework |
| Ab_TemplateInfo.hh | Grafts a cdr onto the template of an antibody framework |
| AntibodyEnum.hh | Enumerators + TypeDefs for Antibody namespace |
| AntibodyEnumManager.cc | Functions for AntibodyEnumerators |
| AntibodyEnumManager.fwd.hh | |
| AntibodyEnumManager.hh | Functions for AntibodyEnumerators |
| AntibodyFeatures.cc | |
| AntibodyFeatures.fwd.hh | |
| AntibodyFeatures.hh | |
| AntibodyFeaturesCreator.cc | |
| AntibodyFeaturesCreator.hh | |
| AntibodyInfo.cc | Class for getting antibody-specific objects and information |
| AntibodyInfo.fwd.hh | AntibodyInfo class forward declarations header |
| AntibodyInfo.hh | Class for getting antibody-specific objects and information |
| AntibodyModelerProtocol.cc | Build a homology model of an antibody |
| AntibodyModelerProtocol.fwd.hh | Forward declaration |
| AntibodyModelerProtocol.hh | Build a homology model of an antibody |
| AntibodyNumberingParser.cc | |
| AntibodyNumberingParser.fwd.hh | |
| AntibodyNumberingParser.hh | Read Antibody Numbering schemes and transform info from the database |
| CDRsMinPackMin.cc | Build a homology model of an antibody |
| CDRsMinPackMin.fwd.hh | Forward declaration |
| CDRsMinPackMin.hh | Main CDR minimization method in protocols/antibody |
| CloseOneCDRLoop.cc | Grafts a cdr onto the template of an antibody framework |
| CloseOneCDRLoop.fwd.hh | |
| CloseOneCDRLoop.hh | |
| GraftCDRLoopsProtocol.cc | Build a homology model of an antibody |
| GraftCDRLoopsProtocol.fwd.hh | Forward declaration |
| GraftCDRLoopsProtocol.hh | Build a homology model of an antibody |
| GraftedStemOptimizer.cc | Optimize the CDR Grafted stem |
| GraftedStemOptimizer.fwd.hh | |
| GraftedStemOptimizer.hh | Optimize the CDR Grafted stem |
| GraftOneCDRLoop.cc | Grafts a cdr onto the template of an antibody framework |
| GraftOneCDRLoop.fwd.hh | |
| GraftOneCDRLoop.hh | Grafts a cdr onto the template of an antibody framework |
| H3CterInsert.cc | Build a homology model of an antibody |
| H3CterInsert.fwd.hh | Build a homology model of an antibody |
| H3CterInsert.hh | Build a homology model of an antibody |
| H3PerturbCCD.cc | Build a homology model of an antibody |
| H3PerturbCCD.fwd.hh | Forward declaration |
| H3PerturbCCD.hh | Build a homology model of an antibody |
| H3RefineCCD.cc | Build a homology model of an antibody |
| H3RefineCCD.fwd.hh | Forward declaration |
| H3RefineCCD.hh | Build a homology model of an antibody |
| LHRepulsiveRamp.cc | Build a homology model of an antibody |
| LHRepulsiveRamp.fwd.hh | Forward declaration |
| LHRepulsiveRamp.hh | Build a homology model of an antibody |
| metrics.cc | Routines to measure antibodies |
| metrics.hh | Routines to measure antibodies |
| ModelCDRH3.cc | Models CDR H3 loop using loop modeling |
| ModelCDRH3.fwd.hh | Build a homology model of an antibody |
| ModelCDRH3.hh | |
| RefineBetaBarrel.cc | Build a homology model of an antibody |
| RefineBetaBarrel.fwd.hh | Forward declaration |
| RefineBetaBarrel.hh | Build a homology model of an antibody |
| RefineOneCDRLoop.cc | Build a homology model of an antibody |
| RefineOneCDRLoop.fwd.hh | Forward declaration |
| RefineOneCDRLoop.hh | Build a homology model of an antibody |
| RefineOneCDRLoopCentroid.cc | Build a homology model of an antibody |
| RefineOneCDRLoopCentroid.fwd.hh | Forward declaration |
| RefineOneCDRLoopCentroid.hh | Build a homology model of an antibody |
| util.cc | |
| util.hh | Utility functions for the Antibody namespace |
| ► antibody_legacy | |
| AntibodyClass.cc | |
| AntibodyClass.fwd.hh | Antibody class forward declarations header |
| AntibodyClass.hh | |
| AntibodyModeler.cc | |
| AntibodyModeler.fwd.hh | Forward declaration |
| AntibodyModeler.hh | Build a homology model of an antibody |
| CDRH3Modeler.cc | Models CDR H3 loop using loop modeling |
| CDRH3Modeler.hh | |
| GraftMover.cc | Grafts a cdr onto the template of an antibody framework |
| GraftMover.hh | |
| LHRepulsiveRampLegacy.cc | Build a homology model of an antibody |
| LHRepulsiveRampLegacy.fwd.hh | Forward declaration |
| LHRepulsiveRampLegacy.hh | Build a homology model of an antibody |
| LHSnugFitLegacy.cc | Build a homology model of an antibody |
| LHSnugFitLegacy.fwd.hh | Forward declaration |
| LHSnugFitLegacy.hh | Build a homology model of an antibody |
| Ubiquitin_E2C_Modeler.cc | |
| Ubiquitin_E2C_Modeler.fwd.hh | Forward declaration |
| Ubiquitin_E2C_Modeler.hh | Build model for di-ubiquitin and e2c enzyme complex |
| ► backrub | |
| BackrubMover.cc | Implementation of BackrubMover class and functions |
| BackrubMover.fwd.hh | |
| BackrubMover.hh | Definition of BackrubMover class and functions |
| BackrubMoverCreator.hh | This class will create instances of Mover BackrubMover for the MoverFactory |
| BackrubSegment.cc | Implmentation of BackrubSegment class |
| BackrubSegment.hh | Definition/implmentation of BackrubSegment class |
| BackrubSidechainMover.cc | BackrubSidechainMover methods implemented |
| BackrubSidechainMover.fwd.hh | BackrubSidechainMover forward declarations header |
| BackrubSidechainMover.hh | |
| BackrubSidechainMoverCreator.hh | This class will create instances of Mover BackrubSidechainMover for the MoverFactory |
| ► boinc | |
| boinc.cc | Wrappers to make BOINC work |
| boinc.hh | Wrappers to make BOINC work |
| boinc_shmem.hh | Boinc shared memory structure for graphics |
| BoincPoseObserver.cc | BoincPoseObserver class |
| BoincPoseObserver.fwd.hh | |
| BoincPoseObserver.hh | BoincPoseObserver class |
| util.cc | Utility functions for filtering boinc outputs |
| util.hh | Utility functions for filtering boinc outputs |
| watchdog.cc | |
| watchdog.hh | |
| ► branch_angle | |
| BranchAngleOptimizer.cc | Implementation of BranchAgnleOptimizer methods |
| BranchAngleOptimizer.fwd.hh | BranchAngleOptimizer class forward declaration |
| BranchAngleOptimizer.hh | Definition of BranchAgnleOptimizer class and methods |
| BranchCoef1.fwd.hh | BranchCoef1 class forward declaration |
| BranchCoef1.hh | Definition/implementation of BranchCoef1 class and methods |
| BranchCoef2.fwd.hh | BranchCoef2 class forward declaration |
| BranchCoef2.hh | Definition/implementation of BranchCoef2 class and methods |
| BranchParam1.fwd.hh | BranchParam1 class forward declaration |
| BranchParam1.hh | Definition/implementation of BranchParam1 class and methods |
| BranchParam2.fwd.hh | BranchParam2 class forward declaration |
| BranchParam2.hh | Definition/implementation of BranchParam2 class and methods |
| ► canonical_sampling | |
| ► mc_convergence_checks | |
| Heat_ConvergenceCheck.hh | |
| HierarchicalLevel.cc | |
| HierarchicalLevel.fwd.hh | |
| HierarchicalLevel.hh | |
| HPool.cc | Hierarchical pool |
| HPool.fwd.hh | Hierarchical pool |
| HPool.hh | Hierarchical pool |
| MPIBPool_ConvergenceCheck.cc | |
| MPIBPool_ConvergenceCheck.fwd.hh | |
| MPIBPool_ConvergenceCheck.hh | |
| MPIHPool_ConvergenceCheck.cc | |
| MPIHPool_ConvergenceCheck.fwd.hh | |
| MPIHPool_ConvergenceCheck.hh | |
| MPIPool_ConvergenceCheck.cc | |
| MPIPool_ConvergenceCheck.fwd.hh | |
| MPIPool_ConvergenceCheck.hh | |
| Pool_ConvergenceCheck.cc | |
| Pool_ConvergenceCheck.hh | |
| pool_util.cc | |
| pool_util.hh | |
| util.cc | |
| util.hh | |
| AsyncMPITemperingBase.cc | AsyncMPITemperingBase methods implemented |
| AsyncMPITemperingBase.hh | |
| BiasedMonteCarlo.cc | BiasedMonteCarlo methods implemented |
| BiasedMonteCarlo.fwd.hh | |
| BiasedMonteCarlo.hh | |
| BiasEnergy.cc | BiasEnergy methods implemented |
| BiasEnergy.fwd.hh | |
| BiasEnergy.hh | |
| BiasEnergy.tmpl.hh | BiasEnergy methods implemented |
| CanonicalSamplingApplication.cc | |
| CanonicalSamplingApplication.hh | |
| CanonicalSamplingMover.cc | |
| CanonicalSamplingMover.fwd.hh | |
| CanonicalSamplingMover.hh | |
| DbTrajectoryReader.cc | |
| DbTrajectoryReader.fwd.hh | |
| DbTrajectoryReader.hh | |
| DbTrajectoryRecorder.cc | |
| DbTrajectoryRecorder.fwd.hh | |
| DbTrajectoryRecorder.hh | |
| DbTrajectoryRecorderCreator.hh | This class will create instances of Mover DbTrajectoryRecorder for the MoverFactory |
| HamiltonianExchange.cc | HamiltonianExchange methods implemented |
| HamiltonianExchange.fwd.hh | |
| HamiltonianExchange.hh | Implement replica exchange in the MetropolisHastingsMover Framework |
| HamiltonianExchangeCreator.hh | This class will create instances of Mover HamiltonianExchange for the MoverFactory |
| MetricRecorder.cc | |
| MetricRecorder.fwd.hh | Forward declarations for class MetricRecorder |
| MetricRecorder.hh | |
| MetricRecorderCreator.hh | This class will create instances of Mover MetricRecorder for the MoverFactory |
| MetropolisHastingsMover.cc | MetropolisHastingsMover methods implemented |
| MetropolisHastingsMover.fwd.hh | MetropolisHastingsMover forward declarations header |
| MetropolisHastingsMover.hh | |
| MetropolisHastingsMoverCreator.hh | This class will create instances of Mover MetropolisHastingsMover for the MoverFactory |
| MultiTemperatureTrialCounter.cc | |
| MultiTemperatureTrialCounter.hh | |
| ParallelTempering.cc | ParallelTempering methods implemented |
| ParallelTempering.fwd.hh | |
| ParallelTempering.hh | Implement replica exchange in the MetropolisHastingsMover Framework |
| ParallelTemperingCreator.hh | This class will create instances of Mover ParallelTempering for the MoverFactory |
| PDBTrajectoryRecorder.cc | |
| PDBTrajectoryRecorder.fwd.hh | Forward declarations for class TrajectoryRecorder |
| PDBTrajectoryRecorder.hh | |
| PDBTrajectoryRecorderCreator.hh | This class will create instances of Mover PDBTrajectoryRecorder for the MoverFactory |
| ProgressBarObserver.cc | |
| ProgressBarObserver.fwd.hh | |
| ProgressBarObserver.hh | |
| ProgressBarObserverCreator.hh | |
| readme.hh | |
| SidechainMetropolisHastingsMover.cc | SidechainMetropolisHastingsMover methods implemented |
| SidechainMetropolisHastingsMover.fwd.hh | MetropolisHastingsMover forward declarations header |
| SidechainMetropolisHastingsMover.hh | |
| SidechainMetropolisHastingsMoverCreator.hh | This class will create instances of Mover SidechainMetropolisHastingsMover for the MoverFactory |
| SilentTrajectoryRecorder.cc | |
| SilentTrajectoryRecorder.fwd.hh | Forward declarations for class SilentTrajectoryRecorder |
| SilentTrajectoryRecorder.hh | |
| SilentTrajectoryRecorderCreator.hh | This class will create instances of Mover SilentTrajectoryRecorder for the MoverFactory |
| SimulatedTempering.cc | SimulatedTempering methods implemented |
| SimulatedTempering.fwd.hh | |
| SimulatedTempering.hh | |
| SimulatedTemperingCreator.hh | This class will create instances of Mover SimulatedTempering for the MoverFactory |
| TemperatureController.cc | TemperatureController methods implemented |
| TemperatureController.fwd.hh | |
| TemperatureController.hh | |
| TemperingBase.cc | TemperingBase methods implemented |
| TemperingBase.fwd.hh | |
| TemperingBase.hh | |
| ThermodynamicMover.cc | ThermodynamicMover methods implemented |
| ThermodynamicMover.fwd.hh | ThermodynamicMover forward declarations header |
| ThermodynamicMover.hh | |
| ThermodynamicObserver.cc | ThermodynamicObserver methods implemented |
| ThermodynamicObserver.fwd.hh | ThermodynamicObserver forward declarations header |
| ThermodynamicObserver.hh | |
| TrajectoryRecorder.cc | |
| TrajectoryRecorder.fwd.hh | Forward declarations for class TrajectoryRecorder |
| TrajectoryRecorder.hh | |
| TrialCounterObserver.cc | Protocols::canonical_sampling::TrialCounterObserver methods implemented |
| TrialCounterObserver.hh | |
| TrialCounterObserverCreator.hh | This class will create instances of Mover TrialCounterObserver for the MoverFactory |
| WTEBiasEnergy.cc | WTEBiasEnergy methods implemented |
| WTEBiasEnergy.hh | |
| ► cartesian | |
| md.cc | |
| md.hh | Atom tree minimization functions |
| ► checkpoint | |
| Checkpoint.cc | |
| Checkpoint.fwd.hh | |
| Checkpoint.hh | |
| CheckPointer.cc | |
| CheckPointer.fwd.hh | |
| CheckPointer.hh | Application-level code for Abrelax, fold_cst and JumpingFoldCst protocols |
| ► cluster | |
| APCluster.cc | |
| APCluster.fwd.hh | |
| APCluster.hh | |
| cluster.cc | |
| cluster.hh | |
| ► coarse_rna | |
| CoarseRNA_DeNovoProtocol.cc | Protocols that are specific to CoarseRNA_DeNovoProtocol |
| CoarseRNA_DeNovoProtocol.hh | |
| CoarseRNA_Fragments.cc | Protocols that are specific to RNA_Fragments |
| CoarseRNA_Fragments.hh | |
| CoarseRNA_LoopCloser.cc | Protocols that are specific to CoarseRNA_LoopCloser |
| CoarseRNA_LoopCloser.fwd.hh | Pose forward declarations header |
| CoarseRNA_LoopCloser.hh | |
| ► comparative_modeling | |
| ► features | |
| ResidueFeature.cc | Abstract base class for per-residue features used in comparative modeling |
| ResidueFeature.fwd.hh | Forward declaration for ResidueFeature class |
| ResidueFeature.hh | Abstract base class for per-residue features used in comparative modeling |
| ResidueFeatureFactory.cc | Factory for creating various types of ResidueFeatures |
| ResidueFeatureFactory.hh | Factory for creating various types of constraints |
| SSFeature.cc | |
| SSFeature.fwd.hh | Forward declaration for SSFeature class |
| SSFeature.hh | |
| TorsionFeature.cc | |
| TorsionFeature.fwd.hh | Forward declaration for TorsionFeature class |
| TorsionFeature.hh | |
| Align_RmsdEvaluator.cc | |
| Align_RmsdEvaluator.fwd.hh | Forward declaration for Align_RmsdEvaluator class |
| Align_RmsdEvaluator.hh | |
| Align_RotamerEvaluator.cc | |
| Align_RotamerEvaluator.fwd.hh | Forward declaration for Align_RotamerEvaluator class |
| Align_RotamerEvaluator.hh | |
| AlignmentClustering.cc | Divide input alns into clusters based on gdtmm comparison of partial models using ranked alignments |
| AlignmentClustering.fwd.hh | |
| AlignmentClustering.hh | Divide input alns into clusters based on gdtmm comparison of partial models. Uses the top e-value or hh-value sample as the cluster center |
| AlignmentSet.cc | |
| AlignmentSet.fwd.hh | Forward declaration for AlignmentSet class |
| AlignmentSet.hh | |
| AlignRmsdTargetEvaluatorCreator.cc | Header for AlignRmsdTargetEvaluatorCreator |
| AlignRmsdTargetEvaluatorCreator.hh | Header for AlignRmsdTargetEvaluatorCreator |
| cm_main.cc | |
| cm_main.hh | |
| coord_util.cc | |
| coord_util.hh | |
| ExtraThreadingMover.cc | Method declarations for ExtraThreadingMover |
| ExtraThreadingMover.hh | Class for copying extra stuff (ligands,dna,peptides,etc) from a template Pose |
| GenericJobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class GenericJobInputter |
| GenericJobInputter.fwd.hh | Header file for GenericJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| GenericJobInputter.hh | Header file for GenericJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| GenericJobInputterCreator.hh | |
| IgnoreSubsetConstraintSet.cc | |
| IgnoreSubsetConstraintSet.fwd.hh | Forward declaration for IgnoreSubsetConstraintSet class |
| IgnoreSubsetConstraintSet.hh | |
| LoopRelaxMover.cc | |
| LoopRelaxMover.fwd.hh | Forward declaration for LoopRelaxMover class |
| LoopRelaxMover.hh | |
| LoopRelaxMoverCreator.hh | |
| LoopRelaxThreadingMover.cc | |
| LoopRelaxThreadingMover.fwd.hh | Forward declaration for LoopRelaxThreadingMover class |
| LoopRelaxThreadingMover.hh | |
| MultiThreadingMover.cc | |
| MultiThreadingMover.hh | |
| PartialThreadingMover.cc | |
| PartialThreadingMover.hh | |
| RecoverSideChainsMover.cc | |
| RecoverSideChainsMover.fwd.hh | Forward declaration for RecoverSideChainsMover class |
| RecoverSideChainsMover.hh | |
| StealLigandMover.cc | |
| StealLigandMover.fwd.hh | Forward declaration for StealLigandMover class |
| StealLigandMover.hh | |
| StealSideChainsMover.cc | |
| StealSideChainsMover.fwd.hh | Forward declaration for StealSideChainsMover class |
| StealSideChainsMover.hh | |
| ThreadingJob.cc | |
| ThreadingJob.fwd.hh | Header file for ThreadingJob classes |
| ThreadingJob.hh | Header file for ThreadingJob classes |
| ThreadingJobInputter.cc | |
| ThreadingJobInputter.fwd.hh | Header file for ThreadingJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| ThreadingJobInputter.hh | |
| ThreadingJobInputterCreator.hh | |
| ThreadingMover.cc | Method declarations for ThreadingMover |
| ThreadingMover.hh | |
| util.cc | Set of utilities used in comparative modeling of protein structures |
| util.hh | Small bundle of utilities for comparative modeling |
| ► constraints_additional | |
| AdditionalConstraintCreators.cc | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| AdditionalConstraintCreators.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| AmbiguousMultiConstraint.cc | Declarations for a type of constraint that holds a number of constraints |
| AmbiguousMultiConstraint.fwd.hh | |
| AmbiguousMultiConstraint.hh | Declarations for a type of constraint that holds multiple other |
| BindingSiteConstraint.cc | |
| BindingSiteConstraint.hh | |
| CombinedConstraintEvaluator.cc | PoseEvaluator |
| CombinedConstraintEvaluator.hh | |
| CombinedConstraintEvaluatorCreator.cc | Header for CombinedConstraintsEvaluatorCreator |
| CombinedConstraintEvaluatorCreator.hh | Header for CombinedConstraintsEvaluatorCreator |
| COMCoordinateConstraint.cc | |
| COMCoordinateConstraint.hh | |
| ConstraintEvaluator.cc | PoseEvaluator |
| ConstraintEvaluator.fwd.hh | |
| ConstraintEvaluator.hh | |
| ConstraintEvaluatorCreator.cc | Header for ConstraintsEvaluatorCreator |
| ConstraintEvaluatorCreator.hh | Header for ConstraintsEvaluatorCreator |
| MaxSeqSepConstraintSet.cc | |
| MaxSeqSepConstraintSet.fwd.hh | Forward declaration for MaxSeqSepConstraintSet class |
| MaxSeqSepConstraintSet.hh | Helper class for FoldConstraints Protocol, filters constraints by sequence separation |
| SequenceCoupling1BDConstraint.cc | This is a constraint that refers to a core::sequence::SequenceProfile? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design). A note about the SequenceProfile::read_from_checkpoint function that is used to read in scores for amino acid types: the first line of the file will be ignored |
| SequenceCoupling1BDConstraint.fwd.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCoupling1BDConstraint.hh | This is a constraint that refers to a core::sequence::SequenceCoupling1BD? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCouplingConstraint.cc | This is a constraint that refers to a core::sequence::SequnceCopuling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design). A note about the SequenceProfile::read_from_checkpoint function that is used to read in scores for amino acid types: the first line of the file will be ignored |
| SequenceCouplingConstraint.fwd.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCouplingConstraint.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| ► contact_map | |
| ContactMap.cc | Method code and full headers for ContactMapCreator, ContactMap, ContactPartner and contact |
| ContactMap.fwd.hh | ContactMap forward declarations header |
| ContactMap.hh | Mover to create a ContactMap |
| ContactMapCreator.hh | |
| ► cryst | |
| cryst_movers.cc | Protocols for folding into density |
| cryst_movers.hh | |
| cryst_movers_creator.hh | |
| ► cyclic_peptide | |
| CreateAngleConstraint.cc | Add angle constraints to the current pose conformation |
| CreateAngleConstraint.hh | Add angle constraints to the current pose conformation |
| CreateAngleConstraintCreator.hh | Add angle constraints to the current pose conformation. This class will create instances of mover CreateAngleConstraint for the MoverFactory |
| CreateDistanceConstraint.cc | Add distance constraints to the current pose conformation |
| CreateDistanceConstraint.hh | Add distance constraints to the current pose conformation |
| CreateDistanceConstraintCreator.hh | Add distance constraints to the current pose conformation. This class will create instances of mover CreateDistanceConstraint for the MoverFactory |
| CreateTorsionConstraint.cc | Add torsion constraints to the current pose conformation |
| CreateTorsionConstraint.hh | Add torsion constraints to the current pose conformation |
| CreateTorsionConstraintCreator.hh | Add torsion constraints to the current pose conformation. This class will create instances of mover CreateTorsionConstraint for the MoverFactory |
| DeclareBond.cc | Add constraints to the current pose conformation |
| DeclareBond.hh | Add constraints to the current pose conformation |
| DeclareBondCreator.hh | |
| PeptideStubMover.cc | Add constraints to the current pose conformation |
| PeptideStubMover.hh | Add constraints to the current pose conformation |
| PeptideStubMoverCreator.hh | |
| ► ddg | |
| ddG_main.cc | |
| ddG_main.hh | |
| ddGData.cc | |
| ddGData.fwd.hh | |
| ddGData.hh | |
| ddGMover.cc | |
| ddGMover.hh | |
| ► denovo_design | |
| ► filters | |
| ExposedHydrophobicsFilter.cc | Tom's Denovo design protocol |
| ExposedHydrophobicsFilter.fwd.hh | Fwd declarations for Tom's denovo design protocol |
| ExposedHydrophobicsFilter.hh | Tom's Denovo Protocol. This is freely mutable and used for playing around with stuff |
| ExposedHydrophobicsFilterCreator.hh | Creator for Tom's denovo protocol |
| ► design_opt | |
| GreedyOptMutationMover.cc | |
| GreedyOptMutationMover.fwd.hh | |
| GreedyOptMutationMover.hh | |
| GreedyOptMutationMoverCreator.hh | |
| ParetoOptMutationMover.cc | |
| ParetoOptMutationMover.fwd.hh | |
| ParetoOptMutationMover.hh | |
| ParetoOptMutationMoverCreator.hh | This class will create instances of Mover ParetoOptMutationMover for the MoverFactory |
| PointMutationCalculator.cc | |
| PointMutationCalculator.fwd.hh | |
| PointMutationCalculator.hh | |
| ► dna | |
| DesignProteinBackboneAroundDNA.cc | Performs a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.) |
| DesignProteinBackboneAroundDNA.fwd.hh | |
| DesignProteinBackboneAroundDNA.hh | Performs a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.) |
| DesignProteinBackboneAroundDNACreator.hh | |
| DnaChains.cc | |
| DnaChains.fwd.hh | |
| DnaChains.hh | Descriptive but lightweight class to keep track of (usually basepaired) dna chains |
| DnaDesignDef.cc | |
| DnaDesignDef.fwd.hh | |
| DnaDesignDef.hh | |
| DnaInterfaceFinder.cc | |
| DnaInterfaceFinder.fwd.hh | |
| DnaInterfaceFinder.hh | |
| DnaInterfaceMinMover.cc | |
| DnaInterfaceMinMover.fwd.hh | |
| DnaInterfaceMinMover.hh | A mover that minimizes protein residues near DNA |
| DnaInterfaceMinMoverCreator.hh | |
| DnaInterfaceMultiStateDesign.cc | |
| DnaInterfaceMultiStateDesign.fwd.hh | |
| DnaInterfaceMultiStateDesign.hh | |
| DnaInterfaceMultiStateDesignCreator.hh | |
| DnaInterfacePacker.cc | |
| DnaInterfacePacker.fwd.hh | |
| DnaInterfacePacker.hh | Intended to perform anything one would want to do in a DNA interface that uses a single incarnation of the RotamerSets/InteractionGraph combo |
| DnaInterfacePackerCreator.hh | |
| DNAParameters.cc | A class to query for base-paired partners as well as base pair and base step parameters |
| DNAParameters.fwd.hh | A class to query for base-paired partners as well as base pair and base step parameters |
| DNAParameters.hh | A class to query for base-paired partners as well as base pair and base step parameters |
| PDBOutput.cc | |
| PDBOutput.fwd.hh | |
| PDBOutput.hh | |
| RestrictDesignToProteinDNAInterface.cc | |
| RestrictDesignToProteinDNAInterface.fwd.hh | |
| RestrictDesignToProteinDNAInterface.hh | When operated on a PackerTask, pack/design is limited to the protein-DNA interface |
| RestrictDesignToProteinDNAInterfaceCreator.hh | |
| RotamerDNAHBondFilter.cc | Filters rotamers for contact to DNA in an -ex dependent manner |
| RotamerDNAHBondFilter.fwd.hh | Filters rotamers for contact to DNA in an -ex dependent manner |
| RotamerDNAHBondFilter.hh | When passed to a PackerTask, filters rotamers for contact to DNA in an -ex dependent manner |
| SeparateDnaFromNonDna.cc | |
| SeparateDnaFromNonDna.fwd.hh | |
| SeparateDnaFromNonDna.hh | |
| SeparateDnaFromNonDnaCreator.hh | |
| typedefs.hh | Non-class and non-pointer typedefs for this namespace |
| util.cc | |
| util.hh | |
| WatsonCrickRotamerCouplings.cc | |
| WatsonCrickRotamerCouplings.fwd.hh | |
| WatsonCrickRotamerCouplings.hh | When operated on a PackerTask, adds RotamerCouplings to it that will trigger the use of a FixbbCoupledRotamerAnnealer by pack_rotamers, which will make base-paired DNA rotamer substitutions |
| WatsonCrickRotamerCouplingsCreator.hh | |
| ► docking | |
| ► membrane | |
| MPDockingMover.cc | Dock two membrane proteins |
| MPDockingMover.fwd.hh | Dock two proteins, which are made into membrane proteins |
| MPDockingMover.hh | Dock two membrane proteins |
| MPDockingMoverCreator.hh | Dock two membrane proteins |
| MPDockingSetupMover.cc | Reads in 2 poses and 2 spanfiles, concatenates them, and prints them out CURRENTLY ONLY WORKS FOR 2 POSES!!! |
| MPDockingSetupMover.fwd.hh | Reads in 2 poses and 2 spanfiles, concatenates them, and prints them out CURRENTLY ONLY WORKS FOR 2 POSES!!! |
| MPDockingSetupMover.hh | Reads in 2 poses and 2 spanfiles, concatenates them, and prints them out CURRENTLY ONLY WORKS FOR 2 POSES!!! |
| MPDockingSetupMoverCreator.hh | Setup MPDock protocol |
| ► stateless | |
| SaneDockingProtocol.cc | |
| SaneDockingProtocol.fwd.hh | |
| SaneDockingProtocol.hh | DockingProtocol class that doesn't use the more esoteric features of the Mover base class (e.g get_input_pose()) |
| ConformerSwitchMover.cc | Code for the conformer switch mover in ensemble docking |
| ConformerSwitchMover.fwd.hh | ConformerSwitchMover forward declarations header |
| ConformerSwitchMover.hh | Code for the conformer switch mover in ensemble docking |
| ConformerSwitchMoverCreator.hh | |
| DockFilters.cc | Filters for docking |
| DockFilters.fwd.hh | Forward declarations for low-res docking |
| DockFilters.hh | Filters for docking |
| DockingEnsemble.cc | Container class for ensemble docking information to be used with ConformerSwitchMover |
| DockingEnsemble.fwd.hh | DockingEnsemble forward declarations header |
| DockingEnsemble.hh | Container class for ensemble docking information to be used with ConformerSwitchMover |
| DockingEnsemblePrepackProtocol.cc | Prepacking of the bound structure before docking with ensembles |
| DockingEnsemblePrepackProtocol.fwd.hh | |
| DockingEnsemblePrepackProtocol.hh | Prepacking of the bound structure before docking with ensembles |
| DockingHighRes.cc | Protocols that are specific to high resolution docking |
| DockingHighRes.fwd.hh | Forward declarations for low-res docking |
| DockingHighRes.hh | Initialization protocols for docking |
| DockingHighResLegacy.cc | Protocols that are specific to high resolution docking |
| DockingHighResLegacy.fwd.hh | Forward declarations for DockingHighResLegacy (high resolution docking protocol as it existed in mini before the GrayLab refactor) |
| DockingHighResLegacy.hh | Initialization protocols for docking |
| DockingInitialPerturbation.cc | Initial position functions |
| DockingInitialPerturbation.fwd.hh | |
| DockingInitialPerturbation.hh | Initialization protocols for docking |
| DockingInitialPerturbationCreator.hh | |
| DockingLowRes.cc | Protocols that are specific to docking low resolution |
| DockingLowRes.fwd.hh | Forward declarations for low-res docking |
| DockingLowRes.hh | Low resolution mode for docking |
| DockingLowResEnsemble.cc | Protocols that are specific to low resolution ensemble docking |
| DockingLowResEnsemble.fwd.hh | Forward declarations for low-res ensemble docking |
| DockingLowResEnsemble.hh | Low resolution mode for ensemble docking |
| DockingPrepackProtocol.cc | Prepacking of the bound sturcture before docking |
| DockingPrepackProtocol.fwd.hh | |
| DockingPrepackProtocol.hh | Prepacking of the bound structure before docking |
| DockingProtocol.cc | |
| DockingProtocol.fwd.hh | |
| DockingProtocol.hh | |
| DockingProtocolCreator.hh | Declaration of the MoverCreator class for the DockAndRetrieveSidechains |
| DockMCMCycle.cc | Protocols that are specific to high resolution docking |
| DockMCMCycle.fwd.hh | Forward declarations for DockMCMCycle (high resolution min) docking |
| DockMCMCycle.hh | Initialization protocols for docking |
| DockMCMProtocol.cc | Protocols that are specific to high resolution docking |
| DockMCMProtocol.fwd.hh | Forward declarations for DockMCMProtocol (high resolution min) docking |
| DockMCMProtocol.hh | Initialization protocols for docking |
| DockMinMover.cc | |
| DockMinMover.fwd.hh | Forward declarations for DockMinMover (high resolution min) docking |
| DockMinMover.hh | |
| DockSetupMover.cc | |
| DockSetupMover.fwd.hh | |
| DockSetupMover.hh | Allows low-resolution docking using simulated or parallel tempering |
| DockSetupMoverCreator.hh | Declaration of the MoverCreator class for the DockAndRetrieveSidechains |
| DockTaskFactory.cc | Sets up the task factory for docking movers |
| DockTaskFactory.fwd.hh | Forward declarations for DockTaskFactory |
| DockTaskFactory.hh | Sets up the task factory for docking movers |
| EllipsoidalRandomizationMover.cc | |
| EllipsoidalRandomizationMover.fwd.hh | Forward declarations for EllipsoidalRandomizationMover (docking initial placement mover) |
| EllipsoidalRandomizationMover.hh | |
| metrics.cc | Protocols that are specific to docking low resolution |
| metrics.hh | Protocols that are specific to docking low resolution |
| RigidBodyInfo.cc | |
| RigidBodyInfo.fwd.hh | |
| RigidBodyInfo.hh | |
| SidechainMinMover.cc | |
| SidechainMinMover.fwd.hh | |
| SidechainMinMover.hh | |
| TemperedDocking.cc | Low resolution docking using parallel or simulated tempering |
| TemperedDocking.fwd.hh | |
| TemperedDocking.hh | Allows low-resolution docking using simulated or parallel tempering |
| TemperedDockingCreator.hh | Declaration of the MoverCreator class for the DockAndRetrieveSidechains |
| types.hh | Additionl types for Docking protocol |
| util.cc | |
| util.hh | Protocols that are specific to docking low resolution |
| ► domain_assembly | |
| AddAssemblyConstraints.cc | |
| AddAssemblyConstraints.fwd.hh | Adds constraints for the assembling process |
| AddAssemblyConstraints.hh | Adds constraints for the assembling process |
| AssembleLinkerMover.cc | A mover for assembling domains |
| AssembleLinkerMover.fwd.hh | A mover for assembling domains |
| AssembleLinkerMover.hh | A mover for assembling domains |
| CombineChainsMover.cc | Takes a multichain pose and returns a single-chain one |
| CombineChainsMover.fwd.hh | A mover for assembling chains |
| CombineChainsMover.hh | A mover for assembling domains |
| PostDockAssemblyScorer.cc | Computes crmsd of the assembly to the staring point |
| PostDockAssemblyScorer.fwd.hh | Computes crmsd of the assembly to the staring point |
| PostDockAssemblyScorer.hh | Computes crmsd of the assembly to the staring point |
| ► electron_density | |
| BfactorFittingMover.cc | Set up morphing with electron density map |
| BfactorFittingMover.hh | |
| BfactorFittingMoverCreator.hh | |
| DensityMorphingMover.cc | Set up morphing with electron density map |
| DensityMorphingMover.hh | Add constraints to the current pose conformation |
| DensityMorphingMoverCreator.hh | |
| ReportFSC.cc | |
| ReportFSC.hh | |
| ReportFSCCreator.hh | |
| ScaleMapIntensities.cc | |
| ScaleMapIntensities.hh | |
| ScaleMapIntensitiesCreator.hh | |
| SetupForDensityScoringMover.cc | Protocols for folding into density |
| SetupForDensityScoringMover.hh | Protocols for folding into density |
| SetupForDensityScoringMoverCreator.hh | |
| util.cc | Protocols for folding into density |
| util.hh | Protocols for folding into density |
| ► elscripts | |
| ► modules | |
| MonteCarlo.hh | MonteCarlo module for ElScripts |
| BaseRole.cc | BaseRole, which handles a lot of common functions between all the elscripts roles including a lot of lua stuff |
| BaseRole.fwd.hh | Foward decls for BaseRole, base class of ElScripts |
| BaseRole.hh | BaseRole, which handles a lot of common functions between all the elscripts roles including a lot of lua stuff |
| Master.cc | The Master role in elscripts, handles trajectories, generating workunits, processing of results |
| Master.fwd.hh | Foward decls for Master, the master role of elscripts |
| Master.hh | The Master role in elscripts, handles trajectories, generating workunits, processing of results This is the non MPI version of the master, which is used by the Single Node Role Splitting this from MPI_Master so Single Node can be compiled without MPI |
| MPI_Master.cc | The MPI_Master role in elscripts, handles trajectories, generating workunits, processing of results |
| MPI_Master.fwd.hh | Foward decls for MPI_Master, the master role of elscripts |
| MPI_Master.hh | The MPI_Master role in elscripts, handles trajectories, generating workunits, processing of results Has additional functions related to boost mpi world and MPI_EndPoint |
| MPI_Slave.cc | Slave role of elscripts |
| MPI_Slave.fwd.hh | Foward decls for MPI_Slave, the slave role of elscripts |
| MPI_Slave.hh | Slave role of elscripts |
| SingleNode.cc | Slave role of elscripts |
| SingleNode.fwd.hh | Foward decls for SingleNode, the non mpi version of elscripts |
| SingleNode.hh | Singlenode role of elscripts |
| Slave.cc | Slave role of elscripts |
| Slave.fwd.hh | Foward decls for Slave, the slave role of elscripts |
| Slave.hh | Non_mpi slave role of elscripts used by single node, shares fxns with MPI_Slave |
| util.cc | Utility functions useful in elscripts |
| util.hh | Utility functions useful in elscripts |
| ► environment | |
| ► claims | |
| BrokerElements.cc | Some implementation details of the BrokerElements (such as they are) |
| BrokerElements.hh | |
| ClaimStrength.cc | ClaimStrength tracks the prioirty of a particular claim with respect to its initialization |
| ClaimStrength.fwd.hh | |
| ClaimStrength.hh | Header file for ClaimStrength, which tracks the prioirty of a particular claim with respect to its initialization |
| CutBiasClaim.cc | Claims access to a torsional angle |
| CutBiasClaim.fwd.hh | |
| CutBiasClaim.hh | |
| EnvClaim.cc | Abstract class for implementing an EnvClaim (e.g. TorsionClaim) |
| EnvClaim.fwd.hh | |
| EnvClaim.hh | Virtual base class for all claims used with environment claiming system |
| EnvLabelSelector.cc | The EnvLabelSelector holds a selection that another object can set inside of it |
| EnvLabelSelector.fwd.hh | The EnvLabelSelector holds a selection that another object can set inside of it |
| EnvLabelSelector.hh | The EnvLabelSelector holds a set of local positions that are converted to seqids at apply |
| JumpClaim.cc | Claims access to a jump |
| JumpClaim.fwd.hh | Forward declaration for JumpClaim in environment |
| JumpClaim.hh | |
| TorsionClaim.cc | Implementation file for TorsionClaim |
| TorsionClaim.fwd.hh | |
| TorsionClaim.hh | An EnvClaim object for claiming arbitrary regions and types of torsional angles within a pose |
| VirtResClaim.cc | Claims access to a torsional angle |
| VirtResClaim.fwd.hh | Forward declaration for VirtResClaim in environment |
| VirtResClaim.hh | A claim for expressing the desire for new sequence to be inserted at a particular point |
| XYZClaim.cc | Claims access to a torsional angle |
| XYZClaim.fwd.hh | |
| XYZClaim.hh | |
| AutoCutData.cc | |
| AutoCutData.fwd.hh | Definition of the AutoCutData class |
| AutoCutData.hh | |
| AutoCutDataCreator.hh | |
| ClientMover.cc | |
| ClientMover.fwd.hh | Definition of the ClientMover class |
| ClientMover.hh | An environment that automatically distributes rights to shared degrees of freedom (e.g. fold tree) |
| CoMTrackerCM.cc | |
| CoMTrackerCM.fwd.hh | Definition of the CoMTrackerCM class |
| CoMTrackerCM.hh | Header file for CoMTracker |
| CoMTrackerCMCreator.hh | |
| DofUnlock.cc | |
| DofUnlock.fwd.hh | Definition of the DofUnlock class |
| DofUnlock.hh | A class that is used to express a mover-specific DoF-unlock on a ProtectedPose. Its destruction expresses a re-locking |
| EnvClaimBroker.cc | |
| EnvClaimBroker.fwd.hh | Definition of the EnvClaimBroker class |
| EnvClaimBroker.hh | A class responsible for managing claims from ClientMovers, and retaining important information about the result of the brokering process |
| EnvExcn.hh | Subclasses of EXCN_Env_Exception that require inclusion of the stuff in protocols |
| Environment.cc | |
| Environment.fwd.hh | Definition of the BrokeredEnvironment class |
| Environment.hh | An environment that automatically distributes rights to shared degrees of freedom (e.g. fold tree) |
| EnvMover.cc | |
| EnvMover.fwd.hh | Definition of the EnvMover class |
| EnvMover.hh | |
| EnvMoverCreator.hh | This class will create instances of the EnvMover for the MoverFactory |
| ProtectedConformation.cc | |
| ProtectedConformation.fwd.hh | Definition of the ProtectedConformation class |
| ProtectedConformation.hh | A conformation built by the environment to be protected |
| ScriptCM.cc | |
| ScriptCM.fwd.hh | Definition of the ScriptCM class |
| ScriptCM.hh | Header file for CoMTracker |
| ScriptCMCreator.hh | |
| ► enzdes | |
| AddLigandMotifRotamersOperationCreator.hh | |
| AddorRemoveCsts.cc | |
| AddorRemoveCsts.hh | |
| AddOrRemoveMatchCstsCreator.hh | |
| AddRigidBodyLigandConfsCreator.hh | |
| BackboneSampler.cc | |
| BackboneSampler.hh | Adapted from backrub mover in protein interface design |
| BackboneSamplerCreator.hh | Declaration of the MoverCreator class for the BackboneSampler |
| DesignVsNativeComparison.cc | |
| DesignVsNativeComparison.hh | |
| DetectProteinLigandInterfaceOperationCreator.hh | |
| enzdes_util.cc | Bunch of utility functions used in enzdes |
| enzdes_util.hh | Bunch of utility functions used in enzdes |
| EnzdesBaseProtocol.cc | |
| EnzdesBaseProtocol.fwd.hh | |
| EnzdesBaseProtocol.hh | |
| EnzdesFixBBProtocol.cc | |
| EnzdesFixBBProtocol.hh | |
| EnzdesFlexBBProtocol.cc | |
| EnzdesFlexBBProtocol.hh | |
| EnzdesJobInputter.cc | Job inputter that adds some stuff for enzdes to the pose |
| EnzdesJobInputter.fwd.hh | |
| EnzdesJobInputter.hh | |
| EnzdesJobInputterCreator.hh | |
| EnzdesJobOutputter.cc | Implementation for EnzdesJobOutputter |
| EnzdesJobOutputter.fwd.hh | Forward declaration for EnzdesJobOutputters |
| EnzdesJobOutputter.hh | Header file for EnzdesJobOutputter |
| EnzdesJobOutputterCreator.hh | |
| EnzdesMovers.cc | Collection of movers that are used at different stages in enzyme design |
| EnzdesMovers.fwd.hh | |
| EnzdesMovers.hh | Collection of movers that are used at different stages in enzyme design |
| EnzdesMoversCreator.hh | |
| EnzdesTaskOperations.cc | Various task operations used in enzyme design |
| EnzdesTaskOperations.fwd.hh | |
| EnzdesTaskOperations.hh | Collection of Task operations used in enzyme design |
| EnzFilterCreators.hh | FilterCreators for the enzyme design filters |
| EnzFilters.cc | |
| EnzFilters.fwd.hh | |
| EnzFilters.hh | Definition of filter classes for enzdes in rosetta_scripts framework |
| EnzRepackMinimize.cc | Repack/minimize class for rosetta_scripts-compatible enzdes |
| EnzRepackMinimize.fwd.hh | |
| EnzRepackMinimize.hh | |
| EnzRepackMinimizeCreator.hh | |
| ModifyStoredLigandRBConfsMovers.cc | |
| ModifyStoredLigandRBConfsMovers.fwd.hh | |
| ModifyStoredLigandRBConfsMovers.hh | |
| PackRotamersMoverPartGreedy.cc | Partly greedy pack rotamers mover. given a set of target residues, choose their neighbors greedily and then |
| PackRotamersMoverPartGreedy.hh | |
| PackRotamersMoverPartGreedyCreator.hh | |
| ProteinLigandInterfaceUpweighterOperationCreator.hh | |
| RemoveLigandFilter.cc | |
| RemoveLigandFilter.fwd.hh | |
| RemoveLigandFilter.hh | |
| RemoveLigandFilterCreator.hh | |
| SecondaryMatchProtocol.cc | |
| SecondaryMatchProtocol.hh | |
| SetCatalyticResPackBehaviorCreator.hh | |
| ► evaluation | |
| AlignEvaluator.cc | |
| AlignEvaluator.fwd.hh | Forward declaration for AlignEvaluator class |
| AlignEvaluator.hh | Base class for evaluators that evaluate based on some sort of sequence alignment |
| EvaluatorCreator.fwd.hh | Forward Header for base class for EvaluatorCreators for the Evaluator load-time factory registration scheme |
| EvaluatorCreator.hh | Base class for EvaluatorCreators for the Evaluator load-time factory registration scheme |
| EvaluatorFactory.cc | Factory for creating Evaluators objects |
| EvaluatorFactory.fwd.hh | Report data to database |
| EvaluatorFactory.hh | Factory for creating Evaluator objects |
| PCA.cc | |
| PCA.fwd.hh | Initialization protocols for relax |
| PCA.hh | Initialization protocols for relax |
| PoseEvaluator.cc | PoseEvaluator |
| PoseEvaluator.fwd.hh | |
| PoseEvaluator.hh | Initialization protocols for relax |
| TimeEvaluator.cc | Initialization protocols for relax |
| TimeEvaluator.fwd.hh | |
| TimeEvaluator.hh | Initialization protocols for relax |
| util.cc | Initialization protocols for relax |
| util.hh | Initialization protocols for relax |
| ► farna | |
| BasePairStep.cc | |
| BasePairStep.fwd.hh | |
| BasePairStep.hh | |
| BasePairStepLibrary.cc | |
| BasePairStepLibrary.fwd.hh | |
| BasePairStepLibrary.hh | |
| FullAtomRNA_Fragments.cc | RNA fragments from database, |
| FullAtomRNA_Fragments.fwd.hh | Pose forward declarations header |
| FullAtomRNA_Fragments.hh | |
| MultipleDomainMover.cc | Protocols that are specific to MultipleDomainMover |
| MultipleDomainMover.fwd.hh | Forward declarations header |
| MultipleDomainMover.hh | |
| RNA_ChunkLibrary.cc | |
| RNA_ChunkLibrary.fwd.hh | Forward declarations header |
| RNA_ChunkLibrary.hh | |
| RNA_DeNovoProtocol.cc | Protocols that are specific to RNA_DeNovoProtocol |
| RNA_DeNovoProtocol.hh | |
| RNA_FragmentMover.cc | Protocols that are specific to RNA_FragmentMover |
| RNA_FragmentMover.fwd.hh | |
| RNA_FragmentMover.hh | Protocols that are specific to RNA_FragmentMover |
| RNA_Fragments.cc | |
| RNA_Fragments.fwd.hh | RNA_Fragments forward declarations header |
| RNA_Fragments.hh | |
| RNA_FragmentsClasses.fwd.hh | |
| RNA_JumpLibrary.cc | Protocols that are specific to RNA_JumpLibrary |
| RNA_JumpLibrary.fwd.hh | Pose forward declarations header |
| RNA_JumpLibrary.hh | |
| RNA_LoopCloser.cc | Protocols that are specific to RNA_LoopCloser |
| RNA_LoopCloser.fwd.hh | |
| RNA_LoopCloser.hh | |
| RNA_MatchType.hh | |
| RNA_Minimizer.cc | Protocols that are specific to RNA_Minimizer |
| RNA_Minimizer.fwd.hh | |
| RNA_Minimizer.hh | |
| RNA_Relaxer.cc | Protocols that are specific to RNA_Relaxer |
| RNA_Relaxer.fwd.hh | |
| RNA_Relaxer.hh | |
| RNA_SecStructInfo.cc | Statistically derived rotamer pair potential class implementation |
| RNA_SecStructInfo.fwd.hh | |
| RNA_SecStructInfo.hh | Statistically derived rotamer pair potential class implementation |
| RNA_StructureParameters.cc | User input parameters for RNA structure inference |
| RNA_StructureParameters.fwd.hh | Pose forward declarations header |
| RNA_StructureParameters.hh | |
| util.cc | Protocols that are specific to RNA_FragmentMover |
| util.hh | |
| ► features | |
| ► helixAssembly | |
| ConcurrencyTest.cc | |
| ConcurrencyTest.fwd.hh | |
| ConcurrencyTest.hh | |
| ConcurrencyTestCreator.cc | |
| ConcurrencyTestCreator.hh | |
| HelicalFragment.cc | |
| HelicalFragment.fwd.hh | |
| HelicalFragment.hh | Small helper class that stores the start and end of a helix secondary structure |
| HelixBundleFeatures.cc | Search through a pose for sets of 3 helices and generate RMSD calculations between all pairs of them |
| HelixBundleFeatures.fwd.hh | |
| HelixBundleFeatures.hh | |
| HelixBundleFeaturesCreator.cc | |
| HelixBundleFeaturesCreator.hh | |
| ► strand_assembly | |
| CheckForSandwichFeatures.cc | Check various properties for SandwichFeatures |
| CheckForSandwichFeatures.hh | Check various properties for SandwichFeatures |
| SandwichFeatures.cc | Extract and analyze beta-sandwich features |
| SandwichFeatures.fwd.hh | |
| SandwichFeatures.hh | |
| SandwichFeaturesCreator.cc | |
| SandwichFeaturesCreator.hh | |
| SandwichFragment.cc | |
| SandwichFragment.hh | Small helper class that stores the start and end of a strand secondary structure |
| StrandAssemblyCommon.hh | Has most basic inclusions and namespace usings |
| StrandBundleFeatures.cc | Extract beta strand, strand pairs, sandwiches in pdb file, see wiki.rosettacommons.org/index.php/MultiBodyFeaturesReporters#StrandBundleFeatures for detail |
| StrandBundleFeatures.fwd.hh | |
| StrandBundleFeatures.hh | Extract beta strand, strand pairs, sandwiches in pdb file, see wiki.rosettacommons.org/index.php/MultiBodyFeaturesReporters#StrandBundleFeatures for detail |
| StrandBundleFeaturesCreator.cc | |
| StrandBundleFeaturesCreator.hh | |
| StrandFragment.cc | |
| StrandFragment.hh | Small helper class that stores the start and end of a strand secondary structure |
| WriteToDBFromSandwichFeatures.cc | Write to a DB after SandwichFeatures |
| WriteToDBFromSandwichFeatures.hh | Write to a DB after SandwichFeatures |
| WriteToFileFromSandwichFeatures.cc | Write to a file after SandwichFeatures |
| WriteToFileFromSandwichFeatures.hh | Write to a file after SandwichFeatures |
| AtomAtomPairFeatures.cc | Report atom-atom pair geometry and scores to features statistics scientific benchmark |
| AtomAtomPairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomAtomPairFeatures.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomAtomPairFeaturesCreator.cc | Header for AtomAtomPairFeaturesCreator for the AtomAtomPairFeatures load-time factory registration scheme |
| AtomAtomPairFeaturesCreator.hh | Header for AtomAtomPairFeaturesCreator for the AtomAtomPairFeatures load-time factory registration scheme |
| AtomInResidueAtomInResiduePairFeatures.cc | Report atom-atom pair geometry and scores to features statistics scientific benchmark |
| AtomInResidueAtomInResiduePairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomInResidueAtomInResiduePairFeatures.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomInResidueAtomInResiduePairFeaturesCreator.cc | Header for AtomInResidueAtomInResiduePairFeaturesCreator for the AtomInResidueAtomInResiduePairFeatures load-time factory registration scheme |
| AtomInResidueAtomInResiduePairFeaturesCreator.hh | Header for AtomInResidueAtomInResiduePairFeaturesCreator for the AtomInResidueAtomInResiduePairFeatures load-time factory registration scheme |
| AtomTypesFeatures.cc | Report AtomType properties to features Statistics Scientific Benchmark |
| AtomTypesFeatures.fwd.hh | Report AtomTypes geometry and scores to features Statistics Scientific Benchmark |
| AtomTypesFeatures.hh | Report AtomType features Statistics Scientific Benchmark |
| AtomTypesFeaturesCreator.cc | Header for AtomTypesFeaturesCreator for the AtomTypesFeatures load-time factory registration scheme |
| AtomTypesFeaturesCreator.hh | Header for AtomTypesFeaturesCreator for the AtomTypesFeatures load-time factory registration scheme |
| BatchFeatures.cc | |
| BatchFeatures.fwd.hh | |
| BatchFeatures.hh | |
| BetaTurnDetection.cc | Determine the presence and type of beta turn at a specific postion in a pose |
| BetaTurnDetection.fwd.hh | Determine if there is a beta turn at particular postion |
| BetaTurnDetection.hh | Determine the presence and type of beta turn at a specific postion in a pose |
| BetaTurnDetectionFeatures.cc | Report beta turns to a DB |
| BetaTurnDetectionFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| BetaTurnDetectionFeatures.hh | Report beta turns to a DB |
| BetaTurnDetectionFeaturesCreator.cc | Header for BetaTurnDetectionFeaturesCreator for the BetaTurnDetectionFeatures load-time factory registration scheme |
| BetaTurnDetectionFeaturesCreator.hh | Header for BetaTurnDetectionFeaturesCreator for the BetaTurnDetectionFeatures load-time factory registration scheme |
| ChargeChargeFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| ChargeChargeFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| ChargeChargeFeatures.hh | Report comments stored with each pose |
| ChargeChargeFeaturesCreator.cc | Header for ChargeChargeFeaturesCreator for the ChargeChargeFeatures load-time factory registration scheme |
| ChargeChargeFeaturesCreator.hh | Header for ChargeChargeFeaturesCreator for the ChargeChargeFeatures load-time factory registration scheme |
| DatabaseFilters.cc | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| DatabaseFilters.fwd.hh | Report data to database |
| DatabaseFilters.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| DatabaseJobInputter.cc | |
| DatabaseJobInputter.fwd.hh | |
| DatabaseJobInputter.hh | Header file for DatabaseJobInputter class |
| DatabaseJobInputterCreator.hh | |
| DatabaseJobOutputter.cc | Job Outputter to a database |
| DatabaseJobOutputter.fwd.hh | Header file for DatabaseJobOutputter class |
| DatabaseJobOutputter.hh | Header file for DatabaseJobOutputter class |
| DatabaseJobOutputterCreator.hh | |
| DatabaseStatements.cc | |
| DatabaseStatements.hh | |
| DdGFeatures.cc | Report the per-residue ddG score to the features database |
| DdGFeatures.fwd.hh | Report the per-residue ddG score to the features database |
| DdGFeatures.hh | Report the per-residue ddG score to the features database |
| DdGFeaturesCreator.cc | Header for DdGFeaturesCreator for the FeaturesReporter load-time factory registration scheme |
| DdGFeaturesCreator.hh | Header for DdGFeaturesCreator for the DdGFeatures load-time factory registration scheme |
| FeaturesReporter.cc | Base class to report geometry and scores to features Statistics Scientific Benchmark |
| FeaturesReporter.fwd.hh | Report data to database |
| FeaturesReporter.hh | Base class to report geometry and scores to features Statistics Scientific Benchmark |
| FeaturesReporterCreator.fwd.hh | Forward Header for base class for FeaturesReporterCreators for the FeaturesReporter load-time factory registration scheme |
| FeaturesReporterCreator.hh | Base class for FeaturesReporterCreators for the FeaturesReporter load-time factory registration scheme |
| FeaturesReporterFactory.cc | Factory for creating FeaturesReporters objects |
| FeaturesReporterFactory.fwd.hh | Report data to database |
| FeaturesReporterFactory.hh | Factory for creating FeaturesReporter objects |
| GeometricSolvationFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| GeometricSolvationFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| GeometricSolvationFeatures.hh | Report hydrogen bonding based solvation model to a features database |
| GeometricSolvationFeaturesCreator.cc | Header for GeometricSolvationFeaturesCreator for the GeometricSolvationFeatures load-time factory registration scheme |
| GeometricSolvationFeaturesCreator.hh | Header for GeometricSolvationFeaturesCreator for the GeometricSolvationFeatures load-time factory registration scheme |
| HBondFeatures.cc | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeatures.fwd.hh | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeatures.hh | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeaturesCreator.cc | Header for HBondFeaturesCreator for the HBondFeatures load-time factory registration scheme |
| HBondFeaturesCreator.hh | Header for HBondFeaturesCreator for the HBondFeatures load-time factory registration scheme |
| HBondParameterFeatures.cc | Report HBond Parameters to features Statistics Scientific Benchmark |
| HBondParameterFeatures.fwd.hh | Report HBondParameter geometry and scores to features Statistics Scientific Benchmark |
| HBondParameterFeatures.hh | Report HBond Parameter features Statistics Scientific Benchmark |
| HBondParameterFeaturesCreator.cc | Header for HBondParameterFeaturesCreator for the HBondParameterFeatures load-time factory registration scheme |
| HBondParameterFeaturesCreator.hh | Header for HBondParameterFeaturesCreator for the HBondParameterFeatures load-time factory registration scheme |
| HelixCapFeatures.cc | |
| HelixCapFeatures.fwd.hh | |
| HelixCapFeatures.hh | |
| HelixCapFeaturesCreator.cc | |
| HelixCapFeaturesCreator.hh | |
| InterfaceFeatures.cc | |
| InterfaceFeatures.fwd.hh | |
| InterfaceFeatures.hh | Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover |
| InterfaceFeaturesCreator.cc | |
| InterfaceFeaturesCreator.hh | |
| JobDataFeatures.cc | |
| JobDataFeatures.fwd.hh | |
| JobDataFeatures.hh | |
| JobDataFeaturesCreator.cc | Header for JobDataFeaturesCreator for the JobDataFeatures load-time factory registration scheme |
| JobDataFeaturesCreator.hh | Header for JobDataFeaturesCreator for the JobDataFeatures load-time factory registration scheme |
| LoopAnchorFeatures.cc | Report loop anchor features to a features database |
| LoopAnchorFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| LoopAnchorFeatures.hh | Report comments stored with each pose |
| LoopAnchorFeaturesCreator.cc | Header for LoopAnchorFeaturesCreator for the LoopAnchorFeatures load-time factory registration scheme |
| LoopAnchorFeaturesCreator.hh | Header for LoopAnchorFeaturesCreator for the LoopAnchorFeatures load-time factory registration scheme |
| OrbitalsFeatures.cc | Report orbital geometry and scores to features statistics scientific benchmark |
| OrbitalsFeatures.fwd.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| OrbitalsFeatures.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| OrbitalsFeaturesCreator.cc | Header for OrbitalsFeaturesCreator for the OrbitalsFeatures load-time factory registration scheme |
| OrbitalsFeaturesCreator.hh | Header for OrbitalsFeaturesCreator for the OrbitalsFeatures load-time factory registration scheme |
| PairFeatures.cc | Report orbital geometry and scores to features statistics scientific benchmark |
| PairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| PairFeatures.hh | Report residue and atom pair geometry and scores to features Statistics Scientific Benchmark |
| PairFeaturesCreator.cc | Header for PairFeaturesCreator for the PairFeatures load-time factory registration scheme |
| PairFeaturesCreator.hh | Header for PairFeaturesCreator for the PairFeatures load-time factory registration scheme |
| PdbDataFeatures.cc | |
| PdbDataFeatures.fwd.hh | |
| PdbDataFeatures.hh | |
| PdbDataFeaturesCreator.cc | Header for PdbDataFeaturesCreator for the PdbDataFeatures load-time factory registration scheme |
| PdbDataFeaturesCreator.hh | Header for PdbDataFeaturesCreator for the PdbDataFeatures load-time factory registration scheme |
| PoseCommentsFeatures.cc | Report comments stored with each pose |
| PoseCommentsFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| PoseCommentsFeatures.hh | Report comments stored with each pose |
| PoseCommentsFeaturesCreator.cc | Header for PoseCommentsFeaturesCreator for the PoseCommentsFeatures load-time factory registration scheme |
| PoseCommentsFeaturesCreator.hh | Header for PoseCommentsFeaturesCreator for the PoseCommentsFeatures load-time factory registration scheme |
| PoseConformationFeatures.cc | Report comments stored with each pose |
| PoseConformationFeatures.fwd.hh | Report pose fold tree related features |
| PoseConformationFeatures.hh | Report comments stored with each pose |
| PoseConformationFeaturesCreator.cc | Header for PoseConformationFeaturesCreator for the PoseConformationFeatures load-time factory registration scheme |
| PoseConformationFeaturesCreator.hh | Header for PoseConformationFeaturesCreator for the PoseConformationFeatures load-time factory registration scheme |
| ProteinBackboneAtomAtomPairFeatures.cc | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeatures.fwd.hh | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeatures.hh | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeaturesCreator.cc | Header for ProteinBackboneAtomAtomPairFeaturesCreator for the ProteinBackboneAtomAtomPairFeatures load-time factory registration scheme |
| ProteinBackboneAtomAtomPairFeaturesCreator.hh | Header for ProteinBackboneAtomAtomPairFeaturesCreator for the ProteinBackboneAtomAtomPairFeatures load-time factory registration scheme |
| ProteinBackboneTorsionAngleFeatures.cc | Report Backbone Torsional Angle features |
| ProteinBackboneTorsionAngleFeatures.fwd.hh | Report protein backbone torsion angle features |
| ProteinBackboneTorsionAngleFeatures.hh | Report protein backbone torsion angle features |
| ProteinBackboneTorsionAngleFeaturesCreator.cc | Header for ProteinBackboneTorsionAngleFeaturesCreator for the ProteinBackboneTorsionAngleFeatures load-time factory registration scheme |
| ProteinBackboneTorsionAngleFeaturesCreator.hh | Header for ProteinBackboneTorsionAngleFeaturesCreator for the ProteinBackboneTorsionAngleFeatures load-time factory registration scheme |
| ProteinBondGeometryFeatures.cc | Report Backbone Torsional Angle features |
| ProteinBondGeometryFeatures.fwd.hh | Report protein bond geometry features |
| ProteinBondGeometryFeatures.hh | Report protein backbone torsion angle features |
| ProteinBondGeometryFeaturesCreator.cc | Header for ProteinBondGeometryFeaturesCreator for the ProteinBondGeometryFeatures load-time factory registration scheme |
| ProteinBondGeometryFeaturesCreator.hh | Header for ProteinBondGeometryFeaturesCreator for the ProteinBondGeometryFeatures load-time factory registration scheme |
| ProteinResidueConformationFeatures.cc | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ProteinResidueConformationFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ProteinResidueConformationFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ProteinResidueConformationFeaturesCreator.cc | Header for ProteinResidueConformationFeaturesCreator for the ProteinResidueConformationFeatures load-time factory registration scheme |
| ProteinResidueConformationFeaturesCreator.hh | Header for ProteinResidueConformationFeaturesCreator for the ProteinResidueConformationFeatures load-time factory registration scheme |
| ProteinRMSDFeatures.cc | Report the root mean squared deviation between two poses |
| ProteinRMSDFeatures.fwd.hh | Report RMSD similarity of a protein structure against supplied reference structure |
| ProteinRMSDFeatures.hh | Report ProteinRMSD similarity of structure against supplied reference structure |
| ProteinRMSDFeaturesCreator.cc | Header for ProteinRMSDFeaturesCreator for the ProteinRMSDFeatures load-time factory registration scheme |
| ProteinRMSDFeaturesCreator.hh | Header for ProteinRMSDFeaturesCreator for the ProteinRMSDFeatures load-time factory registration scheme |
| ProteinRMSDNoSuperpositionFeatures.cc | Report the root mean squared deviation (without superposition) between two poses |
| ProteinRMSDNoSuperpositionFeatures.fwd.hh | Report (no superposition) RMSD similarity of a protein structure against supplied reference structure |
| ProteinRMSDNoSuperpositionFeatures.hh | Report ProteinRMSD similarity of structure against supplied reference structure without superposition |
| ProteinRMSDNoSuperpositionFeaturesCreator.cc | Header for ProteinRMSDNoSuperpositionFeaturesCreator for the ProteinRMSDNoSuperpositionFeatures load-time factory registration scheme |
| ProteinRMSDNoSuperpositionFeaturesCreator.hh | Header for ProteinRMSDNoSuperpositionFeaturesCreator for the ProteinRMSDNoSuperpositionFeatures load-time factory registration scheme |
| ProteinSilentReport.cc | Report feature data to database |
| ProteinSilentReport.fwd.hh | Report pose fold tree related features |
| ProteinSilentReport.hh | Report feature data to database |
| ProtocolFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| ProtocolFeatures.fwd.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| ProtocolFeatures.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.cc | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.fwd.hh | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.hh | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeaturesCreator.cc | Header for RadiusOfGyrationFeaturesCreator for the RadiusOfGyrationFeatures load-time factory registration scheme |
| RadiusOfGyrationFeaturesCreator.hh | Header for RadiusOfGyrationFeaturesCreator for the RadiusOfGyrationFeatures load-time factory registration scheme |
| Report.cc | Report feature data to database |
| Report.fwd.hh | Report pose fold tree related features |
| Report.hh | Report feature data to database |
| ReportToDB.cc | Report all data to a database |
| ReportToDB.fwd.hh | Report data to sqlite database |
| ReportToDB.hh | Report feature data to sqlite database |
| ReportToDBCreator.hh | This class will create instances of Mover ReportToDB for the MoverFactory |
| ResidueBurialFeatures.cc | Report residue burial to features statistics scientific benchmark |
| ResidueBurialFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ResidueBurialFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| ResidueBurialFeaturesCreator.cc | Header for ResidueBurialFeaturesCreator for the ResidueBurialFeatures load-time factory registration scheme |
| ResidueBurialFeaturesCreator.hh | Header for ResidueBurialFeaturesCreator for the ResidueBurialFeatures load-time factory registration scheme |
| ResidueConformationFeatures.cc | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ResidueConformationFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ResidueConformationFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ResidueConformationFeaturesCreator.cc | Header for ResidueConformationFeaturesCreator for the ResidueConformationFeatures load-time factory registration scheme |
| ResidueConformationFeaturesCreator.hh | Header for ResidueConformationFeaturesCreator for the ResidueConformationFeatures load-time factory registration scheme |
| ResidueFeatures.cc | Report residue features to features Statistics Scientific Benchmark |
| ResidueFeatures.fwd.hh | Report residue features to features Statistics Scientific Benchmark |
| ResidueFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| ResidueFeaturesCreator.cc | Header for ResidueFeaturesCreator for the ResidueFeatures load-time factory registration scheme |
| ResidueFeaturesCreator.hh | Header for ResidueFeaturesCreator for the ResidueFeatures load-time factory registration scheme |
| ResidueGridScoresFeatures.cc | Detailed per atom scores of Scoring Grids |
| ResidueGridScoresFeatures.fwd.hh | Detailed per atom scores of Scoring Grids |
| ResidueGridScoresFeatures.hh | Detailed per atom scores of Scoring Grids |
| ResidueGridScoresFeaturesCreator.hh | Detailed per atom scores of Scoring Grids |
| ResidueScoresFeatures.cc | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeatures.fwd.hh | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeatures.hh | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeaturesCreator.cc | Header for ResidueScoresFeaturesCreator for the ResidueScoresFeatures load-time factory registration scheme |
| ResidueScoresFeaturesCreator.hh | Header for ResidueScoresFeaturesCreator for the ResidueScoresFeatures load-time factory registration scheme |
| ResidueSecondaryStructureFeatures.cc | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeatures.fwd.hh | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeatures.hh | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeaturesCreator.cc | Header for ResidueSecondaryStructureFeaturesCreator for the ResidueSecondaryStructureFeatures load-time factory registration scheme |
| ResidueSecondaryStructureFeaturesCreator.hh | Header for ResidueSecondaryStructureFeaturesCreator for the ResidueSecondaryStructureFeatures load-time factory registration scheme |
| ResidueTotalScoresFeatures.cc | Report the total per residue score to a features database |
| ResidueTotalScoresFeatures.fwd.hh | Report the total per residue score to a features database |
| ResidueTotalScoresFeatures.hh | Report the total per residue score to a features database |
| ResidueTotalScoresFeaturesCreator.cc | Header for ResidueTotalScoresFeaturesCreator for the FeaturesReporter load-time factory registration scheme |
| ResidueTotalScoresFeaturesCreator.hh | Header for ResidueTotalScoresFeaturesCreator for the ResidueTotalScoresFeatures load-time factory registration scheme |
| ResidueTypesFeatures.cc | Report ResidueTypes to features Statistics Scientific Benchmark |
| ResidueTypesFeatures.fwd.hh | Report ResidueTypes geometry and scores to features Statistics Scientific Benchmark |
| ResidueTypesFeatures.hh | Report ResidueTypes features Statistics Scientific Benchmark |
| ResidueTypesFeaturesCreator.cc | Header for ResidueTypesFeaturesCreator for the ResidueTypesFeatures load-time factory registration scheme |
| ResidueTypesFeaturesCreator.hh | Header for ResidueTypesFeaturesCreator for the ResidueTypesFeatures load-time factory registration scheme |
| RotamerBoltzmannWeightFeatures.cc | Report residue burial to features statistics scientific benchmark |
| RotamerBoltzmannWeightFeatures.fwd.hh | Report rotamer boltzmann weights to features Statistics Scientific Benchmark |
| RotamerBoltzmannWeightFeatures.hh | Report rotamer boltzmann weights to features Statistics Scientific Benchmark |
| RotamerBoltzmannWeightFeaturesCreator.cc | Header for RotamerBoltzmannWeightFeaturesCreator for the RotamerBoltzmannWeightFeatures load-time factory registration scheme |
| RotamerBoltzmannWeightFeaturesCreator.hh | Header for RotamerBoltzmannWeightFeaturesCreator for the RotamerBoltzmannWeightFeatures load-time factory registration scheme |
| RotamerFeatures.cc | Report rotamer library features to the database |
| RotamerFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| RotamerFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| RotamerFeaturesCreator.cc | Header for RotamerFeaturesCreator for the RotamerFeatures load-time factory registration scheme |
| RotamerFeaturesCreator.hh | Header for RotamerFeaturesCreator for the RotamerFeatures load-time factory registration scheme |
| RotamerRecoveryFeatures.cc | Report rotamer recover features and scores to features Statistics Scientific Benchmark |
| RotamerRecoveryFeatures.fwd.hh | Report Rotamer Recovery features to features Statistics Scientific Benchmark |
| RotamerRecoveryFeatures.hh | Report Rotamer Recovery Statistics Scientific Benchmark |
| RotamerRecoveryFeaturesCreator.cc | Header for RotamerRecoveryFeaturesCreator for the RotamerRecoveryFeatures load-time factory registration scheme |
| RotamerRecoveryFeaturesCreator.hh | Header for RotamerRecoveryFeaturesCreator for the RotamerRecoveryFeatures load-time factory registration scheme |
| RuntimeFeatures.cc | |
| RuntimeFeatures.fwd.hh | |
| RuntimeFeatures.hh | |
| RuntimeFeaturesCreator.hh | |
| SaltBridgeFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| SaltBridgeFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| SaltBridgeFeatures.hh | Report comments stored with each pose |
| SaltBridgeFeaturesCreator.cc | Header for SaltBridgeFeaturesCreator for the SaltBridgeFeatures load-time factory registration scheme |
| SaltBridgeFeaturesCreator.hh | Header for SaltBridgeFeaturesCreator for the SaltBridgeFeatures load-time factory registration scheme |
| ScoreFunctionFeatures.cc | Report the score parameters to a features database |
| ScoreFunctionFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreFunctionFeatures.hh | Add score function parameters to a features database |
| ScoreFunctionFeaturesCreator.cc | Header for ScoreFunctionFeaturesCreator for the ScoreFunctionFeatures load-time factory registration scheme |
| ScoreFunctionFeaturesCreator.hh | Header for ScoreFunctionFeaturesCreator for the ScoreFunctionFeatures load-time factory registration scheme |
| ScoreTypeFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| ScoreTypeFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreTypeFeatures.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreTypeFeaturesCreator.cc | Header for ScoreTypeFeaturesCreator for the ScoreTypeFeatures load-time factory registration scheme |
| ScoreTypeFeaturesCreator.hh | Header for ScoreTypeFeaturesCreator for the ScoreTypeFeatures load-time factory registration scheme |
| ScreeningFeatures.cc | Report JSON object with information needed for vHTS postprocessing |
| ScreeningFeatures.fwd.hh | Forward headers for ScreeningFeatuers |
| ScreeningFeatures.hh | Report JSON object with information needed for vHTS postprocessing |
| ScreeningFeaturesCreator.cc | |
| ScreeningFeaturesCreator.hh | |
| SecondaryStructureSegmentFeatures.cc | |
| SecondaryStructureSegmentFeatures.fwd.hh | |
| SecondaryStructureSegmentFeatures.hh | |
| SecondaryStructureSegmentFeaturesCreator.cc | |
| SecondaryStructureSegmentFeaturesCreator.hh | |
| SmotifFeatures.cc | Calculate 4 geometric values used to classify smotifs. Reference (http://www.ncbi.nlm.nih.gov/pubmed/20421995) |
| SmotifFeatures.fwd.hh | |
| SmotifFeatures.hh | |
| SmotifFeaturesCreator.cc | |
| SmotifFeaturesCreator.hh | |
| StructureFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| StructureFeatures.fwd.hh | Report structure features to features Statistics Scientific Benchmark |
| StructureFeatures.hh | Report structure identifiers to a features database |
| StructureFeaturesCreator.cc | Header for StructureFeaturesCreator for the StructureFeatures load-time factory registration scheme |
| StructureFeaturesCreator.hh | Header for StructureFeaturesCreator for the StructureFeatures load-time factory registration scheme |
| StructureScoresFeatures.cc | Report structure score features to a features database |
| StructureScoresFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| StructureScoresFeatures.hh | Structure scores to features Statistics Scientific Benchmark |
| StructureScoresFeaturesCreator.cc | Header for StructureScoresFeaturesCreator for the StructureScoresFeatures load-time factory registration scheme |
| StructureScoresFeaturesCreator.hh | Header for StructureScoresFeaturesCreator for the StructureScoresFeatures load-time factory registration scheme |
| TaskOperationFeatures.cc | Report |
| TaskOperationFeatures.fwd.hh | Report |
| TaskOperationFeatures.hh | Report |
| TaskOperationFeaturesCreator.cc | Header |
| TaskOperationFeaturesCreator.hh | Header |
| TotalScoreFeatures.cc | |
| TotalScoreFeatures.fwd.hh | |
| TotalScoreFeatures.hh | |
| TotalScoreFeaturesCreator.hh | |
| TrajectoryMapFeatures.cc | Map trajectory structure_ids to cycle number |
| TrajectoryMapFeatures.fwd.hh | Map trajectory structure_ids to cycle number |
| TrajectoryMapFeatures.hh | Map trajectory structure_ids to cycle number |
| TrajectoryMapFeaturesCreator.cc | Header for TrajectoryMapFeaturesCreator for the TrajectoryMapFeatures load-time factory registration scheme |
| TrajectoryMapFeaturesCreator.hh | Header for TrajectoryMapFeaturesCreator for the TrajectoryMapFeatures load-time factory registration scheme |
| TrajectoryReportToDB.cc | Report features data to database multiple times per structure, creating a trajectory |
| TrajectoryReportToDB.fwd.hh | Report features data to database multiple times per structure, creating a trajectory |
| TrajectoryReportToDB.hh | Report features data to database multiple times per structure, creating a trajectory |
| TrajectoryReportToDBCreator.hh | This class will create instances of Mover TrajectoryReportToDB for the MoverFactory |
| UnrecognizedAtomFeatures.cc | Report unrecognized atoms features to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeatures.fwd.hh | Report residue features to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeaturesCreator.cc | Header for UnrecognizedAtomFeaturesCreator for the UnrecognizedAtomFeatures load-time factory registration scheme |
| UnrecognizedAtomFeaturesCreator.hh | Header for UnrecognizedAtomFeaturesCreator for the UnrecognizedAtomFeatures load-time factory registration scheme |
| util.cc | |
| util.hh | |
| WaterFeatures.cc | |
| WaterFeatures.fwd.hh | |
| WaterFeatures.hh | Report geometry between water and hbond sites |
| WaterFeaturesCreator.cc | Header for WaterFeaturesCreator for the WaterFeatures load-time factory registration scheme |
| WaterFeaturesCreator.hh | Header for WaterFeaturesCreator for the WaterFeatures load-time factory registration scheme |
| ► fibril | |
| fibril_util.cc | Utility functions for handling of fibril symmetry modeling |
| fibril_util.hh | Utility functions for handling with symmetric fibril |
| SetupForFibrilMover.cc | |
| SetupForFibrilMover.fwd.hh | |
| SetupForFibrilMover.hh | |
| ► filters | |
| BasicFilterCreators.hh | FilterCreators for the most basic of filters |
| BasicFilters.cc | |
| BasicFilters.fwd.hh | Forward declaration for Filter base class |
| BasicFilters.hh | Header file for very simple Filter classes |
| CalculatorFilter.cc | Combine several filters in a (semi) arbitrary calculation |
| CalculatorFilter.fwd.hh | Forward declaration for CalculatorFilter |
| CalculatorFilter.hh | Combine several filters in a (semi) arbitrary calculation |
| CalculatorFilterCreator.hh | FilterCreator for the CalculatorFilter |
| ContingentFilter.cc | |
| ContingentFilter.fwd.hh | Forward declaration for ContingentFilter |
| ContingentFilter.hh | A filter that is contingent on some other mover to set its pass/fail value |
| ContingentFilterCreator.hh | FilterCreator for the ContingentFilter |
| Filter.cc | |
| Filter.fwd.hh | Forward declaration for Filter base class |
| Filter.hh | Header file for Filter base class |
| FilterCreator.cc | |
| FilterCreator.hh | Base class for FilterCreators for the Filter load-time factory registration scheme |
| FilterFactory.cc | |
| FilterFactory.fwd.hh | Forward declaration of Factory class for Filters |
| FilterFactory.hh | |
| ReplicateFilter.cc | Repeat a subfilter multiple times, and pass a value based on the aggregate results |
| ReplicateFilter.fwd.hh | Forward declaration for ReplicateFilter |
| ReplicateFilter.hh | Repeat a subfilter multiple times, and pass a value based on the aggregate results |
| ReplicateFilterCreator.hh | FilterCreator for the ReplicateFilter |
| TimeFilter.cc | |
| TimeFilter.hh | |
| TimeFilterCreator.hh | FilterCreator for the TimeFilter |
| ► fldsgn | |
| ► filters | |
| CoreDunbrackFilter.cc | Filter structures by packstat score |
| CoreDunbrackFilter.fwd.hh | |
| CoreDunbrackFilter.hh | Header file for CoreDunbrackFilter class |
| CoreDunbrackFilterCreator.hh | FilterCreators for the CoreDunbrackFilter |
| FragQualFilter.cc | Filter structures by packstat score |
| FragQualFilter.fwd.hh | |
| FragQualFilter.hh | Header file for FragQualFilter class |
| FragQualFilterCreator.hh | FilterCreators for the FragQualFilter |
| HelixKinkFilter.cc | |
| HelixKinkFilter.fwd.hh | |
| HelixKinkFilter.hh | Header file for HelixKinkFilter class |
| HelixKinkFilterCreator.hh | FilterCreators for the HelixKinkFilter |
| HelixPairingFilter.cc | Filter structures by sheet topology |
| HelixPairingFilter.fwd.hh | |
| HelixPairingFilter.hh | Header file for HelixPairingFilter class |
| HelixPairingFilterCreator.hh | FilterCreators for the HelixPairingFilter |
| HSSTripletFilter.cc | Filter structures by hsstriplets angle and distance |
| HSSTripletFilter.fwd.hh | |
| HSSTripletFilter.hh | Header file for HSSTripletFilter class |
| HSSTripletFilterCreator.hh | FilterCreators for the HSSTripletFilter |
| InterlockingAromaFilter.cc | Filter structures by packstat score |
| InterlockingAromaFilter.fwd.hh | |
| InterlockingAromaFilter.hh | Header file for InterlockingAromaFilter class |
| InterlockingAromaFilterCreator.hh | FilterCreators for the InterlockingAromaFilter |
| NcontactsFilter.cc | Filter structures by sheet topology |
| NcontactsFilter.fwd.hh | |
| NcontactsFilter.hh | Header file for NcontactsFilter class |
| NcontactsFilterCreator.hh | FilterCreators for the NcontactsFilter |
| ParallelBetaPairingPreferenceFilter.cc | Filter structures by parallel beta pairing preference |
| ParallelBetaPairingPreferenceFilter.fwd.hh | |
| ParallelBetaPairingPreferenceFilter.hh | Header file for ParallelBetaPairingPreferenceFilter class |
| ParallelBetaPairingPreferenceFilterCreator.hh | FilterCreators for the ParallelBetaPairingPreferenceFilter |
| SecondaryStructureCountFilter.cc | Filter structures by number of secondary structures |
| SecondaryStructureCountFilter.fwd.hh | |
| SecondaryStructureCountFilter.hh | Header file for SecondaryStructureCountFilter class |
| SecondaryStructureCountFilterCreator.hh | FilterCreators for the SecondaryStructureCountFilter |
| SecondaryStructureFilter.cc | Filter structures by sheet topology |
| SecondaryStructureFilter.fwd.hh | |
| SecondaryStructureFilter.hh | Header file for SecondaryStructureFilter class |
| SecondaryStructureFilterCreator.hh | FilterCreators for the SecondaryStructureFilter |
| SecondaryStructureHasResidueFilter.cc | Filter structures by number of secondary structures |
| SecondaryStructureHasResidueFilter.fwd.hh | |
| SecondaryStructureHasResidueFilter.hh | Header file for SecondaryStructureHasResidueFilter class |
| SecondaryStructureHasResidueFilterCreator.hh | FilterCreators for the SecondaryStructureHasResidueFilter |
| SheetTopologyFilter.cc | Filter structures by sheet topology |
| SheetTopologyFilter.fwd.hh | |
| SheetTopologyFilter.hh | Header file for SheetTopologyFilter class |
| SheetTopologyFilterCreator.hh | FilterCreators for the SheetTopologyFilter |
| ► potentials | |
| ► sspot | |
| HSPairPotential.cc | |
| HSPairPotential.fwd.hh | |
| HSPairPotential.hh | |
| NatbiasHelicesSheetPotential.cc | Native-biased centroid score for helices on sheets |
| NatbiasHelicesSheetPotential.fwd.hh | |
| NatbiasHelicesSheetPotential.hh | Centroid score for helices on sheet |
| NatbiasHelixPairPotential.cc | Calss for helix-pairing potential |
| NatbiasHelixPairPotential.fwd.hh | |
| NatbiasHelixPairPotential.hh | Header file of NatbiasHelixPairPotential |
| NatbiasSecondaryStructureEnergy.cc | Native biased centroid score for secondary structures |
| NatbiasSecondaryStructureEnergy.fwd.hh | |
| NatbiasSecondaryStructureEnergy.hh | Native biased centroid score for secondary structure |
| NatbiasSecondaryStructureEnergyCreator.hh | Declaration for the class that connects NatbiasSecondaryStructureEnergy with the ScoringManager |
| NatbiasStrandPairPotential.cc | |
| NatbiasStrandPairPotential.fwd.hh | |
| NatbiasStrandPairPotential.hh | Native biased centroid score for strand pairings |
| SSPairPotential.cc | |
| SSPairPotential.fwd.hh | |
| SSPairPotential.hh | |
| util.cc | |
| util.hh | Helper functions for SSPairPotential and HSPairPotential |
| AACompositionEnergy.cc | |
| AACompositionEnergy.fwd.hh | |
| AACompositionEnergy.hh | Amino acid composition energy |
| AACompositionEnergyCreator.hh | Declaration for the class that connects AACompositionEnergy with the ScoringManager |
| SetAACompositionPotential.cc | |
| SetAACompositionPotential.fwd.hh | Forward declaration for SetAACompositionPotential |
| SetAACompositionPotential.hh | |
| SetAACompositionPotentialCreator.hh | |
| SetSecStructEnergies.cc | Mover for setting centroid score of secondary structure through parser |
| SetSecStructEnergies.fwd.hh | Forward declaration for SetSecStructEnergies |
| SetSecStructEnergies.hh | Mover for setting centroid score of secondary structure through parser |
| SetSecStructEnergiesCreator.hh | |
| ► topology | |
| BB_Pos.cc | |
| BB_Pos.fwd.hh | |
| BB_Pos.hh | Bb_pos class header |
| BetaAlphaBetaMotif.cc | Class for beta alpha beta motifs |
| BetaAlphaBetaMotif.fwd.hh | |
| BetaAlphaBetaMotif.hh | |
| DimerPairing.cc | |
| DimerPairing.fwd.hh | |
| DimerPairing.hh | |
| HelixPairing.cc | Class for helix pairings |
| HelixPairing.fwd.hh | |
| HelixPairing.hh | Header file of HelixPairing.cc |
| HSSTriplet.cc | |
| HSSTriplet.fwd.hh | |
| HSSTriplet.hh | |
| Sheet.cc | |
| Sheet.fwd.hh | |
| Sheet.hh | |
| SheetFoldTypeManager.cc | |
| SheetFoldTypeManager.fwd.hh | |
| SheetFoldTypeManager.hh | |
| SS_Info2.cc | |
| SS_Info2.fwd.hh | |
| SS_Info2.hh | |
| StrandPairing.cc | |
| StrandPairing.fwd.hh | |
| StrandPairing.hh | |
| util.cc | Utilities for fldsgn/topology |
| util.hh | |
| BluePrintBDR.cc | |
| BluePrintBDR.fwd.hh | Forward declaration for BluePrintBDR |
| BluePrintBDR.hh | |
| BluePrintBDRCreator.hh | This class will create instances of Mover BluePrintBDR for the MoverFactory |
| CircularPermutation.cc | Perform circularpermutation give a pose ( under development ) |
| CircularPermutation.fwd.hh | Forward declaration for CircularPermutation |
| CircularPermutation.hh | |
| CircularPermutationCreator.hh | |
| MatchResidues.cc | |
| MatchResidues.hh | Header file for MatchResidues class |
| MatchResiduesMover.cc | |
| MatchResiduesMover.fwd.hh | |
| MatchResiduesMover.hh | Header file for MatchResiduesMover class |
| MatchResiduesMoverCreator.hh | MoverCreator for the MatchResiduesMover |
| NcontactsCalculator.cc | Calculate #atom contacts divided by pose.total_residue() in a given pose |
| NcontactsCalculator.hh | Header file for NcontactsCalculator class |
| SheetConstraintsRCG.cc | |
| SheetConstraintsRCG.fwd.hh | |
| SheetConstraintsRCG.hh | |
| SheetCstGeneratorCreator.hh | This class will create instances of the SheetConstraintsRCG mover |
| ► flexpack | |
| ► annealer | |
| FlexbbSimAnnealer.cc | Annealer for optimizing both backbone and sidechain conformations implementation |
| FlexbbSimAnnealer.fwd.hh | Forward declarations and typedefs for the FlexbbSimAnnealer class |
| FlexbbSimAnnealer.hh | |
| ► interaction_graph | |
| FlexbbIGFactory.cc | |
| FlexbbIGFactory.fwd.hh | |
| FlexbbIGFactory.hh | |
| FlexbbInteractionGraph.cc | Declaration for flexible-backbone-packing interaction graph interface & base classes |
| FlexbbInteractionGraph.fwd.hh | Forward declaration of base-class FlexbbIG and associated typedefs |
| FlexbbInteractionGraph.hh | Declaration for flexible-backbone-packing interaction graph interface & base classes |
| FlexbbSparseMatrixIndex.hh | Declaration of class for maintaining sparse matrix indices for flexbb states |
| MinimalistFlexbbInteractionGraph.cc | Class implementation for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| MinimalistFlexbbInteractionGraph.fwd.hh | Class forward declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| MinimalistFlexbbInteractionGraph.hh | Class declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| OTFFlexbbInteractionGraph.cc | Class implementation for OTF flexbb IG |
| OTFFlexbbInteractionGraph.fwd.hh | |
| OTFFlexbbInteractionGraph.hh | Declaration for on-the-fly flexible-backbone-packing interaction graph interface & base classes |
| PrecomputedFlexbbInteractionGraph.cc | |
| PrecomputedFlexbbInteractionGraph.fwd.hh | |
| PrecomputedFlexbbInteractionGraph.hh | |
| ► rotamer_set | |
| FlexbbRotamerSet.cc | Declaration for a class to hold rotamers for a single backbone conformation in a flexible packing run |
| FlexbbRotamerSet.fwd.hh | |
| FlexbbRotamerSet.hh | Declaration for a class to hold rotamers for a single backbone conformation in a flexible packing run |
| FlexbbRotamerSets.cc | |
| FlexbbRotamerSets.fwd.hh | |
| FlexbbRotamerSets.hh | Declaration for a class to hold a set of rotamers for a flexible packing run |
| FlexPacker.cc | |
| FlexPacker.fwd.hh | |
| FlexPacker.hh | |
| OtherContextScoreFunction.cc | |
| OtherContextScoreFunction.hh | |
| ► flexpep_docking | |
| FlexPepDockingAbInitio.cc | Low-resolution part of docking protocol |
| FlexPepDockingAbInitio.fwd.hh | |
| FlexPepDockingAbInitio.hh | Low-resolution agressive ab-initio folding and docking of peptide |
| FlexPepDockingFlags.cc | Flags structure for FlexPepDocking protocols |
| FlexPepDockingFlags.fwd.hh | Flags structure for FlexPepDocking protocols - forward declarations |
| FlexPepDockingFlags.hh | Flags structure for FlexPepDocking protocols |
| FlexPepDockingLowRes.cc | Low-resolution part of docking protocol |
| FlexPepDockingLowRes.fwd.hh | |
| FlexPepDockingLowRes.hh | Low-resolution part of docking protocol |
| FlexPepDockingPoseMetrics.cc | Metrics calculations specific for FlexPepDock (at least for now) |
| FlexPepDockingPoseMetrics.fwd.hh | |
| FlexPepDockingPoseMetrics.hh | Metrics calculations specific for FlexPepDock (at least for now) |
| FlexPepDockingProtocol.cc | Protocol for docking flexible peptides onto globular proteins |
| FlexPepDockingProtocol.hh | Protocol for docking flexible peptides onto globular proteins |
| FlexPepDockingProtocolCreator.hh | |
| ► floppy_tail | |
| FloppyTail_publication.cc | FloppyTail extra functions from original publication - this calculates some statistics used for the first published use of the code (Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379.) |
| FloppyTail_publication.hh | FloppyTail extra functions from original publication - this calculates some statistics used for the first published use of the code (Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379.) |
| FloppyTailMover.cc | This app was initially intended for modeling the binding of a long unstructured C-terminal tail to some other part of a protein. It now works for N-terminal, C-terminal, and internal flexible regions. It works best as a method for sampling space to see what is possible, preferably in conjunction with extensive experimental constraints. It is not meant to produce ab-initio style models of folded complexes |
| FloppyTailMover.fwd.hh | FloppyTail forward declaration |
| FloppyTailMover.hh | FloppyTail headers |
| ► flxbb | |
| DesignTask.cc | |
| DesignTask.fwd.hh | |
| DesignTask.hh | |
| FilterStructs.cc | |
| FilterStructs.fwd.hh | |
| FilterStructs.hh | Filter structures |
| FlxbbDesign.cc | Perform cycles of design and relax with filter |
| FlxbbDesign.fwd.hh | Perform cycles of design and relax with filter |
| FlxbbDesign.hh | Perform cycles of design and relax with filter |
| FlxbbDesign_main.cc | |
| FlxbbDesign_main.hh | |
| FlxbbDesignCreator.hh | |
| InterlockAroma.cc | Place interlocking aromatic residues |
| InterlockAroma.fwd.hh | |
| InterlockAroma.hh | Perform cycles of design and relax with filter |
| InterlockAromaCreator.hh | This class will create instances of Mover InterlockAroma for the MoverFactory |
| LayerDesignOperation.cc | Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB |
| LayerDesignOperation.fwd.hh | |
| LayerDesignOperation.hh | Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA |
| LayerDesignOperationCreator.hh | |
| utility.cc | |
| utility.hh | |
| ► forge | |
| ► build | |
| ► SegmentInsertConnectionScheme | |
| SegmentInsertConnectionScheme_Enum.hh | |
| Bridge.cc | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| Bridge.fwd.hh | Forward declaration for Bridge |
| Bridge.hh | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| BuildInstruction.cc | Tracks modifications to be made and is capable of residue length changes on a Pose |
| BuildInstruction.fwd.hh | Forward declaration for BuildInstruction |
| BuildInstruction.hh | Tracks modifications to be made and is capable of residue length changes on a Pose |
| BuildManager.cc | Container for managing BuildInstructions |
| BuildManager.fwd.hh | Forward declaration for BuildManager |
| BuildManager.hh | Container for managing BuildInstructions |
| ConnectRight.cc | Instruction to connect one Pose onto the right side of another |
| ConnectRight.fwd.hh | Forward declaration for ConnectRight |
| ConnectRight.hh | Instruction to connect one Pose onto the right side of another |
| GrowLeft.cc | Instruction to create an n-side extension |
| GrowLeft.fwd.hh | Forward declaration for GrowLeft |
| GrowLeft.hh | Instruction to create an n-side extension |
| GrowRight.cc | Instruction to create a c-side extension |
| GrowRight.fwd.hh | Forward declaration for GrowRight |
| GrowRight.hh | Instruction to create a c-side extension |
| Interval.fwd.hh | Forward declaration for Interval |
| Interval.hh | Simple struct defining a closed interval of residues |
| RelativeConnectRight.cc | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeConnectRight.fwd.hh | Forward declaration for RelativeConnectRight |
| RelativeConnectRight.hh | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeSequencePosition.fwd.hh | Forward declaration for RelativeSequencePosition |
| RelativeSequencePosition.hh | Function objects to compute relative positions for RelativeConnectRight |
| SegmentInsert.cc | Insert an external segment flanked by new regions |
| SegmentInsert.fwd.hh | Forward declaration for SegmentInsert |
| SegmentInsert.hh | Insert an external segment flanked by new regions |
| SegmentRebuild.cc | Instruction to rebuild a segment |
| SegmentRebuild.fwd.hh | Forward declaration for SegmentRebuild |
| SegmentRebuild.hh | Instruction to rebuild a segment |
| SegmentSwap.cc | Instruction to swap a segment with an external segment |
| SegmentSwap.fwd.hh | Forward declaration for SegmentSwap |
| SegmentSwap.hh | Instruction to swap a segment with an external segment |
| ► components | |
| BDR.cc | |
| BDR.fwd.hh | Forward declaration for BDR |
| BDR.hh | |
| VarLengthBuild.cc | Component that performs a simplified version of a protocol for variable length remodeling of protein backbone segments |
| VarLengthBuild.fwd.hh | Forward declaration for protocols::forge::components::VarLengthBuild |
| VarLengthBuild.hh | Component that performs a simplified version of a protocol for variable length remodeling of protein backbone segments |
| ► constraints | |
| ConstraintFileCstGeneratorCreator.hh | This class will create instances of the ConstraintFileRCG mover |
| ConstraintFileRCG.cc | |
| ConstraintFileRCG.fwd.hh | |
| ConstraintFileRCG.hh | |
| InverseRotamersCstGeneratorCreator.hh | This class will create instances of the InverseRotamersRCG mover |
| InverseRotamersRCG.cc | |
| InverseRotamersRCG.fwd.hh | |
| InverseRotamersRCG.hh | |
| InvrotTreeCstGeneratorCreator.hh | This class will create instances of the InvrotTreeRCG mover |
| InvrotTreeRCG.cc | |
| InvrotTreeRCG.fwd.hh | |
| InvrotTreeRCG.hh | |
| NtoC_RCG.cc | |
| NtoC_RCG.fwd.hh | |
| NtoC_RCG.hh | |
| NtoCCstGeneratorCreator.hh | This class will create instances of the NtoC_RCG mover |
| RemoveCsts.cc | |
| RemoveCsts.hh | |
| RemoveCstsCreator.hh | This class will create instances of the RemoveCsts mover |
| ► methods | |
| chainbreak_eval.cc | Methods for chainbreak evaluation |
| chainbreak_eval.hh | Methods for chainbreak evaluation |
| fold_tree_functions.cc | Methods for manipulating FoldTrees |
| fold_tree_functions.hh | Methods for manipulating FoldTrees |
| fragment_functions.cc | Methods for manipulating fragments |
| fragment_functions.hh | Methods for manipulating fragments |
| pose_mod.cc | Methods for Pose modifications |
| pose_mod.hh | Methods for Pose modifications |
| util.cc | Miscellaneous utility functions for forge |
| util.hh | Miscellaneous utility functions for forge |
| ► remodel | |
| RemodelAccumulator.cc | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelAccumulator.hh | |
| RemodelConstraintGenerator.cc | |
| RemodelConstraintGenerator.fwd.hh | Abstract base class that generates constraints during forge loop remodelling |
| RemodelConstraintGenerator.hh | Abstract base class that generates constraints during forge loop remodelling |
| RemodelData.cc | |
| RemodelData.hh | |
| RemodelDesignMover.cc | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelDesignMover.hh | |
| RemodelEnzdesCstModule.cc | This file handles merging constraint defined by enzdes type cstfile |
| RemodelEnzdesCstModule.fwd.hh | This file handles merging constraint defined by enzdes type cstfile |
| RemodelEnzdesCstModule.hh | This file handles merging constraint defined by enzdes type cstfile |
| RemodelGlobalFrame.cc | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelGlobalFrame.fwd.hh | Forward declaration for RemodelGlobalFrame |
| RemodelGlobalFrame.hh | |
| RemodelLoopMover.cc | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelLoopMover.fwd.hh | Forward declaration for RemodelLoopMover |
| RemodelLoopMover.hh | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelMover.cc | |
| RemodelMover.fwd.hh | Forward declaration for RemodelMover |
| RemodelMover.hh | |
| RemodelMoverCreator.hh | |
| RemodelRotamerLinks.cc | |
| RemodelRotamerLinks.fwd.hh | |
| RemodelRotamerLinks.hh | When operated on a PackerTask, adds RotamerLinks to it that will |
| RemodelRotamerLinksCreator.hh | |
| RemodelWorkingSet.cc | |
| RemodelWorkingSet.hh | |
| ResidueVicinityCstGeneratorCreator.hh | This class will create instances of the ResidueVicinityRCG mover |
| ResidueVicinityRCG.cc | |
| ResidueVicinityRCG.hh | |
| ► frag_picker | |
| ► nonlocal | |
| NonlocalFrags.cc | |
| NonlocalFrags.fwd.hh | |
| NonlocalFrags.hh | |
| NonlocalFragsMain.cc | |
| NonlocalFragsMain.hh | |
| NonlocalPair.fwd.hh | Forward declaration for NonlocalPair |
| NonlocalPair.hh | Nonlocal fragment pair |
| ► quota | |
| ABEGO_SS_Config.cc | Reads a config file for quota selector |
| ABEGO_SS_Config.hh | Selector that picks best fragments based on their total score |
| ABEGO_SS_Map.cc | Map ABEGO vs. SS combinations |
| ABEGO_SS_Map.fwd.hh | |
| ABEGO_SS_Map.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| ABEGO_SS_Pool.cc | Quota selector based on difefrent secondary structure predicitons |
| ABEGO_SS_Pool.fwd.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| ABEGO_SS_Pool.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| QuotaCollector.cc | Pure virtual base class for a container holding fragment candidates |
| QuotaCollector.fwd.hh | Forward declaration for QuotaCollector |
| QuotaCollector.hh | Pure virtual base class for a container holding fragment candidates |
| QuotaConfig.cc | Reads a config file for quota selector |
| QuotaConfig.hh | Selector that picks best fragments based on their total score |
| QuotaPool.fwd.hh | Base class for a quota pool |
| QuotaPool.hh | Single pool used by quota |
| QuotaSelector.cc | Quota selector based on difefrent secondary structure predicitons |
| QuotaSelector.fwd.hh | |
| QuotaSelector.hh | Selector that picks best fragments based on their total score |
| SecondaryStructurePool.cc | Quota selector based on difefrent secondary structure predicitons |
| SecondaryStructurePool.fwd.hh | Class for a quota pool based on secondary structure prediction |
| SecondaryStructurePool.hh | Quota pool based on secondary structure prediction |
| ► scores | |
| ABEGO_SS_Score.cc | Scores a fragment by secondary structure similarity |
| ABEGO_SS_Score.hh | Scores a fragment by secondary structure similarity |
| AdaptiveScoreHistogram.cc | |
| AdaptiveScoreHistogram.fwd.hh | AdaptiveScoreHistogram forward declaration |
| AdaptiveScoreHistogram.hh | A very basic histogram to keep statistics of scores |
| AmbigCSScore.cc | Object that scores a fragment by target-observed/vall-predicted chemical shift distances |
| AmbigCSScore.hh | Object that scores a fragment by its crmsd to the native |
| AtomBasedConstraintsScore.cc | |
| AtomBasedConstraintsScore.fwd.hh | AtomBasedConstraintsScore forward declaration |
| AtomBasedConstraintsScore.hh | |
| AtomPairConstraintsScore.cc | |
| AtomPairConstraintsScore.fwd.hh | FragmentScoreManager forward declaration |
| AtomPairConstraintsScore.hh | |
| BFactor.cc | Base class for fragment scoring |
| BFactor.hh | Base class for fragment scoring |
| CachingScoringMethod.hh | Adds cashing functionality to a FragmentScoringMethod object |
| ConstScore.hh | Score that adds a constant (so basically it does nothing!) |
| CSScore.cc | Object that scores a fragment by target-observed/vall-predicted chemical shift distances |
| CSScore.hh | Object that scores a fragment by its crmsd to the native |
| DihedralConstraintsScore.cc | Calculates a score based on how close are dihdral angles in a Vall chunk to their target values |
| DihedralConstraintsScore.fwd.hh | DihedralConstraintsScore forward declaration |
| DihedralConstraintsScore.hh | |
| DisulfideDistance.cc | Scores fragments by disulfide-linke Calpha distances |
| DisulfideDistance.hh | Scores fragments by disulfide-linke Calpha distances |
| DisulfideIdentity.cc | Base class for fragment scoring |
| DisulfideIdentity.hh | Base class for fragment scoring |
| FourAtomsConstraintData.cc | Holder for data necessary to create a single constraint based on four atoms |
| FourAtomsConstraintData.fwd.hh | DihedralConstraintsScore forward declaration |
| FourAtomsConstraintData.hh | Holder for data necessary to create a single constraint based on four atoms |
| fragment_scoring_utilities.cc | Functions and data types common for fragment scoring |
| fragment_scoring_utilities.hh | Functions and data types common for fragment scoring |
| FragmentAllAtomCrmsd.cc | Object that scores a fragment by its crmsd to the native |
| FragmentAllAtomCrmsd.hh | Object that scores a fragment by its crmsd to the native |
| FragmentChunkCrms.cc | |
| FragmentChunkCrms.hh | Object that scores a fragment by its tmscore to the native |
| FragmentCrmsd.cc | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsd.hh | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsdResDepth.cc | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsdResDepth.hh | Object that scores a fragment by its crmsd and residue depth to the native |
| FragmentDME.cc | Object that scores a fragment by its Distance Matrix Error (DME) to the native |
| FragmentDME.hh | Object that scores a fragment by its Distance Matrix Error (DME) to the native |
| FragmentScoreManager.cc | |
| FragmentScoreManager.fwd.hh | FragmentScoreManager forward declaration |
| FragmentScoreManager.hh | Score manager |
| FragmentScoreMap.fwd.hh | FragmentScoreMap forward declaration |
| FragmentScoreMap.hh | |
| FragmentScoringMethod.fwd.hh | FragmentScoringMethod forward declaration |
| FragmentScoringMethod.hh | Base class for fragment scoring |
| GunnCost.cc | |
| GunnCost.hh | |
| GunnCostScore.cc | Object that scores a fragment by its crmsd to the native |
| GunnCostScore.hh | Object that scores a fragment by Gunn cost function (how it fits to the local structure) |
| HydrophobicityProfileSimilarity.cc | Base class for fragment scoring |
| HydrophobicityProfileSimilarity.hh | Object that scores a fragment by hydrophobicity |
| HydrophobicitySimilarity.cc | Base class for fragment scoring |
| HydrophobicitySimilarity.hh | Object that scores a fragment by hydrophobicity |
| InterbondAngleScore.cc | |
| InterbondAngleScore.fwd.hh | DihedralConstraintsScore forward declaration |
| InterbondAngleScore.hh | |
| JCoupling.cc | Object that scores a fragment by root mean square deviation of Phi && Psi dihedrals |
| JCoupling.hh | Object that scores a fragment by its crmsd to the native |
| LAMBEGO_Similarity.cc | |
| LAMBEGO_Similarity.hh | Scores a fragment based on scores for a probability over torsion bins |
| MidPhiOut.cc | Object that scores a fragment by root mean square deviation of Phi && Psi dihedrals |
| MidPhiOut.hh | Object that scores a fragment by its crmsd to the native |
| MidPsiOut.cc | Object that scores a fragment by root mean square deviation of Psi && Psi dihedrals |
| MidPsiOut.hh | Object that scores a fragment by its crmsd to the native |
| PartialSecondarySimilarity.cc | Scores a fragment by secondary structure similarity but throws out the worst 20% of the residue matches |
| PartialSecondarySimilarity.hh | Scores a fragment by secondary structure similarity but throws out the worst 20% of the residue matches |
| PCS_FragDistance.cc | Scores fragments by disulfide-linke Calpha distances |
| PCS_FragDistance.hh | Scores fragments by disulfide-linke Calpha distances |
| Phi.cc | Base class for fragment scoring |
| Phi.hh | Object that scores a fragment by predicted Phi torsions |
| PhiPsiRmsd.cc | Object that scores a fragment by root mean square deviation of Phi && Psi dihedrals |
| PhiPsiRmsd.hh | Object that scores a fragment by its crmsd to the native |
| PhiPsiSquareWell.cc | Object that scores a fragment by root mean square deviation of Phi && Psi dihedrals |
| PhiPsiSquareWell.hh | Object that scores a fragment by its crmsd to the native |
| ProfileScore.cc | Scores a fragment by an amino acid sequence identity |
| ProfileScore.fwd.hh | FragmentScoringMethod forward declaration |
| ProfileScore.hh | Scores a fragment by an amino acid sequence identity |
| ProfileScoreBlosum62.cc | Scores a fragment by an amino acid sequence identity |
| ProfileScoreBlosum62.hh | Scores a fragment by Blosum62 profile score |
| ProfileScoreDistWeight.cc | Scores a fragment by weighting L1 profile distances by residue type |
| ProfileScoreDistWeight.hh | Scores a fragment by weighting L1 profile distances by residue type |
| ProfileScoreL1.cc | Scores a fragment by an amino acid sequence identity |
| ProfileScoreL1.hh | Scores a fragment by L1 profile score |
| ProfileScoreStructL1.cc | Scores a fragment using structure based profiles |
| ProfileScoreStructL1.hh | Scores a fragment by L1 structure based profile score |
| ProfileScoreSubMatrix.cc | Scores a fragment by substitution matrix (e.g. Blosum62) profile score |
| ProfileScoreSubMatrix.hh | Scores a fragment by substitution matrix (e.g. Blosum62) profile score |
| ProlinePhiScore.cc | Base class for fragment scoring |
| ProlinePhiScore.hh | Base class for fragment scoring |
| Psi.cc | Base class for fragment scoring |
| Psi.hh | Object that scores a fragment by predicted Psi torsions |
| PValuedFragmentScoreManager.cc | |
| PValuedFragmentScoreManager.hh | Score manager that stores statistics of all scores. This allows estimate p-value for a score |
| RamaScore.cc | Ramachandran surface scores for fragment picking |
| RamaScore.hh | Base class for fragment scoring |
| RDCScore.cc | Object that scores a fragment by its RDC |
| RDCScore.hh | Object that scores a fragment by its crmsd to the native |
| ScoreEValuator.cc | Scores a fragment by an amino acid sequence identity |
| ScoreEValuator.hh | Object that scores a fragment by its crmsd to the native |
| SecondaryIdentity.cc | Scores a fragment by an amino acid sequence identity |
| SecondaryIdentity.hh | Scores a fragment by an amino acid sequence identity |
| SecondarySimilarity.cc | Scores a fragment by secondary structure similarity |
| SecondarySimilarity.hh | Scores a fragment by secondary structure similarity |
| SequenceIdentity.cc | Base class for fragment scoring |
| SequenceIdentity.hh | Base class for fragment scoring |
| SolventAccessibility.cc | Base class for fragment scoring |
| SolventAccessibility.hh | Object that scores a fragment by predicted solvent accessibility |
| TalosSSSimilarity.cc | Scores a fragment by secondary structure similarity |
| TalosSSSimilarity.hh | Scores a fragment by secondary structure similarity |
| TorsionBinSimilarity.cc | |
| TorsionBinSimilarity.hh | Scores a fragment based on scores for a probability over torsion bins |
| BestTotalScoreSelector.cc | Selector that picks best fragments based on their total score |
| BestTotalScoreSelector.fwd.hh | |
| BestTotalScoreSelector.hh | Selector that picks best fragments based on their total score |
| BoundedCollector.fwd.hh | |
| BoundedCollector.hh | |
| CandidatesCollector.fwd.hh | Forward declaration for CandidatesCollector |
| CandidatesCollector.hh | Pure virtual base class for a container holding fragment candidates |
| CommonFragmentComparators.fwd.hh | Few ways to compare fragment candidates (forward definitions) |
| CommonFragmentComparators.hh | Few ways to compare fragment candidates |
| CompositeFragmentSelector.cc | Selector that picks best fragments based on their total score |
| CompositeFragmentSelector.hh | Selector that picks best fragments based on their total score |
| Contact.fwd.hh | Forward declaration for a Contact |
| Contact.hh | A contact |
| ContactCounts.fwd.hh | Forward declaration for a ContactCounts |
| ContactCounts.hh | Contact counts |
| ContactTypes.cc | Fragment picker contact types |
| ContactTypes.hh | Fragment picker type declarations |
| CS2ndShift.cc | |
| CS2ndShift.hh | Class that converts Talos object into secondary shifts list |
| CSTalosIO.cc | |
| CSTalosIO.hh | Class that reads and writes chemical shifts in TALOS format |
| CustomScoreSelector.cc | Selector that picks best fragments based on their total score |
| CustomScoreSelector.fwd.hh | |
| CustomScoreSelector.hh | Selector that picks best fragments based on their total score |
| DiversifyCrmsdByClustering.cc | Selector that picks fragments diferent enough from the fragments that have been already picked |
| DiversifyCrmsdByClustering.hh | Selector that picks fragments diversified by crmsd (by means of hierarchical clustering) |
| DiversifyCrmsdSelector.cc | Selector that picks fragments diferent enough from the fragments that have been already picked |
| DiversifyCrmsdSelector.hh | Selector that picks best fragments based on their total score |
| DiversifyDihedralsSelector.cc | Selector that picks fragments diferent enough from the fragments that have been already picked |
| DiversifyDihedralsSelector.hh | Selector that picks best fragments based on their total score |
| Faraggi_SA.cc | Faraggi maximum SA values from Faraggi et al. Proteins 2008 |
| Faraggi_SA.hh | Faraggi maximum SA values from Faraggi et al. Proteins 2008 |
| FragmentCandidate.cc | Something that might become a fragment if its scores will be good enough |
| FragmentCandidate.fwd.hh | |
| FragmentCandidate.hh | Something that might become a fragment if its scores will be good enough |
| FragmentComparatorBase.fwd.hh | Few ways to compare fragment candidates (forward definitions) |
| FragmentComparatorBase.hh | Defines a base class for all fragment comparators |
| FragmentPicker.cc | Fragment picker - the core part of picking machinery |
| FragmentPicker.fwd.hh | Fragment picker - forward declaration |
| FragmentPicker.hh | Fragment picker - the core part of picking machinery |
| FragmentSelectingRule.fwd.hh | |
| FragmentSelectingRule.hh | Selector that picks best fragments based on their total score |
| GrabAllCollector.hh | |
| JCouplingIO.cc | |
| JCouplingIO.hh | Class that reads and writes chemical shifts in TALOS format |
| LAMBEGO_IO.cc | |
| LAMBEGO_IO.hh | Reader for a probability distribution over A,B,E,G,O torsion bins |
| LazySortedVector1.hh | |
| PdbIdChunkFilter.cc | Defines two basic chunk filters based on pdb id |
| PdbIdChunkFilter.fwd.hh | Defines two basic chunk filters based on pdb id |
| PdbIdChunkFilter.hh | Defines two basic chunk filters based on pdb id |
| PhiPsiTalosIO.cc | |
| PhiPsiTalosIO.hh | Class that reads and writes Phi-Psi in TALOS format |
| SidechainContactDistCutoff.cc | Defines sidechain contact distance cutoffs |
| SidechainContactDistCutoff.fwd.hh | |
| SidechainContactDistCutoff.hh | Defines sidechain contact distance cutoffs |
| TorsionBinIO.cc | |
| TorsionBinIO.hh | Reader for a probability distribution over A,B,E,G,O torsion bins |
| VallChunk.cc | Contiguous chunk of residues taken from a vall |
| VallChunk.fwd.hh | Forward declaration for VallChunk |
| VallChunk.hh | Contiguous chunk of residues taken from a vall |
| VallChunkFilter.fwd.hh | Forward declaration for VallChunkFilter |
| VallChunkFilter.hh | Says whether a given chunk is interesting or not |
| VallProvider.cc | Reads a vall library and serves the data in chunks |
| VallProvider.fwd.hh | Forward declaration for VallProvider |
| VallProvider.hh | Reads a vall library and serves the data in chunks |
| VallResidue.cc | Class for managing a line of the Vall fragment library |
| VallResidue.fwd.hh | Forward declaration for core::fragment::picking::vall:VallResidue |
| VallResidue.hh | Class for managing a line of the Vall fragment library |
| ► frags | |
| heap.cc | |
| heap.hh | |
| RMSVallData.hh | |
| TorsionFragment.cc | |
| TorsionFragment.fwd.hh | |
| TorsionFragment.hh | |
| VallData.cc | |
| VallData.fwd.hh | |
| VallData.hh | |
| ► generalized_kinematic_closure | |
| ► filter | |
| GeneralizedKICfilter.cc | Helper class defining success filters for generalized closure of arbitrary segments that could go through side-chains (e.g. disulfides) |
| GeneralizedKICfilter.fwd.hh | Defines owning pointers for GeneralizedKICfilter class |
| GeneralizedKICfilter.hh | Headers for GeneralizedKICfilter class (helper class for the GeneralizedKIC mover that defines filters to accept/reject closure solutions). Filters must be pass/fail (i.e. there are no shades of grey, here.) |
| ► perturber | |
| GeneralizedKICperturber.cc | Helper class for generalized closure of arbitrary segments that could go through side-chains (e.g. disulfides) |
| GeneralizedKICperturber.fwd.hh | Defines owning pointers for GeneralizedKICperturber class |
| GeneralizedKICperturber.hh | Headers for GeneralizedKICperturber class (helper class for the GeneralizedKIC mover) |
| ► selector | |
| GeneralizedKICselector.cc | Helper class for GeneralizedKIC defining how solutions are chosen that pass filters |
| GeneralizedKICselector.fwd.hh | Defines owning pointers for GeneralizedKICselector class |
| GeneralizedKICselector.hh | Headers for GeneralizedKICselector class (helper class for the GeneralizedKIC mover that defines how closure solutions that pass filters are chosen) |
| GeneralizedKIC.cc | Kinematic closure of arbitrary segments that could go through side-chains (e.g. disulfides) |
| GeneralizedKIC.fwd.hh | Defines owning pointers for GeneralizedKIC mover class |
| GeneralizedKIC.hh | Headers for GeneralizedKIC mover class |
| GeneralizedKICCreator.hh | This class will create instances of Mover GeneralizedKIC for the MoverFactory |
| util.cc | Utility functions for generalized kinematic closure |
| util.hh | Headers for GeneralizedKIC utilities |
| ► genetic_algorithm | |
| Entity.cc | Unit employed/optimized by GeneticAlgorithm |
| Entity.fwd.hh | Unit employed/optimized by GeneticAlgorithm |
| Entity.hh | Unit employed/optimized by GeneticAlgorithm |
| EntityRandomizer.cc | Controls the alteration of the traits that define Entity |
| EntityRandomizer.fwd.hh | Fowrad declaration of the class that controls the alteration of the traits that define an Entity |
| EntityRandomizer.hh | Controls the alteration of the traits that define Entity |
| FitnessFunction.hh | Determines the fitness of Entity for GeneticAlgorithm |
| GeneticAlgorithm.cc | Template class for genetic algorithm protocols |
| GeneticAlgorithm.fwd.hh | Genetic algorithm protocols forward declaration |
| GeneticAlgorithm.hh | Template class for genetic algorithm protocols |
| Mutate1Randomizer.cc | Class to mutate only a single position at a time in any given entity |
| Mutate1Randomizer.fwd.hh | Fowrad declaration of the class that controls the alteration of the traits that define an Entity |
| Mutate1Randomizer.hh | Class to mutate only a single position at a time in any given entity |
| ► grafting | |
| ► simple_movers | |
| DeleteRegionMover.cc | |
| DeleteRegionMover.fwd.hh | Forward declarations for DeleteRegionMover class |
| DeleteRegionMover.hh | Base class for graftmovers |
| DeleteRegionMoverCreator.hh | |
| InsertPoseIntoPoseMover.cc | |
| InsertPoseIntoPoseMover.fwd.hh | Forward declarations for InsertPoseIntoPoseMover class |
| InsertPoseIntoPoseMover.hh | Base class for graftmovers |
| InsertPoseIntoPoseMoverCreator.hh | |
| KeepRegionMover.cc | |
| KeepRegionMover.fwd.hh | |
| KeepRegionMover.hh | Keep a region of a pose, delete the rest |
| KeepRegionMoverCreator.hh | |
| ReplaceRegionMover.cc | |
| ReplaceRegionMover.fwd.hh | Forward declarations for ReplaceRegionMover class |
| ReplaceRegionMover.hh | Base class for graftmovers |
| ReplaceRegionMoverCreator.hh | |
| AnchoredGraftMover.cc | Method definitions for AnchoredGraftMover |
| AnchoredGraftMover.fwd.hh | |
| AnchoredGraftMover.hh | Class to graft a piece into a pose. Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com) |
| AnchoredGraftMoverCreator.hh | |
| CCDEndsGraftMover.cc | Method definitions for CCDEndsGraftMover |
| CCDEndsGraftMover.fwd.hh | Forward declarations for GraftMoverBase class |
| CCDEndsGraftMover.hh | Class to graft a piece into a pose. Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com) |
| CCDEndsGraftMoverCreator.hh | |
| GraftMoverBase.cc | Base class for GraftMovers |
| GraftMoverBase.fwd.hh | Forward declarations for GraftMoverBase class |
| GraftMoverBase.hh | Base class for graftmovers |
| util.cc | Utility functions for grafting |
| util.hh | Header for grafting utility functions |
| ► helical_bundle | |
| ► parameters | |
| BundleParameters.cc | A class for holding parameters for parametric helical bundle generation |
| BundleParameters.fwd.hh | Owning pointers and whatnot for the class for holding parameters for parametric helical bundle generation |
| BundleParameters.hh | Prototypes and method declarations for the BundleParameters class, a class for holding parameters for helical bundle backbone generation |
| BundleParametersSet.cc | A class for holding sets of parameters for parametric backbone generation |
| BundleParametersSet.fwd.hh | Owning pointers and whatnot for the class for holding sets of parameters for helical bundle backbone generation |
| BundleParametersSet.hh | Prototypes and method declarations for the BundleParametersSet class, a class for holding sets of parameters for parametric helical bundle generation |
| BundleGridSampler.cc | This mover samples conformations of a helical bundle by performing a grid search in Crick parameter space |
| BundleGridSampler.fwd.hh | Defines owning pointers for BundleGridSampler mover class |
| BundleGridSampler.hh | Headers for BundleGridSampler.cc. Samples conformations of a helical bundle by performing a grid search in Crick parameter space |
| BundleGridSamplerCreator.hh | This class will create instances of Mover BundleGridSampler for the MoverFactory |
| BundleGridSamplerHelper.cc | A class that stores the various parameter perturbations that will be sampled by the BundleGridSampler mover |
| BundleGridSamplerHelper.fwd.hh | Owning pointers and whatnot for BundleGridSamplerHelper class |
| BundleGridSamplerHelper.hh | Prototypes and method declarations for the BundleGridSamplerHelper class |
| FitSimpleHelix.cc | Determines the Crick parameters describing a straight helix, given an input pose |
| FitSimpleHelix.fwd.hh | Defines owning pointers for FitSimpleHelix mover class |
| FitSimpleHelix.hh | Headers for FitSimpleHelix mover class |
| FitSimpleHelixCreator.hh | This class will create instances of Mover FitSimpleHelix for the MoverFactory |
| FitSimpleHelixMultiFunc.cc | Multifunction class implementation for fitting a simple (straight) helix to the Crick parameters |
| FitSimpleHelixMultiFunc.hh | Multifunction class implementation for fitting a simple (straight) helix to the Crick parameters |
| MakeBundle.cc | Builds a helical bundle using the Crick parameters |
| MakeBundle.fwd.hh | Defines owning pointers for MakeBundle mover class |
| MakeBundle.hh | Headers for MakeBundle.cc. Builds a helical bundle using the Crick parameters |
| MakeBundleCreator.hh | This class will create instances of Mover MakeBundle for the MoverFactory |
| MakeBundleHelix.cc | Builds a single helix as part of a helical bundle |
| MakeBundleHelix.fwd.hh | Defines owning pointers for MakeBundleHelix mover class |
| MakeBundleHelix.hh | Headers for MakeBundleHelix.cc. Builds a single helix as part of a helical bundle |
| MakeBundleHelixCreator.hh | This class will create instances of Mover MakeBundleHelix for the MoverFactory |
| PerturbBundle.cc | Perturbs a helical bundle by altering the Crick parameters |
| PerturbBundle.fwd.hh | Defines owning pointers for PerturbBundle mover class |
| PerturbBundle.hh | Headers for PerturbBundle.cc. Perturbs a helical bundle by altering the Crick parameters |
| PerturbBundleCreator.hh | This class will create instances of Mover PerturbBundle for the MoverFactory |
| PerturbBundleHelix.cc | Reads the Crick parameters for a piece of a pose from the input pose and sets the mainchain torsions accordingly. The parameters are presumed to have been perturbed by another mover. This mover is intended to be called by the PerturbBundle mover, which handles the perturbation of the Crick parameters |
| PerturbBundleHelix.fwd.hh | Defines owning pointers for PerturbBundleHelix mover class |
| PerturbBundleHelix.hh | Headers for PerturbBundleHelix.cc. Reads the Crick parameters for a piece of a pose from the input pose and sets the mainchain torsions accordingly. The parameters are presumed to have been perturbed by another mover. This mover is intended to be called by the PerturbBundle mover, which handles the perturbation of the Crick parameters |
| PerturbBundleHelixCreator.hh | This class will create instances of Mover PerturbBundleHelix for the MoverFactory |
| PerturbBundleOptions.cc | A class for options for the PerturbBundle mover |
| PerturbBundleOptions.fwd.hh | Owning pointers and whatnot for PerturbBundleOptions class |
| PerturbBundleOptions.hh | Prototypes and method declarations for the PerturbBundleOptions class |
| util.cc | Utility functions for helical bundle construction |
| util.hh | Headers for utility functions for helical bundle construction |
| ► helix_capper | |
| HelixNCapperMover.cc | Mover to find and fix poorly N-capped helices |
| HelixNCapperMover.hh | |
| ► hotspot_hashing | |
| ► movers | |
| PlaceProbeMover.cc | |
| PlaceProbeMover.hh | |
| PlaceSurfaceProbe.cc | |
| PlaceSurfaceProbe.fwd.hh | Forward declaration for PlaceSurfaceProbe |
| PlaceSurfaceProbe.hh | |
| PlaceSurfaceProbeCreator.hh | Declaration of the MoverCreator class for the AddChainBreak |
| HotspotStub.cc | HotspotStub class |
| HotspotStub.fwd.hh | |
| HotspotStub.hh | |
| HotspotStubSet.cc | HotspotStubSet class |
| HotspotStubSet.fwd.hh | |
| HotspotStubSet.hh | |
| SearchPattern.cc | |
| SearchPattern.fwd.hh | |
| SearchPattern.hh | |
| SearchPatternRotSetOp.cc | Creates rigid body variants from search pattern during repacking |
| SearchPatternRotSetOp.fwd.hh | Creates rigid body variants from search pattern during repacking |
| SearchPatternRotSetOp.hh | Creates rigid body variants from search pattern during repacking |
| SICSearchPattern.cc | |
| SICSearchPattern.hh | |
| StubGenerator.cc | |
| StubGenerator.fwd.hh | |
| StubGenerator.hh | |
| SurfaceSearchPattern.cc | |
| SurfaceSearchPattern.hh | |
| ► hybridization | |
| AllResiduesChanged.hh | |
| BackboneTorsionPerturbation.cc | |
| BackboneTorsionPerturbation.hh | |
| BackboneTorsionPerturbationCreator.hh | Declaration of the MoverCreator class for the BackboneTorsionPerturbation |
| BackboneTorsionSampler.cc | |
| BackboneTorsionSampler.hh | |
| BackboneTorsionSamplerCreator.hh | Declaration of the MoverCreator class for the BackboneTorsionSampler |
| CartesianHybridize.cc | |
| CartesianHybridize.fwd.hh | |
| CartesianHybridize.hh | |
| CartesianHybridizeCreator.hh | |
| CartesianSampler.cc | |
| CartesianSampler.fwd.hh | |
| CartesianSampler.hh | |
| ChunkTrialMover.cc | Wrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one |
| ChunkTrialMover.fwd.hh | |
| ChunkTrialMover.hh | Wrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one |
| DDomainParse.cc | A reimplementation of DDomain domain parsing algorithm, Protein Sci.16,947–955 (2007) |
| DDomainParse.hh | A reimplementation of DDomain domain parsing algorithm, Protein Sci.16,947–955 (2007) |
| DomainAssembly.cc | Domain Assembly |
| DomainAssembly.fwd.hh | |
| DomainAssembly.hh | |
| FoldTreeHybridize.cc | Align a random jump to template |
| FoldTreeHybridize.fwd.hh | |
| FoldTreeHybridize.hh | Align a random jump to template |
| FoldTreeHybridizeCreator.hh | |
| HybridizeFoldtreeDynamic.cc | A mover to dynamically manipulate fold tree during the template hybridization sampling |
| HybridizeFoldtreeDynamic.fwd.hh | |
| HybridizeFoldtreeDynamic.hh | |
| HybridizeProtocol.cc | |
| HybridizeProtocol.fwd.hh | |
| HybridizeProtocol.hh | Add constraints to the current pose conformation |
| HybridizeProtocolCreator.hh | |
| HybridizeSetup.cc | |
| HybridizeSetup.fwd.hh | |
| HybridizeSetup.hh | Add constraints to the current pose conformation |
| HybridizeSetupMoverCreator.hh | |
| InsertChunkMover.cc | Align a random jump to template |
| InsertChunkMover.hh | Align a random jump to template |
| MRMover.cc | |
| MRMover.hh | |
| TemplateHistory.cc | |
| TemplateHistory.fwd.hh | |
| TemplateHistory.hh | |
| TMalign.hh | A reimplementation of TM-align algorithm |
| util.cc | Align a random jump to template |
| util.hh | Align a random jump to template |
| WeightedFragmentSmoothTrialMover.cc | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentSmoothTrialMover.fwd.hh | |
| WeightedFragmentSmoothTrialMover.hh | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentTrialMover.cc | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentTrialMover.fwd.hh | |
| WeightedFragmentTrialMover.hh | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| ► idealize | |
| idealize.cc | |
| idealize.hh | Protocols for idealizing a Pose |
| IdealizeMover.cc | |
| IdealizeMover.fwd.hh | Protocols for idealizing a Pose |
| IdealizeMover.hh | Protocols for idealizing a Pose |
| IdealizeMoverCreator.hh | Declaration of the MoverCreator class for the IdealizeMover |
| ► indexed_structure_store | |
| ► filters | |
| FragmentLookupFilter.cc | FragmentLookupFilter class implementation |
| FragmentLookupFilter.fwd.hh | Header for FragmentLookupFilter class |
| FragmentLookupFilter.hh | Header for FragmentLookupFilter class |
| FragmentLookupFilterCreator.hh | FilterCreators for the FragmentLookupFilter |
| ► init | |
| init.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| init.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init() |
| ► inputter | |
| FastaInputter.cc | An inputter that takes a list of fasta |
| FastaInputter.fwd.hh | An inputter that takes a list of fasta |
| FastaInputter.hh | An inputter that takes a list of fastas |
| Inputter.cc | An inputter, a class that returns a poseSP |
| Inputter.fwd.hh | An inputter, a class that returns a poseSP |
| Inputter.hh | An inputter, a class that returns a poseSP |
| InputterStream.cc | InputterStream holds a list of of streams and does VERY basic things with them like controls whether structures are duplicated across masters and controls whether to take the list sequentially or round robin |
| InputterStream.fwd.hh | InputterStream holds a list of of streams and does VERY basic things with them like controls whether structures are duplicated across masters and controls whether to take the list sequentially or round robin |
| InputterStream.hh | InputterStream holds a list of of streams and does VERY basic things with them like controls whether structures are duplicated across masters and controls whether to take the list sequentially or round robin |
| PDBInputter.cc | An inputter that takes a list of pdbs |
| PDBInputter.fwd.hh | An inputter that takes a list of pdbs |
| PDBInputter.hh | An inputter that takes a list of pdbs |
| SilentFileInputter.cc | An inputter that takes a list of silent files |
| SilentFileInputter.fwd.hh | An inputter that takes a list of silent files |
| SilentFileInputter.hh | An inputter that takes a list of silent files |
| ► interface | |
| util.cc | |
| util.hh | Collection of useful interface functions - both by chain and by groups. In one place. The namespace is for interface classes and functions that are general-use and protocol level. Many more specific classes and functions for interfaces can be found in their appropriate namespaces such as TaskOperations in protocols/toolbox/task_operations |
| ► jd2 | |
| ► archive | |
| ArchiveBase.cc | Implementation of MPIFileBufJobDistributor |
| ArchiveBase.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ArchiveBase.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| ArchiveManager.cc | Implementation of MPIFileBufJobDistributor |
| ArchiveManager.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ArchiveManager.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| EvaluatedArchive.cc | Implementation of MPIFileBufJobDistributor |
| EvaluatedArchive.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| MPIArchiveJobDistributor.cc | Implementation of MPIFileBufJobDistributor |
| MPIArchiveJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIArchiveJobDistributor.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| NormalizedEvaluatedArchive.cc | Implementation of MPIFileBufJobDistributor |
| NormalizedEvaluatedArchive.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| VarianceStatisticsArchive.cc | Iterative protocol starting with abinitio and getting progressively more concerned with full-atom relaxed structures |
| VarianceStatisticsArchive.fwd.hh | |
| VarianceStatisticsArchive.hh | |
| ► parser | |
| BluePrint.cc | Basic idea of BluePrint is on the remodel Possu wrote in rosetta++ |
| BluePrint.fwd.hh | |
| BluePrint.hh | Basic idea of BluePrint is on the remodel Possu wrote in rosetta++ |
| DataLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| DataLoader.fwd.hh | Forward declartion of the XML parser's DataLoader class |
| DataLoader.hh | Declartion of the XML parser's DataLoader class |
| DataLoaderCreator.cc | Creator class for the parser's DataLoader classes |
| DataLoaderCreator.hh | Creator class for the parser's DataLoader classes |
| DataLoaderFactory.cc | Implementation of the factory class for the parser's DataLoader classes |
| DataLoaderFactory.hh | Factory class for the parser's DataLoader classes |
| FragmentReader.cc | |
| FragmentReader.fwd.hh | |
| FragmentReader.hh | |
| FragSetLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| FragSetLoader.hh | Declartion of the XML parser's FragSetLoader class for adding named FragSets to the basic::datacache::DataMap |
| MonteCarloLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| MonteCarloLoader.hh | Declartion of the XML parser's MonteCarloLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| ResidueSelectorLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| ResidueSelectorLoader.hh | Declartion of the XML parser's ResidueSelectorLoader class for adding named ResidueSelectors to the basic::datacache::DataMap |
| ResidueSelectorLoaderCreator.hh | Creator classes for the default DataLoader classes, TaskOperationLoader and ScoreFunctionLoader |
| ScoreFunctionLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| ScoreFunctionLoader.hh | Declartion of the XML parser's ScoreFunctionLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| StandardLoaderCreators.hh | Creator classes for the default DataLoader classes, TaskOperationLoader and ScoreFunctionLoader |
| TaskOperationLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| TaskOperationLoader.hh | Declartion of the XML parser's TaskOperationLoader class |
| AtomTreeDiffJobInputter.cc | |
| AtomTreeDiffJobInputter.fwd.hh | |
| AtomTreeDiffJobInputter.hh | Header file for AtomTreeDiffJobInputter class |
| AtomTreeDiffJobInputterCreator.hh | |
| AtomTreeDiffJobOutputter.cc | AtomTreeDiffJobOutputter |
| AtomTreeDiffJobOutputter.fwd.hh | Header file for AtomTreeDiffJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| AtomTreeDiffJobOutputter.hh | Header file for AtomTreeDiffJobOutputter class |
| AtomTreeDiffJobOutputterCreator.hh | |
| BatchJobInputter.cc | |
| BatchJobInputter.fwd.hh | |
| BatchJobInputter.hh | Header file for BatchJobInputter class |
| BOINCJobDistributor.cc | Implementation of BOINCJobDistributor |
| BOINCJobDistributor.hh | Implementation of BOINCJobDistributor |
| FileJobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - FileJobOutputter |
| FileJobOutputter.fwd.hh | Header file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| FileJobOutputter.hh | Header file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| FileSystemJobDistributor.cc | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| FileSystemJobDistributor.fwd.hh | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| FileSystemJobDistributor.hh | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| InnerJob.cc | August 2008 job distributor as planned at RosettaCon08 - Job classes |
| InnerJob.fwd.hh | Header file for InnerJob class, part of August 2008 job distributor as planned at RosettaCon08 |
| InnerJob.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| InnerMultiThreadingJob.cc | August 2008 job distributor as planned at RosettaCon08 - Job classes |
| InnerMultiThreadingJob.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| InnerMultiThreadingJob.hh | |
| JD2ResourceManager.cc | The ResourceManager that is compatible with the JD2 JobDistributor |
| JD2ResourceManager.fwd.hh | Forward header for the JD2ResourceManager |
| JD2ResourceManager.hh | The ResourceManager that is compatible with the JD2 JobDistributor |
| JD2ResourceManagerCreator.hh | |
| JD2ResourceManagerJobInputter.cc | |
| JD2ResourceManagerJobInputter.hh | |
| JD2ResourceManagerJobInputterCreator.hh | |
| Job.cc | August 2008 job distributor as planned at RosettaCon08 - Job classes |
| Job.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| Job.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| JobDistributor.cc | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributor.fwd.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributor.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributorFactory.cc | JobDistributorFactory class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobDistributorFactory.fwd.hh | JobDistributorFactory class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobDistributorFactory.hh | JobDistributorFactory class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class JobInputter |
| JobInputter.fwd.hh | Header file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputter.hh | Header file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputterCreator.cc | JobInputterCreator base |
| JobInputterCreator.hh | Base class for JobInputterCreators for the JobInputter load-time factory registration scheme |
| JobInputterFactory.cc | JobInputterFactory |
| JobInputterFactory.fwd.hh | JobInputterFactory forward header |
| JobInputterFactory.hh | JobInputterFactory |
| JobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class JobOutputter |
| JobOutputter.fwd.hh | Header file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobOutputter.hh | Header file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobOutputterCreator.cc | JobOutputterCreator base |
| JobOutputterCreator.hh | Base class for JobOutputterCreators for the JobOutputter load-time factory registration scheme |
| JobOutputterFactory.cc | JobOutputterFactory |
| JobOutputterFactory.fwd.hh | JobOutputterFactory forward header |
| JobOutputterFactory.hh | JobOutputterFactory |
| JobOutputterObserver.hh | Classes that want to add score_value pairs to poses before they are output should derive from this Observer class |
| LazySilentFileJobInputter.cc | |
| LazySilentFileJobInputter.fwd.hh | |
| LazySilentFileJobInputter.hh | |
| LazySilentFileJobInputterCreator.hh | |
| MpiFileBuffer.cc | Header file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| MpiFileBuffer.fwd.hh | |
| MpiFileBuffer.hh | Header file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| MPIFileBufJobDistributor.cc | Implementation of MPIFileBufJobDistributor |
| MPIFileBufJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIFileBufJobDistributor.hh | Header for MPIWorkPoolJobDistributor - intended for MPI jobs on large numbers of nodes where the head node is dedicated to handing out new job ids |
| MPIMultiCommJobDistributor.cc | Implementation of MPIMultiCommJobDistributor |
| MPIMultiCommJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIMultiCommJobDistributor.hh | Intended to do JD2-based distribution of jobs where each job can run a parallel MPI protocol |
| MPIWorkPartitionJobDistributor.cc | Implementation of MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user |
| MPIWorkPartitionJobDistributor.fwd.hh | Forward header for MPIWorkPartitonJobDistributor |
| MPIWorkPartitionJobDistributor.hh | Header for MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user |
| MPIWorkPoolJobDistributor.cc | Implementation of MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.hh | Header for MPIWorkPoolJobDistributor - intended for MPI jobs on large numbers of nodes where the head node is dedicated to handing out new job ids |
| MSDJobDistributor.cc | Job distributor subclass for running restrained multistate design |
| MSDJobDistributor.fwd.hh | Job distributor for running constrained multistate design |
| MSDJobDistributor.hh | Job distributor subclass for running restrained multistate design |
| MultiThreadedJobDistributor.cc | Job distributor that launches threads to carry out independant jobs |
| MultiThreadedJobDistributor.fwd.hh | Job distributor that luanches threads to carry out independent jobs |
| MultiThreadedJobDistributor.hh | Job distributor that launches threads to carry out independant jobs |
| MultiThreadingJob.cc | |
| MultiThreadingJob.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| MultiThreadingJob.hh | |
| NoOutputJobOutputter.hh | Header file for NoOutputJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| NoOutputJobOutputterCreator.cc | NoOutputJobOutputCreator class, part of November 2011 XRW2 |
| NoOutputJobOutputterCreator.hh | |
| Parser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| Parser.fwd.hh | Header file for Parser class, part of August 2008 job distributor |
| Parser.hh | Header file for Parser class, part of August 2008 job distributor |
| PDBJobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class PDBJobInputter |
| PDBJobInputter.fwd.hh | Header file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobInputter.hh | Header file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobInputterCreator.hh | |
| PDBJobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - PDBJobOutputter |
| PDBJobOutputter.fwd.hh | Header file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobOutputter.hh | Header file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobOutputterCreator.hh | |
| PoseInputStreamJobInputter.cc | |
| PoseInputStreamJobInputter.fwd.hh | |
| PoseInputStreamJobInputter.hh | Header file for PoseInputStreamJobInputter class |
| PoseInputStreamJobInputterCreator.hh | |
| ScoreMap.cc | A place to put some common functions for scoremap output |
| ScoreMap.hh | A place to put some common functions for scoremap output |
| ScoreOnlyJobOutputter.cc | |
| ScoreOnlyJobOutputter.fwd.hh | |
| ScoreOnlyJobOutputter.hh | Header file for ScoreOnlyJobOutputter class, allows the user to output only score files |
| ScoreOnlyJobOutputterCreator.hh | |
| ScreeningJobInputter.cc | The ScreeningJobInputter |
| ScreeningJobInputter.fwd.hh | The ScreeningJobInputter forward headers |
| ScreeningJobInputter.hh | The ScreeningJobInputter forward headers |
| ScreeningJobInputterCreator.hh | Creator for ScreeningJobInputter |
| ShuffleJobDistributor.cc | |
| ShuffleJobDistributor.hh | Implementation of ShuffleFileSystemJobDistributor |
| SilentFileJobInputter.cc | |
| SilentFileJobInputter.fwd.hh | |
| SilentFileJobInputter.hh | Header file for SilentFileJobInputter class |
| SilentFileJobInputterCreator.hh | |
| SilentFileJobOutputter.cc | |
| SilentFileJobOutputter.fwd.hh | Header file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SilentFileJobOutputter.hh | Header file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SilentFileJobOutputterCreator.hh | |
| SingleFileBuffer.cc | Header file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SingleFileBuffer.fwd.hh | |
| SingleFileBuffer.hh | Header file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| util.cc | August 2008 job distributor as planned at RosettaCon08 - Base class |
| util.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| ► jobdist | |
| JobDistributors.cc | |
| JobDistributors.fwd.hh | |
| JobDistributors.hh | |
| Jobs.cc | |
| Jobs.fwd.hh | Objects representing inputs for the JobDistributor |
| Jobs.hh | Objects representing inputs for the JobDistributor |
| not_universal_main.cc | Simple main method for applying a Mover to a set of input Poses |
| not_universal_main.hh | Simple main method for applying a Mover to a set of input Poses |
| standard_mains.cc | |
| standard_mains.hh | Main methods that implement the typical running patterns for executables |
| ► jumping | |
| DisulfPairingLibrary.cc | |
| DisulfPairingLibrary.hh | Header file for ClassicAbinitio protocol |
| DisulfPairingsList.cc | |
| DisulfPairingsList.fwd.hh | Fwd headers for ns jumping |
| DisulfPairingsList.hh | Header file for ClassicAbinitio protocol |
| JumpSample.cc | |
| JumpSample.hh | Read jump-definition file setups fold tree an chainbreak variants loop code didn't work because fold-tree to complicated ( overlapping loops ) |
| JumpSetup.cc | |
| JumpSetup.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| JumpSetup.hh | Read jump-definition file setups fold tree an chainbreak variants loop code didn't work because fold-tree to complicated ( overlapping loops ) |
| MembraneJump.cc | |
| MembraneJump.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| MembraneJump.hh | Read jump-definition file setups fold tree an chainbreak variants loop code didn't work because fold-tree to complicated ( overlapping loops ) |
| PairingLibrary.cc | |
| PairingLibrary.fwd.hh | Fwd headers for ns jumping |
| PairingLibrary.hh | Header file for ClassicAbinitio protocol |
| RandomSheetBuilder.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| RandomSheetBuilder.hh | Header file for ClassicAbinitio protocol |
| ResiduePairJump.cc | Class to create jump transform from a pair of residues |
| ResiduePairJump.fwd.hh | |
| ResiduePairJump.hh | Class to create jump transform from a pair of residues |
| ResiduePairJumpSetup.cc | |
| ResiduePairJumpSetup.fwd.hh | |
| ResiduePairJumpSetup.hh | Setup jumps specifically to ResiduePairJump, read in definition file |
| SameStrand.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SameStrand.fwd.hh | Fwd headers for ns jumping |
| SameStrand.hh | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SheetBuilder.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SheetBuilder.hh | Header file for ClassicAbinitio protocol |
| util.cc | |
| util.hh | Read jump-definition file setups fold tree an chainbreak variants loop code didn't work because fold-tree to complicated ( overlapping loops ) |
| ► kinematic_closure | |
| ► perturbers | |
| BondAnglePerturber.cc | |
| BondAnglePerturber.fwd.hh | |
| BondAnglePerturber.hh | |
| FragmentPerturber.cc | |
| FragmentPerturber.fwd.hh | |
| FragmentPerturber.hh | |
| IdealizeNonPhiPsi.cc | |
| IdealizeNonPhiPsi.fwd.hh | |
| IdealizeNonPhiPsi.hh | |
| LogFilePerturber.cc | |
| LogFilePerturber.fwd.hh | |
| LogFilePerturber.hh | |
| OmegaPerturber.cc | |
| OmegaPerturber.fwd.hh | |
| OmegaPerturber.hh | |
| Perturber.cc | |
| Perturber.fwd.hh | |
| Perturber.hh | |
| PerturberSet.cc | |
| PerturberSet.fwd.hh | |
| PerturberSet.hh | |
| Rama2bPerturber.cc | |
| Rama2bPerturber.fwd.hh | |
| Rama2bPerturber.hh | |
| RamaPerturber.cc | |
| RamaPerturber.fwd.hh | |
| RamaPerturber.hh | |
| readme.hh | |
| UniformPerturber.cc | |
| UniformPerturber.fwd.hh | |
| UniformPerturber.hh | |
| VicinityPerturber.cc | |
| VicinityPerturber.fwd.hh | |
| VicinityPerturber.hh | |
| WalkingBondAnglePerturber.cc | |
| WalkingBondAnglePerturber.fwd.hh | |
| WalkingBondAnglePerturber.hh | |
| WalkingPerturber.cc | |
| WalkingPerturber.fwd.hh | |
| WalkingPerturber.hh | |
| ► pivot_pickers | |
| EndToEndPivots.cc | |
| EndToEndPivots.fwd.hh | |
| EndToEndPivots.hh | |
| FixedOffsetPivots.cc | |
| FixedOffsetPivots.fwd.hh | |
| FixedOffsetPivots.hh | |
| FixedPivots.cc | |
| FixedPivots.fwd.hh | |
| FixedPivots.hh | |
| LoopPivots.cc | |
| LoopPivots.fwd.hh | |
| LoopPivots.hh | |
| PivotPicker.fwd.hh | |
| PivotPicker.hh | |
| readme.hh | |
| StandardPivots.cc | |
| StandardPivots.fwd.hh | |
| StandardPivots.hh | |
| ► solution_pickers | |
| FilteredSolutions.cc | |
| FilteredSolutions.fwd.hh | |
| FilteredSolutions.hh | |
| RandomSolutions.cc | |
| RandomSolutions.fwd.hh | |
| RandomSolutions.hh | |
| readme.hh | |
| SolutionPicker.fwd.hh | |
| SolutionPicker.hh | |
| BalancedKicMover.cc | |
| BalancedKicMover.fwd.hh | |
| BalancedKicMover.hh | |
| ClosureProblem.cc | Source file for ClosureProblem |
| ClosureProblem.fwd.hh | Forward header for ClosureProblem |
| ClosureProblem.hh | Header file for ClosureProblem |
| ClosureSolution.cc | Source file for ClosureSolution |
| ClosureSolution.fwd.hh | Forward header for ClosureSolution |
| ClosureSolution.hh | Header file for ClosureSolution |
| internal.cc | Source file for internal helpers |
| internal.hh | |
| KicMover.cc | |
| KicMover.fwd.hh | |
| KicMover.hh | |
| KicMoverCreator.hh | |
| readme.hh | |
| types.hh | Header file for shared types |
| ► kinmatch | |
| FunGroupTK.cc | ??? |
| FunGroupTK.hh | ToolKit for rapid IK based functional group placement |
| ► ligand_docking | |
| ► ligand_options | |
| Interface.cc | Implementation of resfile reader and its command classes |
| Interface.fwd.hh | Header of classes for resfile options |
| Interface.hh | Header of classes for resfile options |
| interface_distance_functions.cc | Helper functions for the Interface class |
| interface_distance_functions.hh | Helper functions for the interface class |
| ► rdf | |
| RDFBase.fwd.hh | Forward headers for RDFBase |
| RDFBase.hh | A base class that defines an RDF function. These functions computes one or more RDF values for a pair of atoms |
| RDFFunctionCreator.fwd.hh | Forward Header for base class for RDFFunctionCreator |
| RDFFunctionCreator.hh | Header for base class for RDFFunctionCreator |
| RDFFunctionFactory.cc | Factory for creating RDFBase objects |
| RDFFunctionFactory.fwd.hh | Forward headers for RDFFunctionFactory |
| RDFFunctionFactory.hh | Headers for RDFFunctionFactory |
| StandardRDFFunctions.cc | Headers for standard RDF Functions used by RosettaHTS |
| StandardRDFFunctions.fwd.hh | Forward headers for standard RDF Functions used by RosettaHTS |
| StandardRDFFunctions.hh | Headers for standard RDF Functions used by RosettaHTS |
| AddHydrogen.cc | Lemmon |
| AddHydrogen.fwd.hh | |
| AddHydrogen.hh | |
| AddHydrogens.cc | Lemmon |
| AddHydrogens.fwd.hh | |
| AddHydrogens.hh | |
| AddHydrogensCreator.hh | This class will create instances of Mover AddHydrogens for the MoverFactory |
| AtomCountFilter.cc | Find packing defects at an interface using packstat score terms |
| AtomCountFilter.hh | Find packing defects at an interface using packstat score terms |
| AtomCountFilterCreator.hh | FilterCreator for the AtomCountFilter |
| ChainExistsFilter.cc | Find packing defects at an interface using packstat score terms |
| ChainExistsFilter.hh | Find packing defects at an interface using packstat score terms |
| ChainExistsFilterCreator.hh | FilterCreator for the ChainExistsFilter |
| CompleteConnectionsFilter.cc | Find packing defects at an interface using packstat score terms |
| CompleteConnectionsFilter.hh | Find packing defects at an interface using packstat score terms |
| CompleteConnectionsFilterCreator.hh | FilterCreator for the CompleteConnectionsFilter |
| CompoundTranslate.cc | |
| CompoundTranslate.hh | |
| CompoundTranslateCreator.hh | This class will create instances of Mover CompoundTranslateCreator for the MoverFactory |
| ComputeLigandRDF.cc | A mover for computing RDF functions |
| ComputeLigandRDF.fwd.hh | |
| ComputeLigandRDF.hh | Header file for ComputeLigandRDF mover |
| ComputeLigandRDFCreator.hh | |
| DistributionMap.cc | Enumerate some distributions and map them to strings |
| DistributionMap.hh | Enumerate some distributions and map them to strings |
| FinalMinimizer.cc | Implementation of resfile reader and its command classes |
| FinalMinimizer.fwd.hh | |
| FinalMinimizer.hh | Header of classes for resfile options |
| FinalMinimizerCreator.hh | This class will create instances of Mover FinalMinimizerCreator for the MoverFactory |
| grid_functions.cc | |
| grid_functions.hh | |
| GrowLigand.cc | Lemmon |
| GrowLigand.fwd.hh | |
| GrowLigand.hh | |
| GrowLigandCreator.hh | This class will create instances of Mover GrowLigand for the MoverFactory |
| HBondAcceptorFilter.cc | Find packing defects at an interface using packstat score terms |
| HBondAcceptorFilter.hh | Find packing defects at an interface using packstat score terms |
| HBondAcceptorFilterCreator.hh | FilterCreator for the HBondAcceptorFilter |
| HBondDonorFilter.cc | Find packing defects at an interface using packstat score terms |
| HBondDonorFilter.hh | Find packing defects at an interface using packstat score terms |
| HBondDonorFilterCreator.hh | FilterCreator for the HBondDonorFilter |
| HeavyAtomFilter.cc | Find packing defects at an interface using packstat score terms |
| HeavyAtomFilter.hh | Find packing defects at an interface using packstat score terms |
| HeavyAtomFilterCreator.hh | FilterCreator for the HeavyAtomFilter |
| HighResDocker.cc | Implementation of resfile reader and its command classes |
| HighResDocker.fwd.hh | |
| HighResDocker.hh | Header of classes for resfile options |
| HighResDockerCreator.hh | This class will create instances of Mover HighResDockerCreator for the MoverFactory |
| InterfaceBuilder.cc | Implementation of resfile reader and its command classes |
| InterfaceBuilder.fwd.hh | Makes an interface |
| InterfaceBuilder.hh | Header of classes for resfile options |
| InterfaceScoreCalculator.cc | |
| InterfaceScoreCalculator.fwd.hh | |
| InterfaceScoreCalculator.hh | |
| InterfaceScoreCalculatorCreator.hh | This class will create instances of Mover InterfaceScoreCalculator for the MoverFactory |
| ligand_dock_impl.cc | |
| ligand_dock_impl.hh | |
| ligand_functions.cc | |
| ligand_functions.hh | |
| ligand_scores.cc | Lemmon |
| ligand_scores.hh | |
| LigandArea.cc | Implementation of resfile reader and its command classes |
| LigandArea.fwd.hh | Makes an interface |
| LigandArea.hh | Header of classes for resfile options |
| LigandBaseProtocol.cc | |
| LigandBaseProtocol.hh | |
| LigandDesign.cc | Lemmon |
| LigandDesign.fwd.hh | |
| LigandDesign.hh | |
| LigandDesignCreator.hh | This class will create instances of Mover LigandDesign for the MoverFactory |
| LigandDockingLoaderCreators.hh | Creator classes for the ligand docking DataLoader classes: InterfaceBuilderLoader and MoveMapBuilderLoader |
| LigandDockingLoaders.cc | Implementation of the InterfaceBuilderLoader and MoveMapBuilderLoader classes |
| LigandDockingLoaders.hh | Declartion of the InterfaceBuilderLoader and MoveMapBuilderLoader classes for adding named InterfaceBuilders and MoveMapBuilders into the parser's basic::datacache::DataMap |
| LigandDockProtocol.cc | |
| LigandDockProtocol.fwd.hh | |
| LigandDockProtocol.hh | |
| MinimizeBackbone.cc | Implementation of resfile reader and its command classes |
| MinimizeBackbone.fwd.hh | |
| MinimizeBackbone.hh | Header of classes for resfile options |
| MinimizeBackboneCreator.hh | This class will create instances of Mover MinimizeBackboneCreator for the MoverFactory |
| MinimizeLigand.cc | Implementation of resfile reader and its command classes |
| MinimizeLigand.fwd.hh | |
| MinimizeLigand.hh | Header of classes for resfile options |
| MolarMassFilter.cc | Find packing defects at an interface using packstat score terms |
| MolarMassFilter.hh | Find packing defects at an interface using packstat score terms |
| MolarMassFilterCreator.hh | FilterCreator for the MolarMassFilter |
| MolecularMassFilter.cc | Find packing defects at an interface using packstat score terms |
| MolecularMassFilter.hh | Find packing defects at an interface using packstat score terms |
| MolecularMassFilterCreator.hh | FilterCreator for the MolecularMassFilter |
| MoveMapBuilder.cc | Implementation of resfile reader and its command classes |
| MoveMapBuilder.fwd.hh | |
| MoveMapBuilder.hh | Header of classes for resfile options |
| RandomConformerMover.cc | |
| RandomConformerMover.fwd.hh | |
| RandomConformerMover.hh | |
| RandomConformers.cc | Implementation of resfile reader and its command classes |
| RandomConformers.hh | This class chooses a random conformer for every residue in a specified chain |
| RandomConformersCreator.hh | This class will create instances of Mover RandomConformersCreator for the MoverFactory |
| ResidueTorsionRestraints.cc | |
| ResidueTorsionRestraints.fwd.hh | |
| ResidueTorsionRestraints.hh | |
| RigidSearchMover.cc | |
| RigidSearchMover.fwd.hh | |
| RigidSearchMover.hh | |
| Rotate.cc | Implementation of resfile reader and its command classes |
| Rotate.fwd.hh | |
| Rotate.hh | Header of classes for resfile options |
| RotateCreator.hh | This class will create instances of Mover Rotate for the MoverFactory |
| Rotates.cc | Implementation of resfile reader and its command classes |
| Rotates.fwd.hh | |
| Rotates.hh | Header of classes for resfile options |
| RotatesCreator.hh | This class will create instances of Mover Rotates for the MoverFactory |
| SlideTogether.cc | Implementation of resfile reader and its command classes |
| SlideTogether.hh | Header of classes for resfile options |
| SlideTogetherCreator.hh | This class will create instances of Mover SlideTogether for the MoverFactory |
| StartFrom.cc | Implementation of resfile reader and its command classes |
| StartFrom.fwd.hh | |
| StartFrom.hh | Header of classes for resfile options |
| StartFromCreator.hh | This class will create instances of Mover StartFrom for the MoverFactory |
| TetherLigand.cc | Implementation of resfile reader and its command classes |
| TetherLigand.fwd.hh | |
| TetherLigand.hh | Header of classes for resfile options |
| Transform.cc | |
| Transform.fwd.hh | |
| Transform.hh | |
| TransformCreator.hh | This class will create instances of Mover Transform for the MoverFactory |
| Translate.cc | Implementation of resfile reader and its command classes |
| Translate.fwd.hh | |
| Translate.hh | Header of classes for resfile options |
| TranslateCreator.hh | This class will create instances of Mover Translate for the MoverFactory |
| UnconstrainedTorsionsMover.cc | |
| UnconstrainedTorsionsMover.fwd.hh | |
| UnconstrainedTorsionsMover.hh | |
| WriteLigandMolFile.cc | Ligand MolFile writer |
| WriteLigandMolFile.fwd.hh | Forward header class for Ligand MolFile writer |
| WriteLigandMolFile.hh | Header class for Ligand MolFile writer |
| WriteLigandMolFileCreator.hh | This class will create instances of Mover WriteLigandMolFile for the MoverFactory |
| ► loop_build | |
| LoopBuild.cc | |
| LoopBuild.hh | |
| LoopBuildMover.cc | |
| LoopBuildMover.fwd.hh | |
| LoopBuildMover.hh | |
| LoopmodelWrapper.cc | |
| LoopmodelWrapper.fwd.hh | |
| LoopmodelWrapper.hh | |
| LoopmodelWrapperCreator.hh | |
| LoopMover_SlidingWindow.cc | Kinematic loop closure main protocols |
| LoopMover_SlidingWindow.hh | |
| LoopMover_SlidingWindowCreator.cc | Header for LoopMover_SlidingWindowCreator |
| LoopMover_SlidingWindowCreator.hh | Header for LoopMover_SlidingWindowCreator |
| ► loop_modeling | |
| ► refiners | |
| MinimizationRefiner.cc | |
| MinimizationRefiner.fwd.hh | |
| MinimizationRefiner.hh | |
| MinimizationRefinerCreator.hh | |
| packing_helper.hh | |
| readme.hh | |
| RepackingRefiner.cc | |
| RepackingRefiner.fwd.hh | |
| RepackingRefiner.hh | |
| RepackingRefinerCreator.hh | |
| RotamerTrialsRefiner.cc | |
| RotamerTrialsRefiner.fwd.hh | |
| RotamerTrialsRefiner.hh | |
| RotamerTrialsRefinerCreator.hh | |
| ► samplers | |
| LegacyKicSampler.cc | |
| LegacyKicSampler.fwd.hh | |
| LegacyKicSampler.hh | |
| LegacyKicSamplerCreator.hh | |
| readme.hh | |
| ► utilities | |
| AcceptanceCheck.cc | |
| AcceptanceCheck.fwd.hh | |
| AcceptanceCheck.hh | |
| LoopFilter.cc | |
| LoopFilter.fwd.hh | |
| LoopFilter.hh | |
| LoopMoverGroup.cc | |
| LoopMoverGroup.fwd.hh | |
| LoopMoverGroup.hh | |
| PrepareForCentroid.cc | |
| PrepareForCentroid.fwd.hh | |
| PrepareForCentroid.hh | |
| PrepareForCentroidCreator.hh | |
| PrepareForFullatom.cc | |
| PrepareForFullatom.fwd.hh | |
| PrepareForFullatom.hh | |
| PrepareForFullatomCreator.hh | |
| readme.hh | |
| rosetta_scripts.cc | |
| rosetta_scripts.hh | |
| LoopBuilder.cc | |
| LoopBuilder.fwd.hh | |
| LoopBuilder.hh | |
| LoopBuilderCreator.hh | |
| LoopModeler.cc | |
| LoopModeler.fwd.hh | |
| LoopModeler.hh | |
| LoopModelerCreator.hh | |
| LoopMover.cc | |
| LoopMover.fwd.hh | |
| LoopMover.hh | |
| LoopProtocol.cc | |
| LoopProtocol.fwd.hh | |
| LoopProtocol.hh | |
| LoopProtocolCreator.hh | |
| readme.hh | |
| types.hh | |
| ► loophash | |
| BackboneDB.cc | |
| BackboneDB.hh | I little in the spirit of fragments but way more memory and speed efficient. Backbones are stored as 16bit fixed comma integers. :) |
| Exceptions.hh | |
| FastGapMover.cc | |
| FastGapMover.fwd.hh | Closes gaps |
| FastGapMover.hh | Protocols for closing gaps |
| LocalInserter.cc | |
| LocalInserter.fwd.hh | LoopHashLibrary class forward declarations header |
| LocalInserter.hh | |
| LoopHashDiversifier.cc | Simple mover that uses loophash to replace randomly chosen fragments in a given pose. Heavy inspiration taken by LoophashMoverWrapper |
| LoopHashDiversifier.hh | |
| LoopHashDiversifierCreator.hh | Declaration of the MoverCreator class for the LoopHashDiversifierCreator |
| LoopHashLibrary.cc | |
| LoopHashLibrary.fwd.hh | LocalInserter class forward declarations header |
| LoopHashLibrary.hh | |
| LoopHashLibraryLoader.cc | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoader.fwd.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoader.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoaderCreator.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.cc | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.fwd.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptionsCreator.hh | Load the Loop Hash library using the resource manager |
| LoopHashMap.cc | |
| LoopHashMap.hh | |
| LoopHashMoverWrapper.cc | |
| LoopHashMoverWrapper.hh | |
| LoopHashMoverWrapperCreator.hh | Declaration of the MoverCreator class for the LoopHashMoverWrapper |
| LoopHashRelaxProtocol.cc | |
| LoopHashRelaxProtocol.hh | |
| LoopHashSampler.cc | |
| LoopHashSampler.fwd.hh | LoopHashSampler class forward declarations header |
| LoopHashSampler.hh | |
| Mover_LoopHashRefine.cc | |
| Mover_LoopHashRefine.hh | |
| MPI_LoopHashRefine.cc | |
| MPI_LoopHashRefine.hh | |
| MPI_LoopHashRefine_Emperor.cc | |
| MPI_LoopHashRefine_Emperor.hh | |
| MPI_LoopHashRefine_Master.cc | |
| MPI_LoopHashRefine_Master.hh | |
| WorkUnit_LoopHash.cc | |
| WorkUnit_LoopHash.hh | |
| ► loops | |
| ► loop_closure | |
| ► ccd | |
| ccd_closure.cc | Method definitions for cyclic coordinate descent loop closure |
| ccd_closure.hh | Method declarations for cyclic coordinate descent loop closure |
| CCDLoopClosureMover.cc | Method definitions for CCDLoopClosureMover |
| CCDLoopClosureMover.fwd.hh | Foward declarations for CCDLoopClosureMover |
| CCDLoopClosureMover.hh | Class definition and method declarations for CCDLoopClosureMover |
| CCDLoopClosureMoverCreator.hh | This class will create upcasted instances of CCDLoopClosureMover for the protocols::moves::MoverFactory |
| FASelectSlidingWindowLoopClosure.cc | |
| FASelectSlidingWindowLoopClosure.fwd.hh | Fwd headers for FASelectSlidingWindowLoopClosure |
| FASelectSlidingWindowLoopClosure.hh | Header file for SlidingWindowLoopClosure protocol |
| LoopClosure.cc | |
| LoopClosure.fwd.hh | Fwd headers for ns loops |
| LoopClosure.hh | Header file for LoopClosure protocol |
| RamaCheck.cc | Implementation for RamaCheck classes (RamaCheckBase, RamaCheck1B, RamaCheck2B) |
| RamaCheck.fwd.hh | Forward declaration of RamaCheck classes (RamaCheckBase, RamaCheck1B, RamaCheck2B) |
| RamaCheck.hh | Header for RamaCheck classes (RamaCheckBase, RamaCheck1B, RamaCheck2B) |
| ShortLoopClosure.cc | |
| ShortLoopClosure.fwd.hh | Fwd headers for ShortLoopClosure |
| ShortLoopClosure.hh | |
| SlidingWindowLoopClosure.cc | |
| SlidingWindowLoopClosure.fwd.hh | Fwd headers for ns loops |
| SlidingWindowLoopClosure.hh | Header file for SlidingWindowLoopClosure protocol |
| WidthFirstSlidingWindowLoopClosure.cc | |
| WidthFirstSlidingWindowLoopClosure.fwd.hh | Fwd headers for ns loops |
| WidthFirstSlidingWindowLoopClosure.hh | Header file for SlidingWindowLoopClosure protocol |
| ► kinematic_closure | |
| KinematicMover.cc | |
| KinematicMover.fwd.hh | KinematicMover forward declarations header |
| KinematicMover.hh | |
| KinematicPerturber.cc | Implementations for KinematicPerturbers used by the kinematic mover |
| KinematicPerturber.fwd.hh | KinematicPerturber forward declarations header |
| KinematicPerturber.hh | Header file for KinematicPerturbers used by the kineamtic mover |
| KinematicWrapper.cc | KinematicWrapper methods implemented - this is a mover which simplifies use of KinematicMover loop modeling |
| KinematicWrapper.fwd.hh | KinematicWrapper forward declarations header |
| KinematicWrapper.hh | Wrapper for KinematicMover - useful when only apply() is available |
| ► loop_mover | |
| ► perturb | |
| LoopMover_CCD.cc | Kinematic loop closure main protocols |
| LoopMover_CCD.fwd.hh | LoopMover_Perutrb_CCD forward declaration |
| LoopMover_CCD.hh | |
| LoopMover_CCDCreator.hh | Header for LoopMover_CCDCreator |
| LoopMover_KIC.cc | Kinematic loop closure main protocols |
| LoopMover_KIC.fwd.hh | LoopMover_Perturb_KIC forward declaration |
| LoopMover_KIC.hh | |
| LoopMover_KICCreator.hh | Header for LoopMover_KICCreator |
| LoopMover_QuickCCD.cc | Kinematic loop closure main protocols |
| LoopMover_QuickCCD.fwd.hh | LoopMover_QuickCCD forward declaration |
| LoopMover_QuickCCD.hh | |
| LoopMover_QuickCCD_Moves.cc | Kinematic loop closure main protocols |
| LoopMover_QuickCCD_Moves.fwd.hh | LoopMover_QuickCCD_Moves forward declaration |
| LoopMover_QuickCCD_Moves.hh | |
| LoopMover_QuickCCD_MovesCreator.hh | Header for LoopMover_QuickCCD_MovesCreator |
| LoopMover_QuickCCDCreator.hh | Header for LoopMover_QuickCCDCreator |
| ► refine | |
| LoopMover_Backrub.cc | Backrub loop refine |
| LoopMover_Backrub.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_Backrub.hh | |
| LoopMover_BackrubCreator.hh | Header for LoopMover_BackrubCreator |
| LoopMover_CCD.cc | Kinematic loop closure main protocols |
| LoopMover_CCD.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_CCD.hh | |
| LoopMover_CCDCreator.hh | Header for LoopMover_CCDCreator |
| LoopMover_KIC.cc | Kinematic loop closure main protocols |
| LoopMover_KIC.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_KIC.hh | |
| LoopMover_KICCreator.hh | Header for LoopMover_KICCreator |
| LoopRefineInnerCycle.cc | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| LoopRefineInnerCycle.fwd.hh | Forward declaration |
| LoopRefineInnerCycle.hh | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| LoopRefineInnerCycleContainer.cc | This class is a LoopRefineInnerCycle that contains one or more other LoopRefineInnerCycles to allow a developer to quickly string together existing LoopRefineInnerCycles in new ways to create new loop refinement protocols |
| LoopRefineInnerCycleContainer.fwd.hh | Forward declaration |
| LoopRefineInnerCycleContainer.hh | This class is a LoopRefineInnerCycle that contains one or more other LoopRefineInnerCycles to allow a developer to quickly string together existing LoopRefineInnerCycles in new ways to create new loop refinement protocols |
| LoopRefineInnerCycleContainerCreator.hh | Header for LoopRefineInnerCycleContainerCreator |
| LoopRefineInnerCycleFactory.cc | Factory for creating LoopRefineInnerCycle objects |
| LoopRefineInnerCycleFactory.fwd.hh | Report data to database |
| LoopRefineInnerCycleFactory.hh | Factory for creating LoopRefineInnerCycle objects |
| RepackTrial.cc | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| RepackTrial.fwd.hh | Forward declaration |
| RepackTrial.hh | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| RepackTrialCreator.hh | Header for LoopMover_KICCreator |
| ShearMinCCDTrial.cc | Concrete class derived from LoopRefineInnerCycle to implement the CCD min trial flavor of inner cycle refinement |
| ShearMinCCDTrial.fwd.hh | Forward declaration |
| ShearMinCCDTrial.hh | Concrete class derived from LoopRefineInnerCycle to implement the CCD min trial flavor of inner cycle refinement |
| ShearMinCCDTrialCreator.hh | Header for ShearMinCCDTrialCreator |
| SmallMinCCDTrial.cc | Perform a small move followed CCD closure, packing and minimization |
| SmallMinCCDTrial.fwd.hh | Forward declaration |
| SmallMinCCDTrial.hh | Perform a small move followed CCD closure, packing and minimization |
| SmallMinCCDTrialCreator.hh | Header for SmallMinCCDTrialCreator |
| IndependentLoopMover.cc | Loop mover base class |
| IndependentLoopMover.fwd.hh | IndependentLoopMover base classes |
| IndependentLoopMover.hh | |
| LoopCM.cc | Loop mover base class |
| LoopCM.fwd.hh | LoopCM forward declarations |
| LoopCM.hh | A loop claiming mover that handles KIC and CCD perturb and refine movers |
| LoopCMCreator.hh | This class will create instances of Mover LoopCM for the MoverFactory |
| LoopMover.cc | Loop mover base class |
| LoopMover.fwd.hh | LoopMover base classes |
| LoopMover.hh | |
| ► loops_definers | |
| LoopsDatabaseDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsDatabaseDefiner.fwd.hh | LoopsDatabaseDefiner class forward declarations header |
| LoopsDatabaseDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsDatabaseDefinerCreator.cc | LoopsDatabaseDefinerCreator for the LoosDatabaseDefiner load-time factory registration scheme |
| LoopsDatabaseDefinerCreator.fwd.hh | Forward Header for base class for LoopsDatabaseDefinerCreator |
| LoopsDatabaseDefinerCreator.hh | Header for LoopsDatabaseDefinerCreator for the LoosDatabaseDefiner load-time factory registration scheme |
| LoopsDefiner.fwd.hh | LoopsDefiner class forward declarations header |
| LoopsDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsDefinerCreator.fwd.hh | LoopsDefinerCreator class forward declarations header |
| LoopsDefinerCreator.hh | Base class LoopsDefinerCreator for the load-time factory registration scheme |
| LoopsDefinerFactory.cc | Factory for creating LoopsDefiner objects |
| LoopsDefinerFactory.fwd.hh | Report data to database |
| LoopsDefinerFactory.hh | Factory for creating LoopsDefiner objects |
| LoopsDefinerLoader.cc | Implementation the LoopsDefinerLoader class which implements the DataLoader interface |
| LoopsDefinerLoader.hh | Declartion of the XML loops_definers's LoopsDefinerLoader class |
| LoopsDefinerLoaderCreator.hh | Creator classe for the LoopsDefinerLoader classe |
| LoopsExplicitDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsExplicitDefiner.fwd.hh | LoopsExplicitDefiner class forward declarations header |
| LoopsExplicitDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsExplicitDefinerCreator.cc | LoopsExplicitDefinerCreator for the LoosExplicitDefiner load-time factory registration scheme |
| LoopsExplicitDefinerCreator.fwd.hh | Forward Header for base class for LoopsExplicitDefinerCreator |
| LoopsExplicitDefinerCreator.hh | Header for LoopsExplicitDefinerCreator for the LoosExplicitDefiner load-time factory registration scheme |
| LoopsFileDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsFileDefiner.fwd.hh | LoopsFileDefiner class forward declarations header |
| LoopsFileDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsFileDefinerCreator.cc | LoopsFileDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| LoopsFileDefinerCreator.fwd.hh | Forward Header for base class for LoopsFileDefinerCreator |
| LoopsFileDefinerCreator.hh | Header for LoopsFileDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| util.cc | Utility functions useful in LoopDefiner classes |
| util.hh | Utility functions useful in LoopDefiner classes |
| Exceptions.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| FoldTreeFromLoopsWrapper.cc | |
| FoldTreeFromLoopsWrapper.fwd.hh | FoldTreeFromLoops forward declarations header |
| FoldTreeFromLoopsWrapper.hh | |
| FoldTreeFromLoopsWrapperCreator.hh | Declaration of the MoverCreator class for the FoldTreeFromLoops |
| Loop.cc | |
| Loop.fwd.hh | Loop class forward declarations header |
| Loop.hh | |
| loopfinder.cc | |
| loopfinder.hh | |
| LoopMoverFactory.cc | Factory for creating LoopMovers objects |
| LoopMoverFactory.fwd.hh | Report data to database |
| LoopMoverFactory.hh | Factory for creating LoopMover objects |
| looprelax_protocols.cc | Protocols that are specific to LoopRebuild |
| looprelax_protocols.hh | |
| Loops.cc | |
| Loops.fwd.hh | Loops and Loop class forward declarations header |
| Loops.hh | |
| Loops.tmpl.hh | |
| loops_main.cc | Loop building tools |
| loops_main.hh | |
| LoopsFileFallbackConfiguration.cc | |
| LoopsFileFallbackConfiguration.fwd.hh | Forward hearder for OptionsSystemFallback class |
| LoopsFileFallbackConfiguration.hh | |
| LoopsFileFallbackConfigurationCreator.hh | |
| LoopsFileIO.cc | |
| LoopsFileIO.fwd.hh | LoopsFileIO forward declarations header |
| LoopsFileIO.hh | This class exists to handle the reading and writing of loops files |
| LoopsFileLoader.cc | |
| LoopsFileLoader.fwd.hh | |
| LoopsFileLoader.hh | |
| LoopsFileLoaderCreator.hh | |
| LoopsFileOptions.cc | |
| LoopsFileOptions.fwd.hh | LoopsFileOptions forward declarations header |
| LoopsFileOptions.hh | |
| LoopsFileOptionsCreator.hh | |
| make_loops.cc | |
| make_loops.hh | |
| util.cc | |
| util.hh | |
| ► make_rot_lib | |
| MakeRotLib.cc | |
| MakeRotLib.hh | |
| MakeRotLibJob.cc | Implimentation file for MakeRotLibJob class |
| MakeRotLibJob.fwd.hh | Forward header file for MakeRotLibJob class |
| MakeRotLibJob.hh | Header file for MakeRotLibJob class |
| MakeRotLibJobInputter.cc | Implementation file for MakeRotLibJobInputter class |
| MakeRotLibJobInputter.fwd.hh | Header file for MakeRotLibJobInputter class |
| MakeRotLibJobInputter.hh | Header file for MakeRotLibJobInputter class |
| MakeRotLibJobInputterCreator.hh | MakeRotLibJobInputterCreator function declarations |
| MakeRotLibMover.cc | Implimentation file for MakeRotLibMover |
| MakeRotLibMover.fwd.hh | Forward header file for MakeRotLibMover |
| MakeRotLibMover.hh | Header file for MakeRotLibMover |
| MakeRotLibOptionsData.cc | Implementation file for MakeRotLibOptionsData class |
| MakeRotLibOptionsData.fwd.hh | Forward header file for MakeRotLibOptionsData class |
| MakeRotLibOptionsData.hh | Header file for MakeRotLibOptionsData class |
| RotData.cc | |
| RotData.fwd.hh | Forward header file for RotData |
| RotData.hh | Header file for RotData |
| ► match | |
| ► downstream | |
| ActiveSiteGrid.cc | |
| ActiveSiteGrid.fwd.hh | |
| ActiveSiteGrid.hh | |
| ClassicMatchAlgorithm.cc | |
| ClassicMatchAlgorithm.fwd.hh | |
| ClassicMatchAlgorithm.hh | |
| DownstreamAlgorithm.cc | |
| DownstreamAlgorithm.fwd.hh | |
| DownstreamAlgorithm.hh | Declaration for the base-class algorithm that creates hits from an upstream builder, while managing the logic of their creation. Furthermore, the downstream algorithm manages update of hits from previous rounds should they loose their potential to result in matches |
| DownstreamBuilder.cc | |
| DownstreamBuilder.fwd.hh | |
| DownstreamBuilder.hh | |
| GeometrySecMatchRPE.cc | |
| GeometrySecMatchRPE.fwd.hh | |
| GeometrySecMatchRPE.hh | |
| LigandConformerBuilder.cc | |
| LigandConformerBuilder.fwd.hh | |
| LigandConformerBuilder.hh | |
| RigidLigandBuilder.cc | |
| RigidLigandBuilder.fwd.hh | |
| RigidLigandBuilder.hh | |
| ScoringSecMatchRPE.cc | |
| ScoringSecMatchRPE.fwd.hh | |
| ScoringSecMatchRPE.hh | |
| SecMatchEvaluatorFactory.cc | |
| SecMatchEvaluatorFactory.hh | |
| SecMatchResiduePairEvaluator.cc | |
| SecMatchResiduePairEvaluator.fwd.hh | |
| SecMatchResiduePairEvaluator.hh | |
| SecondaryMatcherToDownstreamResidue.cc | Class implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToDownstreamResidue.fwd.hh | |
| SecondaryMatcherToDownstreamResidue.hh | Class declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToUpstreamResidue.cc | Class implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToUpstreamResidue.fwd.hh | |
| SecondaryMatcherToUpstreamResidue.hh | Class declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| ► output | |
| DownstreamRMSEvaluator.cc | |
| DownstreamRMSEvaluator.fwd.hh | |
| DownstreamRMSEvaluator.hh | |
| LimitHitsPerRotamerFilter.cc | |
| LimitHitsPerRotamerFilter.fwd.hh | Declaration for abstract class to filter matches |
| LimitHitsPerRotamerFilter.hh | Declaration for abstract class to filter matches |
| MatchConsolidator.cc | |
| MatchConsolidator.fwd.hh | |
| MatchConsolidator.hh | |
| MatchEvaluator.cc | |
| MatchEvaluator.fwd.hh | Forward declaration for abstract class to filter matches |
| MatchEvaluator.hh | |
| MatchFilter.cc | Implementation for abstract filter class |
| MatchFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| MatchFilter.hh | Declaration for abstract class to filter matches |
| MatchGrouper.cc | |
| MatchGrouper.fwd.hh | |
| MatchGrouper.hh | |
| MatchOutputter.cc | Implementation of class to write output matches that pass filters This class does not "look ahead" to future matches to decide whether the current match to process should be output, however, filters are able to keep a history of what they've output so far |
| MatchOutputter.fwd.hh | Forward declaration for no-lookahead match processor |
| MatchOutputter.hh | |
| MatchProcessor.cc | |
| MatchProcessor.fwd.hh | |
| MatchProcessor.hh | |
| MatchScoreWriter.cc | |
| MatchScoreWriter.fwd.hh | |
| MatchScoreWriter.hh | |
| OutputWriter.cc | Implementation for the class to write output matches that have (presumably) passed the output filters |
| OutputWriter.fwd.hh | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| OutputWriter.hh | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| PDBWriter.cc | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| PDBWriter.fwd.hh | |
| PDBWriter.hh | |
| PoseInserter.cc | |
| PoseInserter.fwd.hh | |
| PoseInserter.hh | |
| ProcessorFactory.cc | Implementation for a factory class responsible for instantiating MatchProcessor classes |
| ProcessorFactory.fwd.hh | Declaration for a factory class responsible for instantiating MatchProcessor classes |
| ProcessorFactory.hh | Declaration for a factory class responsible for instantiating MatchProcessor classes |
| SameChiBinComboGrouper.cc | |
| SameChiBinComboGrouper.fwd.hh | |
| SameChiBinComboGrouper.hh | |
| SameRotamerComboGrouper.cc | |
| SameRotamerComboGrouper.fwd.hh | |
| SameRotamerComboGrouper.hh | |
| SameSequenceGrouper.cc | |
| SameSequenceGrouper.fwd.hh | |
| SameSequenceGrouper.hh | |
| UpstreamCollisionFilter.cc | Implementation for class to filter matches where the upstream residues collide |
| UpstreamCollisionFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| UpstreamCollisionFilter.hh | Declaration for class to filter matches where the upstream residues collide |
| UpstreamDownstreamCollisionFilter.cc | Implementation for class to filter matches where the upstream residues collide |
| UpstreamDownstreamCollisionFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| UpstreamDownstreamCollisionFilter.hh | Declaration for class to filter matches where the upstream residues collide with the downstream partner |
| UpstreamHitCacher.cc | Declaration for class to cache and recall the conformations of upstream hits |
| UpstreamHitCacher.fwd.hh | Forward declaration for class to cache and recall the conformations of upstream hits |
| UpstreamHitCacher.hh | Declaration for class to cache and recall the conformations of upstream hits |
| WriteKinemageOutputter.cc | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| WriteKinemageOutputter.fwd.hh | |
| WriteKinemageOutputter.hh | |
| WriteUpstreamCoordinateKineamge.cc | |
| WriteUpstreamCoordinateKineamge.fwd.hh | |
| WriteUpstreamCoordinateKineamge.hh | |
| ► upstream | |
| OriginalScaffoldBuildPoint.cc | Class implementations for the launch point geometry on the Scaffold |
| OriginalScaffoldBuildPoint.fwd.hh | Class forward declarations for the launch point geometry on the Scaffold |
| OriginalScaffoldBuildPoint.hh | Class declarations for the launch point geometry on the Scaffold |
| ProteinSCSampler.cc | Class declarations for base class and simple derived class for SC sampling |
| ProteinSCSampler.fwd.hh | Forward declaration for base class and simple derived class for SC sampling in matcher |
| ProteinSCSampler.hh | Class declarations for base class and simple derived class for SC sampling |
| ProteinUpstreamBuilder.cc | |
| ProteinUpstreamBuilder.fwd.hh | |
| ProteinUpstreamBuilder.hh | |
| ScaffoldBuildPoint.cc | Class implementations for the launch point geometry on the Scaffold |
| ScaffoldBuildPoint.fwd.hh | Class forward declarations for the launch point geometry on the Scaffold |
| ScaffoldBuildPoint.hh | Class declarations for the launch point geometry on the Scaffold |
| UpstreamBuilder.cc | |
| UpstreamBuilder.fwd.hh | |
| UpstreamBuilder.hh | |
| UpstreamResTypeGeometry.cc | |
| UpstreamResTypeGeometry.fwd.hh | Forward declaration for class to measure the geometry of a given ResidueType |
| UpstreamResTypeGeometry.hh | |
| BumpGrid.cc | |
| BumpGrid.fwd.hh | |
| BumpGrid.hh | |
| Hit.cc | Constructors for match_dspos1 |
| Hit.fwd.hh | Hit class forward declaration |
| Hit.hh | Hit typedef |
| Matcher.cc | |
| Matcher.fwd.hh | |
| Matcher.hh | |
| MatcherMover.cc | Implementation of mover wrapper for matcher |
| MatcherMover.fwd.hh | Forward file for MatcherMover |
| MatcherMover.hh | Mover wrapper for the matcher |
| MatcherMoverCreator.hh | This class will create instances of Mover FlxbbDesign for the MoverFactory |
| MatcherTask.cc | |
| MatcherTask.fwd.hh | |
| MatcherTask.hh | |
| MatchPositionModifiers.cc | Implementations for MatchPositionModifiers |
| MatchPositionModifiers.fwd.hh | Forward declaration for MatchPositionModifiers |
| MatchPositionModifiers.hh | Header file for MatchPositionModifiers |
| MatchSet.cc | |
| MatchSet.fwd.hh | |
| MatchSet.hh | Declaration for classes in 6D hasher |
| OccupiedSpaceHash.cc | Declaration for classes in 6D hasher |
| OccupiedSpaceHash.fwd.hh | Declaration for classes in 6D hasher |
| OccupiedSpaceHash.hh | Declaration for classes in 6D hasher |
| VoxelSetIterator.cc | Implementation of the VoxelSetIterator class |
| VoxelSetIterator.fwd.hh | Forward declaration for iterator to traverse the 64 bins each hit covers |
| VoxelSetIterator.hh | Declaration for iterator to traverse the 64 bins each hit covers in the OccupiedSpaceHash |
| ► matdes | |
| BuildingBlockInterfaceOperation.cc | Restrict design to only residues at inter-building block interfaces |
| BuildingBlockInterfaceOperation.fwd.hh | Restrict design to only residues at inter-building block interfaces |
| BuildingBlockInterfaceOperation.hh | Restrict design to only residues at inter-building block interfaces |
| BuildingBlockInterfaceOperationCreator.hh | Restrict design to only residues at inter-building block interfaces |
| ClashCheckFilter.cc | Checks to see if any residues defined by the TaskOperations have clashing CA/CBs between interfaces (building block aware) |
| ClashCheckFilter.fwd.hh | |
| ClashCheckFilter.hh | Header file for ClashCheckFilter class |
| ClashCheckFilterCreator.hh | FilterCreator for the ClashCheckFilter |
| ExtractSubposeMover.cc | Extract primary component associated with symdofs and all neighboring components. Note: Currently just dumps extracted PDB and does not modify pose |
| ExtractSubposeMover.fwd.hh | Extract primary component associated with symdofs and all neighboring components |
| ExtractSubposeMover.hh | Extract primary component associated with symdofs and all neighboring components |
| ExtractSubposeMoverCreator.hh | Extract primary component associated with symdofs and all neighboring components |
| GetRBDOFValues.cc | Returns the translation and angle for movable jump |
| GetRBDOFValues.fwd.hh | |
| GetRBDOFValues.hh | Header file for GetRBDOFValues class |
| GetRBDOFValuesCreator.hh | FilterCreator for the GetRBDOFValues |
| InterfacePackingFilter.cc | |
| InterfacePackingFilter.fwd.hh | Forward declaration for InterfacePackingFilter |
| InterfacePackingFilter.hh | Calculates the RosettaHoles score for the atoms within a user-defined cutoff distance (default = 9.0) of the subpose interface. Filters based on lower and upper thresholds, which are set to -/+5 by default |
| InterfacePackingFilterCreator.hh | FilterCreators for the InterfacePackingFilter |
| MatDesGreedyOptMutationMover.cc | |
| MatDesGreedyOptMutationMover.fwd.hh | This is a modified version of Chris King's GreedyOptMutationMover with additional functionality that is currently not compatible with all of the ParetoOpt functionality. Please note that this has been checked into master in its current state in response to requests from others to use this modified version of Chris King's GreedyOptMutationMover. Although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MatDesGreedyOptMutationMover.hh | This is a modified version of Chris King's GreedyOptMutationMover with additional functionality that is currently not compatible with all of the ParetoOpt functionality. Please note that this has been checked into master in its current state in response to requests from others to use this modified version of Chris King's GreedyOptMutationMover. Although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MatDesGreedyOptMutationMoverCreator.hh | |
| MatDesPointMutationCalculator.cc | |
| MatDesPointMutationCalculator.fwd.hh | This is a modified version of chris king's PointMutationCalculator with additional functionality that is currently not compatible with all of the ParetoOpt functionality. please note that this has been checked into master in its current state in response to requests from others to use this modified version of chris king's GreedyOptMutationMover. although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MatDesPointMutationCalculator.hh | This is a modified version of chris king's PointMutationCalculator with additional functionality that is currently not compatible with all of the ParetoOpt functionality. please note that this has been checked into master in its current state in response to requests from others to use this modified version of chris king's GreedyOptMutationMover. although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| OligomericAverageDegreeFilter.cc | Calculates AverageDegree within the context of an unbound oligomer |
| OligomericAverageDegreeFilter.fwd.hh | |
| OligomericAverageDegreeFilter.hh | Header file for OligomericAverageDegreeFilter class |
| OligomericAverageDegreeFilterCreator.hh | FilterCreator for the OligomericAverageDegreeFilter |
| SchemePlaceMotifsMover.cc | |
| SchemePlaceMotifsMover.fwd.hh | |
| SchemePlaceMotifsMover.hh | |
| SchemePlaceMotifsMoverCreator.hh | |
| SymDofMover.cc | |
| SymDofMover.fwd.hh | |
| SymDofMover.hh | |
| SymDofMoverCreator.hh | |
| SymDofMoverSampler.cc | |
| SymDofMoverSampler.hh | |
| SymUnsatHbondFilter.cc | Determine the number of unsatified hydrogen bonds at an interface Works with both symmetric and asymmetric poses |
| SymUnsatHbondFilter.fwd.hh | |
| SymUnsatHbondFilter.hh | Definition of filter class SymUnsatHbondFilter |
| SymUnsatHbondFilterCreator.hh | FilterCreators for the SymUnsatHbondFilterCreator |
| ► md | |
| CartesianMD.cc | Initialization for MD |
| CartesianMD.fwd.hh | Forward declarations for CartesianMD |
| CartesianMD.hh | Cartesian MD |
| CartesianMDCreator.hh | |
| MDBase.cc | Initialization for MD |
| MDBase.fwd.hh | Initialization for MD |
| MDBase.hh | Initialization for MD |
| MDConstants.hh | Protocols/md package type declarations |
| Rattle.hh | Rattle bond length constrainer for CartesianMD |
| thermostat.hh | Thermostat for MD simulation |
| ► medal | |
| MedalExchangeMover.cc | |
| MedalExchangeMover.fwd.hh | |
| MedalExchangeMover.hh | |
| MedalMain.cc | |
| MedalMain.hh | |
| MedalMover.cc | |
| MedalMover.fwd.hh | |
| MedalMover.hh | |
| util.cc | |
| util.hh | |
| ► membrane | |
| ► geometry | |
| Embedding.cc | Methods for Computing Membrane Embeddings |
| Embedding.fwd.hh | Methods for Computing Membrane Embeddings |
| Embedding.hh | Methods for Computing Membrane Embeddings |
| EmbeddingDef.cc | Basic Embedding Definitions for Membrane Embedding |
| EmbeddingDef.fwd.hh | Basic Embedding Definitions for Membrane Embedding |
| EmbeddingDef.hh | Basic Embedding Definitions for Membrane Embedding |
| util.cc | Utility methods for membrane framework |
| util.hh | Utility methods for membrane framework |
| ► io | |
| LipoFileLoader.cc | Loader class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileLoader.fwd.hh | Loader class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileLoader.hh | Loader class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileLoaderCreator.hh | Loader class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileOptions.cc | Options Class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileOptions.fwd.hh | Options class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileOptions.hh | Options class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| LipoFileOptionsCreator.hh | Options creator class - load object that stores Lipid Exposure Data from Membrane Spanning Topology |
| SpanFileLoader.cc | Loader for SpanningTopology object - generating per-chain membrane spanning data |
| SpanFileLoader.fwd.hh | Loader for SpanningTopology object - generating per-chain membrane spanning data |
| SpanFileLoader.hh | Loader for SpanningTopology object - generating per-chain membrane spanning data |
| SpanFileLoaderCreator.hh | Loader for SpanningTopology object - generating per-chain membrane spanning data |
| SpanFileOptions.cc | Options for generating per-chain membrane spanning data |
| SpanFileOptions.fwd.hh | Options for generating per-chain membrane spanning data |
| SpanFileOptions.hh | Options for generating per-chain membrane spanning data |
| SpanFileOptionsCreator.hh | Options for generating per-chain membrane spanning data |
| ► symmetry | |
| SymmetricAddMembraneMover.cc | Add Membrane Representation to a Symmetric starting pose |
| SymmetricAddMembraneMover.fwd.hh | Add Membrane Representation to a Symmetric starting pose |
| SymmetricAddMembraneMover.hh | Add Membrane Representation to a Symmetric starting pose |
| SymmetricAddMembraneMoverCreator.hh | Add Membrane Representation to a Symmetric starting pose |
| util.cc | Quick calculations for symmetrizing membrane proteins |
| util.hh | Quick calculations for symmetrizing membrane proteins |
| ► visualize | |
| VisualizeEmbeddingMover.cc | Visualize Embedding normal and center with Virtual Residues |
| VisualizeEmbeddingMover.fwd.hh | Visualize Embedding normal and center with Virtual Residues |
| VisualizeEmbeddingMover.hh | Visualize Embedding normal and center with Virtual Residues |
| VisualizeEmbeddingMoverCreator.hh | Visualize Embedding normal and center with Virtual Residues |
| VisualizeMembraneMover.cc | Visualize Membrane Planes by many atoms |
| VisualizeMembraneMover.fwd.hh | Visualize Membrane Planes with Virtual Residues |
| VisualizeMembraneMover.hh | Visualize Membrane Planes by many atoms |
| VisualizeMembraneMoverCreator.hh | Visualize Membrane Planes with Virtual Residues |
| AddMembraneMover.cc | Add Membrane Representation to the Pose |
| AddMembraneMover.fwd.hh | Add Membrane Representation to the Pose |
| AddMembraneMover.hh | Add Membrane Representation to the Pose |
| AddMembraneMoverCreator.hh | Add Membrane Representation to the Pose (Rosetta Scripts Creator Hook) |
| FlipMover.cc | Flips a span or protein in the membrane (Rosetta Scripts Hook) |
| FlipMover.fwd.hh | Flips a span or protein in the membrane (Rosetta Scripts Hook) |
| FlipMover.hh | Flips a span or protein in the membrane (Rosetta Scripts Hook) |
| FlipMoverCreator.hh | Flips a span or protein in the membrane (Rosetta Scripts Hook) |
| MembranePositionFromTopologyMover.cc | Computes and sets the initial position of the membrane |
| MembranePositionFromTopologyMover.fwd.hh | Computes and sets the initial position of the membrane |
| MembranePositionFromTopologyMover.hh | Computes and sets the initial position of the membrane |
| MembranePositionFromTopologyMoverCreator.hh | Compute the Initial Position of the membrane |
| metrics.cc | Metrics for membrane framework proteins |
| metrics.hh | Metrics for membrane framework proteins |
| RandomMembranePositionMover.cc | Random membrane position mover |
| RandomMembranePositionMover.fwd.hh | Random membrane position mover |
| RandomMembranePositionMover.hh | Random membrane position mover |
| SetMembranePositionMover.cc | Sets the membrane position normal and center |
| SetMembranePositionMover.fwd.hh | Sets the membrane position normal and center |
| SetMembranePositionMover.hh | Sets the membrane position normal and center |
| SetMembranePositionMoverCreator.hh | Sets the membrane position normal and center |
| TransformIntoMembraneMover.cc | Transform pose into membrane coordinates (Rosetta Scripts Hook) |
| TransformIntoMembraneMover.fwd.hh | Transform pose into membrane coordinates (Rosetta Scripts Hook) |
| TransformIntoMembraneMover.hh | Transform pose into membrane coordinates (Rosetta Scripts Hook) |
| TransformIntoMembraneMoverCreator.hh | Transform pose into membrane coordinates (Rosetta Scripts Hook) |
| TranslationRotationMover.cc | |
| TranslationRotationMover.fwd.hh | |
| TranslationRotationMover.hh | |
| TranslationRotationMoverCreator.hh | |
| ► metal_interface | |
| AddZincSiteConstraints.cc | Adds metal binding site geometry constraints to pose |
| AddZincSiteConstraints.fwd.hh | AddZincSiteConstraints protocol-mover forward declarations header |
| AddZincSiteConstraints.hh | Adds metal binding site geometry constraints to pose |
| FindClosestAtom.cc | Finds the closest atom in a given residue to a point (usually a zinc atom) |
| FindClosestAtom.hh | Finds the closest atom in a given residue to a point (usually a zinc atom) |
| MatchGrafter.cc | Takes a scaffold protein and a match pdb from RosettaMatch, grafts the match onto the protein. For zinc homodimer design, it can then combine two grafted poses by overlaying the zinc atoms |
| MatchGrafter.fwd.hh | MatchGrafter protocol-mover forward declarations header |
| MatchGrafter.hh | Takes a scaffold protein and a match pdb from RosettaMatch, grafts the match onto the protein. For zinc homodimer design, it can then combine two grafted poses by overlaying the zinc atoms |
| MetalSiteResidue.cc | Stores data that describes a metal-coordinating residue |
| MetalSiteResidue.fwd.hh | MetalSiteResidue protocol-mover forward declarations header |
| MetalSiteResidue.hh | Stores data that describes a metal-coordinating residue |
| ZincHeterodimerMover.cc | ZincHeterodimerMover methods implemented - see apps/pilot/rjha/README for details |
| ZincHeterodimerMover.fwd.hh | ZincHeterodimerMover protocol-mover forward declarations header |
| ZincHeterodimerMover.hh | ZincHeterodimerMover protocol main mover |
| ZincSiteFinder.cc | Searches pose for a zinc residue, then fills a vector of MetalSiteResidue objects with info including sequence position of coordinating sidechains, ligand atom xyz, ligand atom name, and atom ids to provide a convenient way for protocols to add metalsite constraints (ligand refers to protein sidechains) |
| ZincSiteFinder.fwd.hh | ZincSiteFinder protocol-mover forward declarations header |
| ZincSiteFinder.hh | Searches pose for a zinc residue, then fills a vector of MetalSiteResidue objects with info including sequence position of coordinating sidechains, ligand atom xyz, ligand atom name, and atom ids to provide a convenient way for protocols to add metalsite constraints (ligand refers to protein sidechains) |
| ► motif_grafting | |
| ► movers | |
| MotifGraftCreator.hh | Declaration of the MoverCreator class for the MotifGraftCreator |
| MotifGraftMover.cc | Declaration of the MoverCreator class for the MotifGraftCreator |
| MotifGraftMover.hh | Declaration of the MoverCreator class for the MotifGraftCreator |
| ► motifs | |
| BuildPosition.cc | Position where motifs are built in MotifSearch |
| BuildPosition.fwd.hh | Forward declaration for position where motifs are built in MotifSearch |
| BuildPosition.hh | Class declaration for position where motifs are built in MotifSearch |
| IRCollection.cc | Implmentation of interaction motifs |
| IRCollection.fwd.hh | Forward declaration for sets of interaction motifis between residues |
| IRCollection.hh | Class declaration for collections of inverse rotamers |
| LigandMotifSearch.cc | Ligand motif searching protocol |
| LigandMotifSearch.fwd.hh | Forward declaration for interaction motif search protocol |
| LigandMotifSearch.hh | Class declaration for ligand motif searching protocol |
| Motif.cc | Implementation of interaction motifs |
| Motif.fwd.hh | Forward declaration for interaction motif between residues |
| Motif.hh | Header for interaction motif between residues |
| motif_utils.cc | Motif helper/conversion/io functions |
| motif_utils.hh | Header for motif helper/conversion/io functions |
| MotifDnaPacker.cc | |
| MotifDnaPacker.fwd.hh | |
| MotifDnaPacker.hh | |
| MotifDnaPackerCreator.hh | This class will create instances of Mover MotifDnaPacker for the MoverFactory |
| MotifHit.cc | Class that holds information about a motif in the context of the search |
| MotifHit.fwd.hh | Forward declaration for class that holds information about a motif in the context of the search |
| MotifHit.hh | Class declaration for class that holds information about a motif in the context of the search |
| MotifLibrary.cc | Implementation of interaction motifs |
| MotifLibrary.fwd.hh | Forward declaration for sets of interaction motifis between residues |
| MotifLibrary.hh | Class declaration for sets of interaction motifs between residues |
| MotifSearch.cc | Motif searching protocol |
| MotifSearch.fwd.hh | Forward declaration for interaction motif search protocol |
| MotifSearch.hh | Class declaration for motif searching protocol |
| SingleMotif.cc | Implementation of interaction motifs |
| SingleMotif.fwd.hh | Forward declaration for interaction motif between residues |
| SingleMotif.hh | Header for interaction motif between residues |
| ► moves | |
| ChangeFoldTreeMover.fwd.hh | |
| ChangeFoldTreeMover.hh | ChangeFoldTreeMover |
| CompositionMover.cc | |
| CompositionMover.fwd.hh | |
| CompositionMover.hh | |
| CyclicMover.cc | |
| CyclicMover.fwd.hh | |
| CyclicMover.hh | |
| DsspMover.cc | Performs dssp and set secondary structure to pose |
| DsspMover.fwd.hh | |
| DsspMover.hh | Header file of DsspMover.cc |
| DsspMoverCreator.hh | |
| DualMonteCarlo.cc | "dual" MonteCarlo wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| DualMonteCarlo.fwd.hh | "dual" MonteCarlo header - wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| DualMonteCarlo.hh | "dual" MonteCarlo header - wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| FilterMover.cc | Apply filter after mover |
| FilterMover.fwd.hh | Performs filtering pose after mover |
| FilterMover.hh | Performs MoverOP and then apply FilterOP |
| FilterReporterMover.cc | A FilterMover that also calls report() on apply() |
| FilterReporterMover.fwd.hh | A FilterMover that also calls report() on apply() |
| FilterReporterMover.hh | A FilterMover that also calls report() on apply() |
| IfMover.cc | |
| IfMover.hh | |
| IfMoverCreator.hh | |
| IteratedConvergenceMover.cc | Implementation of IteratedConvergenceMover, class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMover.fwd.hh | Forward declaration of the mover class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMover.hh | Mover class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMoverCreator.hh | This class will create instances of Mover IteratedConvergenceMover for the MoverFactory |
| JumpOutMover.cc | |
| JumpOutMover.fwd.hh | |
| JumpOutMover.hh | JumpOutMover |
| MonteCarlo.cc | |
| MonteCarlo.fwd.hh | |
| MonteCarlo.hh | |
| MonteCarlo.tmpl.hh | Implentation for MonteCarlo template functions |
| MonteCarloExceptionConverge.fwd.hh | |
| MonteCarloExceptionConverge.hh | |
| MonteCarloStatus.cc | |
| MonteCarloStatus.hh | |
| MoveMapMover.cc | Implementation file for MoveMapMover |
| MoveMapMover.fwd.hh | |
| MoveMapMover.hh | A MoveMapMover is nothing more than a mover that has a function that sets its movemap |
| Mover.cc | Method code and full headers for Mover– keeps heavily-included Mover.hh small and concise to maximize compiling efficiency and to make the class definitions easier to read |
| Mover.fwd.hh | |
| Mover.hh | : A mover is an object that can apply a conformational change to a pose |
| MoverApplyingMover.cc | Implementation file for MoverApplyingMover |
| MoverApplyingMover.fwd.hh | |
| MoverApplyingMover.hh | A MoverApplyingMover is nothing more than a mover that applies another (variable) mover |
| MoverContainer.cc | Apply functions for classes of type MoverContainer |
| MoverContainer.fwd.hh | MoverContainer forward declarations header |
| MoverContainer.hh | Base class for containers of movers such as SequenceMover |
| MoverContainerCreator.hh | |
| MoverCreator.cc | |
| MoverCreator.hh | Base class for MoverCreators for the Mover load-time factory registration scheme |
| MoverFactory.cc | |
| MoverFactory.fwd.hh | |
| MoverFactory.hh | |
| MoverForPoseList.cc | |
| MoverForPoseList.fwd.hh | |
| MoverForPoseList.hh | : In addition to applying to a pose, this mover can apply to a vector1 of poses |
| MoverStatistics.cc | Keeps track of the acceptance_rate of a Mover |
| MoverStatistics.hh | Keeps track of the acceptance_rate of a Mover |
| MoverStatus.cc | |
| MoverStatus.hh | Return status enum for Movers |
| NullMover.cc | |
| NullMover.fwd.hh | |
| NullMover.hh | |
| OutputMovers.cc | File to contain classes that deal with output and pdb dumping |
| OutputMovers.fwd.hh | OutputMovers forward declarations header |
| OutputMovers.hh | File to contain classes that deal with output and pdb dumping |
| PyMolMover.cc | Send infromation to PyMol |
| PyMolMover.fwd.hh | Send infromation to PyMol |
| PyMolMover.hh | Send infromation to PyMol. Contain classes PyMolMover, PyMolObserver and helper classes |
| PyMolMoverCreator.hh | |
| RampingMover.cc | Mover class for ramping the repulsive term of a score function over the course of several apply() evaluations |
| RampingMover.fwd.hh | |
| RampingMover.hh | Mover class for ramping a score function over the course of apply evaluations |
| RampingMoverCreator.hh | This class will create instances of Mover RampingMover for the MoverFactory |
| RepeatMover.cc | Method definitions for RepeatMover |
| RepeatMover.fwd.hh | |
| RepeatMover.hh | Declarations and simple accessor/mutator definitions for RepeatMover |
| ReplicaExchangeMC.cc | Implementing a Recplica Exchange Monte Carlo Mover |
| ReplicaExchangeMC.fwd.hh | Implementing a Recplica Exchange Monte Carlo Mover |
| ReplicaExchangeMC.hh | Implementing a Recplica Exchange Monte Carlo Mover |
| ResId.cc | |
| ResId.fwd.hh | |
| ResId.hh | A simple base class providing common access to a residue identity for movers and filters. The anticipated usage is to derive movers and filters multiply, from the relevant base class and from ResId and make these movers/filters use the residue id encapsulated in this class |
| SimulatedTempering.cc | Light-weight class for simulated tempering |
| SimulatedTempering.fwd.hh | Light-weight class for simulated tempering |
| SimulatedTempering.hh | Light-weight class for simulated tempering |
| StructureRestrictor.cc | Lookup relevant chains for a structure in a table |
| StructureRestrictor.fwd.hh | Lookup relevant chains for a structure in a table |
| StructureRestrictor.hh | Lookup relevant chains for a structure in a table |
| TrialCounter.cc | |
| TrialCounter.fwd.hh | |
| TrialCounter.hh | |
| TrialMover.cc | Performs a move and accepts it according to Monte Carlo accept/reject criterion |
| TrialMover.fwd.hh | TrialMover forward declarations header |
| TrialMover.hh | Performs a move and accepts it according to Monte Carlo accept/reject criterion |
| util.cc | |
| util.hh | |
| VectorPoseMover.cc | |
| VectorPoseMover.fwd.hh | |
| VectorPoseMover.hh | |
| WhileMover.cc | Method code and full headers for Mover– keeps heavily-included Mover.hh small and concise to maximize compiling efficiency and to make the class definitions easier to read |
| WhileMover.fwd.hh | |
| WhileMover.hh | |
| ► mpi_refinement | |
| Clusterer.cc | |
| Clusterer.hh | |
| MPI_Refine_Emperor.cc | |
| MPI_Refine_Emperor.hh | |
| MPI_Refine_Master.cc | |
| MPI_Refine_Master.hh | |
| MPI_Refinement.cc | |
| MPI_Refinement.hh | |
| MultiObjective.cc | |
| MultiObjective.fwd.hh | |
| MultiObjective.hh | |
| Scheduler.cc | |
| Scheduler.hh | |
| Serial_Refine.cc | |
| Serial_Refine.hh | |
| StructAvrgMover.cc | |
| StructAvrgMover.hh | |
| util.cc | |
| util.hh | |
| WorkUnit_Aggressive.cc | |
| WorkUnit_Aggressive.hh | |
| WorkUnit_Loop.cc | |
| WorkUnit_Loop.hh | |
| WorkUnit_Relax.cc | |
| WorkUnit_Relax.hh | |
| WorkUnit_Sampler.cc | |
| WorkUnit_Sampler.hh | |
| ► multistate_design | |
| MetricCalculatorFitnessFunction.cc | |
| MetricCalculatorFitnessFunction.fwd.hh | |
| MetricCalculatorFitnessFunction.hh | |
| MultiStateAggregateFunction.cc | |
| MultiStateAggregateFunction.fwd.hh | |
| MultiStateAggregateFunction.hh | |
| MultiStateEntity.cc | |
| MultiStateEntity.fwd.hh | |
| MultiStateEntity.hh | |
| MultiStateFitnessFunction.cc | |
| MultiStateFitnessFunction.fwd.hh | |
| MultiStateFitnessFunction.hh | |
| MultiStatePacker.cc | |
| MultiStatePacker.fwd.hh | |
| MultiStatePacker.hh | |
| PackingState.cc | |
| PackingState.fwd.hh | |
| PackingState.hh | For multistate design that is based on (re)use of packer information (RotamerSets and InteractionGraph) |
| PartitionAggregateFunction.cc | |
| PartitionAggregateFunction.fwd.hh | |
| PartitionAggregateFunction.hh | |
| SingleState.cc | |
| SingleState.fwd.hh | |
| SingleState.hh | |
| SingleStateEntityData.cc | |
| SingleStateEntityData.fwd.hh | |
| SingleStateEntityData.hh | |
| SingleStateFitnessFunction.cc | |
| SingleStateFitnessFunction.fwd.hh | |
| SingleStateFitnessFunction.hh | |
| util.cc | |
| util.hh | Collection of useful utilities for setting up and using a GeneticAlgorithm with multistate design |
| ► ncbb | |
| ► oop | |
| OopCreatorMover.cc | |
| OopCreatorMover.fwd.hh | |
| OopCreatorMover.hh | |
| OopCreatorMoverCreator.fwd.hh | |
| OopCreatorMoverCreator.hh | |
| OopDockDesignProtocol.cc | |
| OopDockDesignProtocol.fwd.hh | |
| OopDockDesignProtocol.hh | |
| OopDockDesignProtocolCreator.fwd.hh | |
| OopDockDesignProtocolCreator.hh | |
| NcbbDockDesignProtocol.cc | |
| NcbbDockDesignProtocol.fwd.hh | |
| NcbbDockDesignProtocol.hh | |
| NcbbDockDesignProtocolCreator.fwd.hh | |
| NcbbDockDesignProtocolCreator.hh | |
| ► neighbor | |
| Neighborhood.cc | |
| Neighborhood.hh | |
| ► noesy_assign | |
| CovalentCompliance.cc | |
| CovalentCompliance.hh | |
| CrossPeak.cc | Ab-initio fragment assembly protocol for proteins |
| CrossPeak.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| CrossPeak.hh | |
| CrossPeakInfo.cc | Ab-initio fragment assembly protocol for proteins |
| CrossPeakInfo.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| CrossPeakInfo.hh | |
| CrossPeakList.cc | Ab-initio fragment assembly protocol for proteins |
| CrossPeakList.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| CrossPeakList.hh | |
| CrossPeakList.impl.hh | |
| DistanceScoreMover.cc | Ab-initio fragment assembly protocol for proteins |
| DistanceScoreMover.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| DistanceScoreMover.hh | |
| Exceptions.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| FloatingResonance.cc | |
| FloatingResonance.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FloatingResonance.hh | |
| FoldResonance.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FoldResonance.hh | |
| FragsToAtomDist.cc | Simulate fragments and recored atom distances |
| FragsToAtomDist.fwd.hh | Simulate fragments and recored atom distances |
| FragsToAtomDist.hh | Simulate fragments and recored atom distances |
| LabelResonance.cc | |
| LabelResonance.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| LabelResonance.hh | |
| MethylNames.cc | |
| MethylNames.hh | |
| NoesyModule.cc | Main hook-up for the automatic NOESY assignment module |
| NoesyModule.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| NoesyModule.hh | Main hook-up for the automatic NOESY assignment module |
| NoesyModule.impl.hh | |
| PeakAssignment.cc | Ab-initio fragment assembly protocol for proteins |
| PeakAssignment.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| PeakAssignment.hh | |
| PeakAssignmentOptionKeys.hh | Ab-initio fragment assembly protocol for proteins |
| PeakAssignmentParameters.cc | Ab-initio fragment assembly protocol for proteins |
| PeakAssignmentParameters.hh | |
| PeakAssignmentResidueMap.cc | Ab-initio fragment assembly protocol for proteins |
| PeakAssignmentResidueMap.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| PeakAssignmentResidueMap.hh | |
| PeakCalibrator.cc | Ab-initio fragment assembly protocol for proteins |
| PeakCalibrator.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| PeakCalibrator.hh | |
| PeakFileFormat.cc | Ab-initio fragment assembly protocol for proteins |
| PeakFileFormat.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| PeakFileFormat.hh | |
| PeakFileFormat_Sparky.cc | Ab-initio fragment assembly protocol for proteins |
| PeakFileFormat_Sparky.hh | |
| PeakFileFormat_xpk.cc | Ab-initio fragment assembly protocol for proteins |
| PeakFileFormat_xpk.hh | |
| ProtonResonance.cc | |
| ProtonResonance.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ProtonResonance.hh | |
| Resonance.cc | |
| Resonance.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| Resonance.hh | |
| ResonanceList.cc | |
| ResonanceList.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ResonanceList.hh | Table with atomID - chemical shift mapping |
| StructureDependentPeakCalibrator.cc | Ab-initio fragment assembly protocol for proteins |
| StructureDependentPeakCalibrator.hh | |
| StructureIndependentPeakCalibrator.cc | Ab-initio fragment assembly protocol for proteins |
| StructureIndependentPeakCalibrator.hh | |
| util.cc | Ab-initio fragment assembly protocol for proteins |
| util.hh | |
| ► nonlocal | |
| BiasedFragmentMover.cc | |
| BiasedFragmentMover.fwd.hh | |
| BiasedFragmentMover.hh | |
| Chunk.cc | |
| Chunk.fwd.hh | |
| Chunk.hh | |
| HelixRotate.cc | |
| HelixRotate.fwd.hh | |
| HelixRotate.hh | |
| Policy.fwd.hh | |
| Policy.hh | |
| PolicyFactory.cc | |
| PolicyFactory.hh | |
| Region.cc | |
| Region.fwd.hh | |
| Region.hh | |
| SheetTranslate.cc | |
| SheetTranslate.fwd.hh | |
| SheetTranslate.hh | |
| SimpleTreeBuilder.cc | |
| SimpleTreeBuilder.fwd.hh | |
| SimpleTreeBuilder.hh | |
| SingleFragmentMover.cc | |
| SingleFragmentMover.fwd.hh | |
| SingleFragmentMover.hh | |
| SingleFragmentMoverCreator.cc | |
| SingleFragmentMoverCreator.hh | |
| SmoothPolicy.cc | |
| SmoothPolicy.hh | |
| StarTreeBuilder.cc | |
| StarTreeBuilder.fwd.hh | |
| StarTreeBuilder.hh | |
| TreeBuilder.fwd.hh | |
| TreeBuilder.hh | |
| TreeBuilderFactory.cc | |
| TreeBuilderFactory.hh | |
| UniformPolicy.cc | |
| UniformPolicy.hh | |
| util.cc | |
| util.hh | |
| ► normalmode | |
| NormalMode.cc | |
| NormalMode.hh | Initialization for NormalMode |
| NormalModeMinimizer.cc | High-level atom tree minimizer class |
| NormalModeMinimizer.fwd.hh | Protocols::normalmode::NormalModeMinimizer forward declarations |
| NormalModeMinimizer.hh | High-level atom tree minimizer class |
| NormalModeMinimizerCreator.hh | |
| NormalModeMultiFunc.cc | Atom tree multifunction class |
| NormalModeMultiFunc.hh | NormalMode multifunction class |
| NormalModeRelaxMover.cc | Normal Mode Perturbation + Relax |
| NormalModeRelaxMover.fwd.hh | Initialization for NormalMode |
| NormalModeRelaxMover.hh | Initialization for NormalMode |
| ► optimize_weights | |
| DDGBindOptEData.cc | Implementation of the OptEPositionData class that handles interface ddG optimization |
| DDGBindOptEData.fwd.hh | Forward header for a optE position data class that holds interface ddG information |
| DDGBindOptEData.hh | Header file for OptEPositionData class that hold interface ddG information |
| DGBindOptEData.cc | |
| DGBindOptEData.fwd.hh | |
| DGBindOptEData.hh | |
| IterativeOptEDriver.cc | Implementation of iterative weight fitting protocol |
| IterativeOptEDriver.fwd.hh | Forward declaration of iterative weight fitting protocol |
| IterativeOptEDriver.hh | A class for optimizing weights in an iterative weight fitting, sequence recovery test protocol |
| NestedEnergyTermOptEData.cc | |
| NestedEnergyTermOptEData.fwd.hh | Forward header for some special optE position data classes |
| NestedEnergyTermOptEData.hh | Classes to store by-energy-term rotamer data for optE, when using the unfolded state energy term |
| OptEData.cc | |
| OptEData.fwd.hh | Forward declarations for OptE data structures |
| OptEData.hh | Classes to store by-energy-term rotamer data for optE |
| OptEMultifunc.cc | OptE mode multifunction class |
| OptEMultifunc.fwd.hh | Core::optimization::OptEMultifunc forward declarations |
| OptEMultifunc.hh | OptE mode multifunction class |
| PNatLigPoseOptEData.cc | |
| PNatLigPoseOptEData.fwd.hh | |
| PNatLigPoseOptEData.hh | |
| ► outputter | |
| FormatStringOutputter.cc | An abstract base class that implements format string parsing |
| FormatStringOutputter.fwd.hh | An abstract base class that implements format string parsing |
| FormatStringOutputter.hh | An abstract base class that implements format string parsing |
| Outputter.cc | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a file |
| Outputter.fwd.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a file |
| Outputter.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a file |
| PDBOutputter.cc | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| PDBOutputter.fwd.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| PDBOutputter.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| ResFileOutputter.cc | Saves a resfile that is generated by applying the input task operations to the pose |
| ResFileOutputter.fwd.hh | Saves a resfile that is generated by applying the input task operations to the pose |
| ResFileOutputter.hh | Saves a resfile that is generated by applying the input task operations to the pose |
| SilentFileOutputter.cc | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| SilentFileOutputter.fwd.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a silent file (or many!) |
| SilentFileOutputter.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a silent file( or many! ) |
| ► pack_daemon | |
| DynamicAggregateFunction.cc | |
| DynamicAggregateFunction.fwd.hh | Forward declaration of class MultistateAggregateFunction |
| DynamicAggregateFunction.hh | Declaration for a file-driven definition for the active states in a multistate design and the set of mathematical expressions that together define the fitness function for the sequence being designed |
| EntityCorrespondence.cc | Implementation for class EntityCorrespondence |
| EntityCorrespondence.fwd.hh | Forward declaration for class EntityCorrespondence |
| EntityCorrespondence.hh | Declaration for class EntityCorrespondence |
| MultistateAggregateFunction.cc | Implementation for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class) |
| MultistateAggregateFunction.fwd.hh | Forward declaration of class MultistateAggregateFunction |
| MultistateAggregateFunction.hh | Declaration for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class) |
| MultistateFitnessFunction.cc | Implementation of the class MultistateFitnessFunction |
| MultistateFitnessFunction.fwd.hh | Forward declaration of class MultistateFitnessFunction |
| MultistateFitnessFunction.hh | Declaration for class MultistateFitnessFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateFitnessFunction class) |
| PackDaemon.cc | Implementation for class PackDaemon |
| PackDaemon.fwd.hh | Declaration for class PackDaemon |
| PackDaemon.hh | Declaration for class PackDaemon |
| util.cc | Utility functions for working with the multistate-design classes |
| util.hh | Declaration for utility functions for working with the multistate-design classes |
| ► pb_potential | |
| SetupPoissonBoltzmannPotential.cc | Setup for Poisson-Boltzmann energy term use in scorefunction This mover assumes you have a path to the APBS (Adaptive Poisson-Boltzmann Solver) program in the system PATH. The executable name must be "apbs", case-sensitive |
| SetupPoissonBoltzmannPotential.fwd.hh | SetupPoissonBoltzmannPotential class forward delcaration |
| SetupPoissonBoltzmannPotential.hh | Setup for Poisson-Boltzmann energy term use in scorefunction This mover assumes you have a path to the APBS (Adaptive Poisson-Boltzmann Solver) program in the system PATH. The executable name must be "apbs", case-sensitive |
| SetupPoissonBoltzmannPotentialCreator.hh | |
| ► pmut_scan | |
| AlterSpecDisruptionDriver.cc | A protocol that tries to find interface-disrupting mutations as phase 1 of an altered-specificity protocol |
| AlterSpecDisruptionDriver.hh | A protocol that tries to find interface-disrupting mutations as phase 1 of an altered-specificity protocol |
| Mutant.cc | A helper class for the point mut scan protocol which holds data about mutants |
| Mutant.fwd.hh | Forward declaration for Mutant.hh |
| Mutant.hh | A helper class for the point mut scan protocol |
| PointMutScanDriver.cc | A protocol that tries to find stability enhancing mutations |
| PointMutScanDriver.hh | A protocol that tries to find stability enhancing mutations |
| ► pockets | |
| DarcParticleSwarmMinimizer.cc | |
| DarcParticleSwarmMinimizer.fwd.hh | |
| DarcParticleSwarmMinimizer.hh | |
| Fingerprint.cc | Protocols::pockets::Fingerprint functions |
| Fingerprint.fwd.hh | Protocols::pockets::Fingerprint forward declarations header |
| Fingerprint.hh | Protocols::pockets::MultiFingerprint header |
| FingerprintMultifunc.cc | Fingerprint multifunction class |
| FingerprintMultifunc.fwd.hh | Protocols::pockets::FingerprintMultifunc forward declarations |
| FingerprintMultifunc.hh | Fingerprint comparison multifunction class |
| GenPharmacophore.cc | Protocols::pockets::Fingerprint functions |
| GenPharmacophore.fwd.hh | Protocols::pockets::Fingerprint forward declarations header |
| GenPharmacophore.hh | |
| PocketConstraint.cc | |
| PocketConstraint.fwd.hh | Core::grid::Pockets::PocketConstraint forward declarations header |
| PocketConstraint.hh | |
| PocketConstraintCreator.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| PocketExemplarMultifunc.cc | Pocket multifunction class |
| PocketExemplarMultifunc.fwd.hh | Protocols::pockets::PocketExemplarMultifunc forward declarations |
| PocketExemplarMultifunc.hh | Pocket comparison multifunction class |
| PocketGrid.cc | Protocols::pockets::PocketGrid functions |
| PocketGrid.fwd.hh | Protocols::pockets::PocketGrid forward declarations header |
| PocketGrid.hh | Protocols::pockets::PocketGrid header |
| ► pose_reporters | |
| BasicPosePropertyReporterCreators.hh | Collection of PosePropertySelector creators for basic pose reporters |
| BasicPosePropertyReporters.cc | Collection of simple pose property reporters |
| BasicPosePropertyReporters.hh | Collection of simple pose property reporters |
| ► pose_selectors | |
| BasicPoseSelectorCreators.hh | Collection of PoseSelector creators for basic selectors |
| BasicPoseSelectors.cc | Collection of simple pose selectors |
| BasicPoseSelectors.hh | Collection of simple pose selectors |
| ClusterPoseSelector.cc | Cluster pose selector using protocols::cluster |
| ClusterPoseSelector.hh | Cluster pose selector using protocols::cluster |
| ClusterPoseSelectorCreator.hh | Creator for ClusterPoseSelector |
| ► protein_interface_design | |
| ► filters | |
| AtomicContactCountFilter.cc | |
| AtomicContactCountFilter.fwd.hh | Forward declaration for AtomicContactCountFilter |
| AtomicContactCountFilter.hh | |
| AtomicContactCountFilterCreator.hh | FilterCreators for the AtomicContactCountFilter |
| AverageDegreeFilter.cc | |
| AverageDegreeFilter.fwd.hh | Forward declaration for AverageDegreeFilter |
| AverageDegreeFilter.hh | Reports the average degree of connectivity of interface residues |
| AverageDegreeFilterCreator.hh | FilterCreators for the AverageDegreeFilter |
| BindingStrainFilter.cc | |
| BindingStrainFilter.fwd.hh | Forward declaration for BindingStrainFilter |
| BindingStrainFilter.hh | Reports the rotameric energy strain upon binding, by separating the monomers, repacking, minimizing, and measuring the energy difference from the bound but separated state |
| BindingStrainFilterCreator.hh | FilterCreators for the BindingStrainFilter |
| BoltzmannFilter.cc | |
| BoltzmannFilter.fwd.hh | Forward declaration for BoltzmannFilter |
| BoltzmannFilter.hh | Reports the average degree of connectivity of interface residues |
| BoltzmannFilterCreator.hh | FilterCreators for the BoltzmannFilter |
| ClashWithTargetFilter.cc | ClashWithTarget filtering |
| ClashWithTargetFilter.hh | Clash check with Target using motifgrafting |
| ClashWithTargetFilterCreator.hh | FilterCreators for the ClashWithTargetFilter |
| DesignableResiduesFilter.cc | |
| DesignableResiduesFilter.fwd.hh | Forward declaration for DesignableResiduesFilter |
| DesignableResiduesFilter.hh | Reports to Tracer which residues are designable in a taskfactory |
| DesignableResiduesFilterCreator.hh | FilterCreators for the DesignableResiduesFilter |
| DisulfideFilter.cc | Filters for interfaces which could form a disulfide bond between docking partners |
| DisulfideFilter.hh | Filters for interfaces which could form a disulfide bond between docking partners |
| DisulfideFilterCreator.hh | FilterCreators for the DisulfideFilter |
| FilterScan.cc | |
| FilterScan.fwd.hh | Forward declaration for FilterScanFilter |
| FilterScan.hh | Scans a task factory, mutates to each designable residue and evaluates a filter. Mutations that pass the filter are output in a resfile format |
| FilterScanCreator.hh | FilterCreators for the FilterScanFilter |
| FNatFilter.cc | Filtering on fraction of native contacts |
| FNatFilter.hh | Calculate L_RMSD using the method from protocols::docking::metrics |
| FNatFilterCreator.hh | FilterCreators for the FNatFilter |
| HbondsToAtomFilter.cc | |
| HbondsToAtomFilter.fwd.hh | Forward declaration for HbondsToAtomFilter |
| HbondsToAtomFilter.hh | Definition of filter classes for iterations of docking/design |
| HbondsToAtomFilterCreator.hh | FilterCreators for the filters defined in HbondsToAtomFilterCreator.hh |
| HbondsToResidueFilter.cc | |
| HbondsToResidueFilter.fwd.hh | Forward declaration for HbondsToResidueFilter |
| HbondsToResidueFilter.hh | Definition of filter classes for iterations of docking/design |
| HbondsToResidueFilterCreator.hh | FilterCreators for the filters defined in HbondsToResidueFilterCreator.hh |
| InterfaceHolesFilter.cc | Find packing defects at an interface using packstat score terms |
| InterfaceHolesFilter.hh | Find packing defects at an interface using packstat score terms |
| InterfaceHolesFilterCreator.hh | FilterCreators for the InterfaceHolesFilter |
| IRmsdFilter.cc | Rmsd filtering |
| IRmsdFilter.hh | Calculate I_RMSD using the method from protocols::docking::metrics |
| IRmsdFilterCreator.hh | FilterCreators for the IRmsdFilter |
| LRmsdFilter.cc | Rmsd filtering |
| LRmsdFilter.hh | Calculate L_RMSD using the method from protocols::docking::metrics |
| LRmsdFilterCreator.hh | FilterCreators for the LRmsdFilter |
| RelativeSegmentFilter.cc | |
| RelativeSegmentFilter.fwd.hh | Forward declaration for RelativeSegmentFilter |
| RelativeSegmentFilter.hh | |
| RelativeSegmentFilterCreator.hh | FilterCreators for the filters defined in RelativeSegmentFilterCreator.hh |
| RmsdFilter.cc | Rmsd filtering |
| RmsdFilter.hh | Find packing defects at an interface using packstat score terms |
| RmsdFilterCreator.hh | FilterCreators for the RmsdFilter |
| RmsdSimpleFilter.cc | Rmsd filtering |
| RmsdSimpleFilter.hh | Simply calculate RMSD, doesn't assume that poses are statick unmutable objects |
| RmsdSimpleFilterCreator.hh | FilterCreators for the RmsdSimpleFilter |
| SequenceRecoveryFilter.cc | |
| SequenceRecoveryFilter.fwd.hh | Forward declaration for SequenceRecoveryFilter |
| SequenceRecoveryFilter.hh | A filter that is contingent on some other mover to set its pass/fail value |
| SequenceRecoveryFilterCreator.hh | FilterCreators for the SequenceRecoveryFilter |
| SpecificResiduesNearInterfaceFilter.cc | Pass if a specific set of residues are near the interface |
| SpecificResiduesNearInterfaceFilter.fwd.hh | Forward header for SpecificResiduesNearInterface |
| SpecificResiduesNearInterfaceFilter.hh | Reports the average degree of connectivity of interface residues |
| SpecificResiduesNearInterfaceFilterCreator.hh | Pass if a specific set of residues are near the interface |
| SSamountFilter.cc | SS fraction filtering |
| SSamountFilter.hh | Calculate SS fraction, doesn't assume that poses are statick unmutable objects |
| SSamountFilterCreator.hh | FilterCreators for the SSamountFilter |
| StubScoreFilter.cc | |
| StubScoreFilter.fwd.hh | Forward declaration for StubScoreFilter |
| StubScoreFilter.hh | A filter that is contingent on some other mover to set its pass/fail value |
| StubScoreFilterCreator.hh | FilterCreators for the StubScoreFilter |
| StubScoreLoopsFilter.cc | |
| StubScoreLoopsFilter.fwd.hh | Forward declaration for StubScoreLoopsFilter |
| StubScoreLoopsFilter.hh | A filter that is contingent on some other mover to set its pass/fail value |
| StubScoreLoopsFilterCreator.hh | FilterCreators for the StubScoreLoopsFilter |
| TorsionFilter.cc | |
| TorsionFilter.fwd.hh | Forward declaration for Torsion |
| TorsionFilter.hh | Reports the average degree of connectivity of interface residues |
| TorsionFilterCreator.hh | FilterCreators for the Torsion |
| ► movers | |
| AddChainBreak.cc | |
| AddChainBreak.hh | |
| AddChainBreakCreator.hh | Declaration of the MoverCreator class for the AddChainBreak |
| AddSidechainConstraintsToHotspots.cc | |
| AddSidechainConstraintsToHotspots.hh | |
| AddSidechainConstraintsToHotspotsCreator.hh | Declaration of the MoverCreator class for the AddSidechainConstraintsToHotspots |
| BackrubDDMover.cc | |
| BackrubDDMover.hh | Derived class from mover for dock design with backrub moves |
| BackrubDDMoverCreator.hh | Declaration of the MoverCreator class for the BackrubDDMover |
| BestHotspotCstMover.cc | |
| BestHotspotCstMover.hh | |
| BestHotspotCstMoverCreator.hh | Declaration of the MoverCreator class for the BestHotspotCstMover |
| BuildAlaPose.cc | |
| BuildAlaPose.fwd.hh | BuildAlaPose forward declarations header |
| BuildAlaPose.hh | |
| BuildAlaPoseCreator.hh | Declaration of the MoverCreator class for the BuildAlaPose |
| DesignMinimizeHbonds.cc | |
| DesignMinimizeHbonds.hh | |
| DesignMinimizeHbondsCreator.hh | Declaration of the MoverCreator class for the DesignMinimizeHbonds |
| DisulfideMover.cc | |
| DisulfideMover.hh | |
| DisulfideMoverCreator.hh | Declaration of the MoverCreator class for the DisulfideMover |
| DockAndRetrieveSidechains.cc | |
| DockAndRetrieveSidechains.hh | |
| DockAndRetrieveSidechainsCreator.hh | Declaration of the MoverCreator class for the DockAndRetrieveSidechains |
| DockWithHotspotMover.cc | |
| DockWithHotspotMover.fwd.hh | |
| DockWithHotspotMover.hh | |
| DockWithHotspotMoverCreator.hh | This class will create instances of protocols::moves::Mover DockWithHotspotMover for the protocols::moves::MoverFactory |
| FavorNativeResiduePreCycle.cc | |
| FavorNativeResiduePreCycle.hh | |
| FavorNativeResiduePreCycleCreator.hh | Declaration of the MoverCreator class for the FavorNativeResiduePreCycle |
| FavorNonNativeResiduePreCycle.cc | |
| FavorNonNativeResiduePreCycle.hh | |
| FavorNonNativeResiduePreCycleCreator.hh | Declaration of the MoverCreator class for the FavorNonnativeResidue |
| HotspotDisjointedFoldTreeMover.cc | |
| HotspotDisjointedFoldTreeMover.hh | |
| HotspotDisjointedFoldTreeMoverCreator.hh | Declaration of the MoverCreator class for the HotspotDisjointedFoldTreeMover |
| HotspotHasherMover.cc | |
| HotspotHasherMover.hh | |
| HotspotHasherMoverCreator.hh | Declaration of the MoverCreator class for the HotspotHasherMover |
| InterfaceRecapitulationMover.cc | |
| InterfaceRecapitulationMover.hh | |
| InterfaceRecapitulationMoverCreator.hh | Declaration of the MoverCreator class for the InterfaceRecapitulationMover |
| LoopFinder.cc | Finds loops and adds them to the basic::datacache::DataMap. Parseable options to control how loops are found |
| LoopFinder.hh | Header for class to find loops (parseable options to control how loops are found) |
| LoopFinderCreator.hh | Declaration of the MoverCreator class for the LoopFinder |
| LoopLengthChange.cc | |
| LoopLengthChange.fwd.hh | LoopLengthChange forward declarations header |
| LoopLengthChange.hh | |
| LoopLengthChangeCreator.hh | Declaration of the MoverCreator class for the LoopLengthChange |
| LoopMoverFromCommandLine.cc | Parseable class to do full loop remodeling with input fragment files from command line |
| LoopMoverFromCommandLine.fwd.hh | LoopRemodel forward declarations header |
| LoopMoverFromCommandLine.hh | Header for parseable class to build loops from command line |
| LoopMoverFromCommandLineCreator.hh | Declaration of the MoverCreator class for the LoopRemodelFromCommandLine |
| LoopOver.cc | |
| LoopOver.hh | |
| LoopOverCreator.hh | Declaration of the MoverCreator class for the LoopOver |
| LoopRemodel.cc | Parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive). Intended to sample loop conformations at an interface |
| LoopRemodel.fwd.hh | LoopRemodel forward declarations header |
| LoopRemodel.hh | Header for parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive) |
| LoopRemodelCreator.hh | Declaration of the MoverCreator class for the LoopRemodel |
| MapHotspot.cc | |
| MapHotspot.hh | |
| MapHotspotCreator.hh | Declaration of the MoverCreator class for the MapHotspot |
| PatchdockTransform.cc | |
| PatchdockTransform.fwd.hh | PatchdockTransform forward declarations header |
| PatchdockTransform.hh | |
| PatchdockTransformCreator.hh | Declaration of the MoverCreator class for the PatchdockTransform |
| PeptideStapleDesignMover.cc | |
| PeptideStapleDesignMover.hh | |
| PeptideStapleDesignMoverCreator.hh | Declaration of the MoverCreator class for the PeptideStapleDesignMover |
| PlacementAuctionMover.cc | |
| PlacementAuctionMover.fwd.hh | Forward declations for PlacementAuctionMover |
| PlacementAuctionMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| PlacementAuctionMoverCreator.hh | Declaration of the MoverCreator class for the PlacementAuctionMover |
| PlacementMinimizationMover.cc | |
| PlacementMinimizationMover.fwd.hh | Forward declations for PlacementMinimizationMover |
| PlacementMinimizationMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| PlacementMinimizationMoverCreator.hh | Declaration of the MoverCreator class for the PlacementMinimizationMover |
| PlaceOnLoop.cc | |
| PlaceOnLoop.fwd.hh | PlaceOnLoop forward declarations header |
| PlaceOnLoop.hh | |
| PlaceOnLoopCreator.hh | Declaration of the MoverCreator class for the PlaceOnLoop |
| PlaceSimultaneouslyMover.cc | |
| PlaceSimultaneouslyMover.hh | Definition of classes for grafting hotspots into a pose |
| PlaceSimultaneouslyMoverCreator.hh | Declaration of the MoverCreator class for the PlaceSimultaneouslyMover |
| PlaceStubMover.cc | |
| PlaceStubMover.fwd.hh | Forward declarations for PlaceStubMover |
| PlaceStubMover.hh | Definition of classes for grafting hotspots into a pose |
| PlaceStubMoverCreator.hh | Declaration of the MoverCreator class for the PlaceStubMover |
| PlaceUtils.cc | Collection of utility functions for placement classes |
| PlaceUtils.hh | Definition of classes for grafting hotspots into a pose |
| PrepackMover.cc | |
| PrepackMover.hh | |
| PrepackMoverCreator.hh | Declaration of the MoverCreator class for the PrepackMover |
| ProteinInterfaceMultiStateDesignMover.cc | |
| ProteinInterfaceMultiStateDesignMover.fwd.hh | |
| ProteinInterfaceMultiStateDesignMover.hh | |
| ProteinInterfaceMultiStateDesignMoverCreator.hh | Declaration of the MoverCreator class for the ProteinInterfaceMultiStateDesignMover |
| RandomMutation.cc | |
| RandomMutation.fwd.hh | RandomMutation forward declarations header |
| RandomMutation.hh | |
| RandomMutationCreator.hh | Declaration of the MoverCreator class for the RandomMutation |
| RepackMinimize.cc | |
| RepackMinimize.hh | |
| RepackMinimizeCreator.hh | Declaration of the MoverCreator class for the RepackMinimize |
| SaveAndRetrieveSidechains.cc | |
| SaveAndRetrieveSidechains.fwd.hh | SaveAndRetrieveSidechains forward declarations header |
| SaveAndRetrieveSidechains.hh | |
| SaveAndRetrieveSidechainsCreator.hh | Declaration of the MoverCreator class for the SaveAndRetrieveSidechains |
| SetAtomTree.cc | |
| SetAtomTree.hh | |
| SetAtomTreeCreator.hh | Declaration of the MoverCreator class for the SetAtomTree |
| SetTemperatureFactor.cc | |
| SetTemperatureFactor.fwd.hh | SetTemperatureFactor forward declarations header |
| SetTemperatureFactor.hh | |
| SetTemperatureFactorCreator.hh | Declaration of the MoverCreator class for the SetTemperatureFactor |
| SetupHotspotConstraintsLoopsMover.cc | |
| SetupHotspotConstraintsLoopsMover.fwd.hh | SetupHotspotConstraintsLoopsMover forward declarations header |
| SetupHotspotConstraintsLoopsMover.hh | Derived classes from DockDesign for dock design |
| SetupHotspotConstraintsLoopsMoverCreator.hh | Declaration of the MoverCreator class for the SetupHotspotConstraintsLoopsMover |
| SetupHotspotConstraintsMover.cc | |
| SetupHotspotConstraintsMover.fwd.hh | SetupHotspotConstraintsMover forward declarations header |
| SetupHotspotConstraintsMover.hh | Derived classes from DockDesign for dock design |
| SetupHotspotConstraintsMoverCreator.hh | Declaration of the MoverCreator class for the SetupHotspotConstraintsMover |
| ShoveResidueMover.cc | |
| ShoveResidueMover.hh | |
| ShoveResidueMoverCreator.hh | Declaration of the MoverCreator class for the ShoveResidueMover |
| SpinMover.cc | |
| SpinMover.hh | |
| SpinMoverCreator.hh | Declaration of the MoverCreator class for the SpinMover |
| SubroutineMover.cc | |
| SubroutineMover.fwd.hh | Forward declations for SubroutineMover |
| SubroutineMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| SubroutineMoverCreator.hh | Declaration of the MoverCreator class for the SubroutineMover |
| TaskAwareCsts.cc | |
| TaskAwareCsts.fwd.hh | TaskAwareCsts forward declarations header |
| TaskAwareCsts.hh | |
| TaskAwareCstsCreator.hh | Declaration of the MoverCreator class for the TaskAwareCsts |
| TopologyBrokerMover.cc | |
| TopologyBrokerMover.fwd.hh | TopologyBrokerMover forward declarations header |
| TopologyBrokerMover.hh | |
| TopologyBrokerMoverCreator.hh | This class will create instances of protocols::moves::Mover TopologyBrokerMover for the protocols::moves::MoverFactory |
| TryRotamers.cc | |
| TryRotamers.hh | |
| TryRotamersCreator.hh | Declaration of the MoverCreator class for the TryRotamers |
| VLB.cc | |
| VLB.hh | |
| VLBCreator.hh | Declaration of the MoverCreator class for the VLB |
| design_utils.cc | Various utilities for interface design |
| design_utils.hh | Definition of various classes for interface design |
| DockDesignFilterFactory.cc | |
| DockDesignFilterFactory.fwd.hh | |
| DockDesignFilterFactory.hh | |
| ParserJobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class PDBJobInputter |
| ParserJobInputter.fwd.hh | |
| ParserJobInputter.hh | Header file for PatchdockJobInputter. Feeds poses based on a starting structure and a patchdock output file describing the rigid-body transformations to apply to the pose |
| ParserJobInputterCreator.hh | |
| PatchdockReader.fwd.hh | |
| read_patchdock.cc | Various utilities for interface design |
| read_patchdock.hh | |
| ReportPSSMDifference.cc | Calculation of the difference in PSSM score between mutated and native pose |
| ReportPSSMDifference.fwd.hh | Calculation of the difference in PSSM score between mutated and native pose |
| ReportPSSMDifference.hh | Calculation of the difference in PSSM score between mutated and native pose |
| util.cc | |
| util.hh | Definition of classes for iterations of docking/design |
| ► qsar | |
| ► scoring_grid | |
| AtrGrid.cc | |
| AtrGrid.fwd.hh | |
| AtrGrid.hh | |
| AtrGridCreator.hh | |
| ChargeGrid.cc | This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857. doi:10.1021/jm00145a002 |
| ChargeGrid.fwd.hh | |
| ChargeGrid.hh | This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857. doi:10.1021/jm00145a002 |
| ChargeGridCreator.hh | |
| ClassicGrid.cc | |
| ClassicGrid.fwd.hh | |
| ClassicGrid.hh | |
| ClassicGridCreator.hh | |
| ConstantScoreBase.fwd.hh | |
| ConstantScoreBase.hh | This is a base class for defining constant terms which are computed over an entire ligand rather than on a per atom basis The unneeded functions are stubbed out, everything left is pure virtual |
| GridBase.fwd.hh | |
| GridBase.hh | |
| GridCreator.cc | |
| GridCreator.hh | Base class for GridCreators for the Grid load time factory registration scheme |
| GridFactory.cc | |
| GridFactory.fwd.hh | |
| GridFactory.hh | |
| GridInitMover.cc | |
| GridInitMover.fwd.hh | |
| GridInitMover.hh | |
| GridInitMoverCreator.hh | |
| GridManager.cc | |
| GridManager.fwd.hh | |
| GridManager.hh | |
| HbaGrid.cc | |
| HbaGrid.fwd.hh | |
| HbaGrid.hh | |
| HbaGridCreator.hh | |
| HbdGrid.cc | |
| HbdGrid.fwd.hh | |
| HbdGrid.hh | |
| HbdGridCreator.hh | |
| LigandPropertyScore.cc | |
| LigandPropertyScore.fwd.hh | |
| LigandPropertyScore.hh | |
| LigandPropertyScoreCreator.hh | |
| RepGrid.cc | |
| RepGrid.fwd.hh | |
| RepGrid.hh | |
| RepGridCreator.hh | |
| ScoreNormalization.cc | Header file for Score Normalization methods |
| ScoreNormalization.fwd.hh | Report data to database |
| ScoreNormalization.hh | Header file for Score Normalization methods |
| ScoringGridLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| ScoringGridLoader.fwd.hh | |
| ScoringGridLoader.hh | Declartion of the XML parser's ScoringGridLoader class for adding named ScoringGrids to the basic::datacache::DataMap |
| ScoringGridLoaderCreator.hh | Creator classes for the default DataLoader classes, TaskOperationLoader and ScoreFunctionLoader |
| ShapeGrid.cc | |
| ShapeGrid.fwd.hh | |
| ShapeGrid.hh | |
| ShapeGridCreator.hh | |
| SingleGrid.cc | |
| SingleGrid.fwd.hh | |
| SingleGrid.hh | |
| SolvationGrid.cc | |
| SolvationGrid.fwd.hh | |
| SolvationGrid.hh | |
| SolvationGridCreator.hh | |
| SolvationMetaGrid.cc | |
| SolvationMetaGrid.fwd.hh | |
| SolvationMetaGrid.hh | |
| SolvationMetaGridCreator.hh | |
| VdwGrid.cc | |
| VdwGrid.fwd.hh | |
| VdwGrid.hh | |
| VdwGridCreator.hh | |
| qsarMap.cc | |
| qsarMap.fwd.hh | |
| qsarMap.hh | |
| qsarMover.cc | |
| qsarMover.fwd.hh | |
| qsarMover.hh | |
| qsarMoverCreator.hh | |
| qsarOptFunc.cc | |
| qsarOptFunc.fwd.hh | |
| qsarOptFunc.hh | |
| RenderGridsToKinemage.cc | |
| RenderGridsToKinemage.fwd.hh | |
| RenderGridsToKinemage.hh | |
| RenderGridsToKinemageCreator.hh | |
| ► rbsegment_relax | |
| AutoRBRelaxMover.cc | |
| AutoRBRelaxMover.hh | |
| FragInsertAndAlignMover.cc | |
| FragInsertAndAlignMover.hh | |
| IdealizeHelices.cc | Protocols for folding into density |
| IdealizeHelices.hh | |
| IdealizeHelicesCreator.hh | |
| MakeStarTopology.cc | Protocols for folding into density |
| MakeStarTopology.hh | |
| MakeStarTopologyCreator.hh | |
| OptimizeThreading.cc | Protocols for folding into density |
| OptimizeThreading.hh | |
| OptimizeThreadingCreator.hh | |
| RBSegment.cc | |
| RBSegment.fwd.hh | |
| RBSegment.hh | |
| RBSegmentMover.cc | |
| RBSegmentMover.hh | |
| RBSegmentRelax.cc | RBSegmentRelax protocol |
| RBSegmentRelax.hh | RBSegmentRelax protocol |
| RBSegmentRelax_main.cc | |
| RBSegmentRelax_main.hh | |
| util.cc | |
| util.hh | |
| ► relax | |
| ► membrane | |
| MPFastRelaxMover.cc | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPFastRelaxMover.fwd.hh | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPFastRelaxMover.hh | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPFastRelaxMoverCreator.hh | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| AtomCoordinateCstMover.cc | Add coordinate constraints to a pose, as for the relax protocol |
| AtomCoordinateCstMover.fwd.hh | |
| AtomCoordinateCstMover.hh | Coordinate constraints for relax, etc |
| AtomCoordinateCstMoverCreator.hh | |
| CentroidRelax.cc | CentroidRelax Protocol |
| CentroidRelax.fwd.hh | |
| CentroidRelax.hh | Centroid-based relax, using Frank Dimaio's updated centroid statistics |
| ClassicRelax.cc | Protocols that are specific to relax |
| ClassicRelax.hh | Initialization protocols for relax |
| cst_util.cc | Set of functions for adding constraints used in relax |
| cst_util.hh | Small bundle of utilities for incorporating constraints into relax |
| FastRelax.cc | The FastRelax Protocol |
| FastRelax.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FastRelax.hh | The FastRelax Protocol |
| FastRelaxCreator.hh | |
| MiniRelax.cc | |
| MiniRelax.fwd.hh | Forward declaration for MiniRelax class |
| MiniRelax.hh | |
| Ramady.cc | Header for the Rana energy repair code, Ramady |
| Ramady.hh | Header for the Rana energy repair code, Ramady |
| relax_main.cc | Protocols that are specific to relax |
| relax_main.hh | Initialization protocols for relax |
| RelaxProtocolBase.cc | Protocols that are specific to relax |
| RelaxProtocolBase.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| RelaxProtocolBase.hh | Initialization protocols for relax |
| util.cc | Initialization protocols for relax and utility functions |
| util.hh | Initialization protocols for relax and utility functions |
| WorkUnit_BatchRelax.cc | |
| WorkUnit_BatchRelax.hh | |
| ► rigid | |
| PoseMembraneRigidBodyMover.cc | |
| PoseMembraneRigidBodyMover.hh | |
| RB_geometry.cc | Functions that are needed to do geometric functions for rigid body moves |
| RB_geometry.hh | Functions that set up the geometry required for rigid body moves |
| rigid_body_moves.cc | |
| rigid_body_moves.hh | |
| RigidBodyMotionMover.cc | |
| RigidBodyMotionMover.fwd.hh | |
| RigidBodyMotionMover.hh | |
| RigidBodyMover.cc | Initialization protocols for docking |
| RigidBodyMover.fwd.hh | RigidBodyMover forward declarations header |
| RigidBodyMover.hh | |
| RigidBodyMoverCreator.hh | This class will create instances of Movers SmallMover and ShearMover for the MoverFactory |
| RollMover.cc | RollMover methods implemented |
| RollMover.fwd.hh | RollMover forward declarations header |
| RollMover.hh | |
| RollMoverCreator.hh | This class will create instances of Mover RollMover for the MoverFactory |
| RotateJumpAxisMover.cc | RotateJumpAxisMover methods implemented |
| RotateJumpAxisMover.fwd.hh | RotateJumpAxisMover forward declarations header |
| RotateJumpAxisMover.hh | RotateJumpAxisMover header |
| UniformRigidBodyCM.cc | |
| UniformRigidBodyCM.fwd.hh | Definition of the UniformRigidBodyCM class |
| UniformRigidBodyCM.hh | |
| UniformRigidBodyCMCreator.hh | This class will create instances of Mover UniformRigidBodyCM for the MoverFactory |
| UniformRigidBodyMover.cc | |
| UniformRigidBodyMover.fwd.hh | Definition of the FragmentJumpCM class |
| UniformRigidBodyMover.hh | |
| UniformRigidBodyMoverCreator.hh | This class will create instances of Mover UniformRigidBodyMover for the MoverFactory |
| ► rosetta_scripts | |
| AdditionalOutputWrapper.cc | This mover wraps another mover to obtain additional output from it via regular call to apply(). A new instance is created for each call to get_additional_output() on this wrapper |
| AdditionalOutputWrapper.hh | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| AdditionalOutputWrapperCreator.hh | This class will create instances of Mover AdditionalOutputWrapper for the MoverFactory |
| MultipleOutputWrapper.cc | This mover wraps another mover or a ROSETTASCRIPTS block to obtain additional, |
| MultipleOutputWrapper.hh | This mover wraps another mover or a ROSETTASCRIPTS block to obtain additional, |
| MultipleOutputWrapperCreator.hh | This class will create instances of Mover MultipleOutputWrapper for the MoverFactory |
| MultiplePoseMover.cc | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| MultiplePoseMover.hh | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| MultiplePoseMoverCreator.hh | This class will create instances of Mover MultiplePoseMover for the MoverFactory |
| ParsedProtocol.cc | A mover that applies a protocol parsed from a ROSETTASCRIPTS script |
| ParsedProtocol.fwd.hh | Forward declarations for ParsedProtocol |
| ParsedProtocol.hh | |
| ParsedProtocolCreator.hh | This class will create instances of Mover DockDesign for the MoverFactory |
| PosePropertyReporter.cc | Base class for pose selectors used by MultiplePoseMover |
| PosePropertyReporter.fwd.hh | Forward declarations for PosePropertyReporter |
| PosePropertyReporter.hh | Base class for pose selectors used by MultiplePoseMover |
| PosePropertyReporterCreator.cc | Base class for PosePropertyReporters for the load-time factory registration scheme |
| PosePropertyReporterCreator.hh | Base class for PosePropertyReporters for the load-time factory registration scheme |
| PosePropertyReporterFactory.cc | Factory for PosePropertyReporters |
| PosePropertyReporterFactory.fwd.hh | Factory for PosePropertyReporters forward definitions |
| PosePropertyReporterFactory.hh | Factory for PosePropertyReporters |
| PoseSelector.cc | Base class for pose selectors used by MultiplePoseMover |
| PoseSelector.fwd.hh | Forward declarations for PoseSelector |
| PoseSelector.hh | Base class for pose selectors used by MultiplePoseMover |
| PoseSelectorCreator.cc | |
| PoseSelectorCreator.hh | Base class for PoseSelectors for the load-time factory registration scheme |
| PoseSelectorFactory.cc | Factory for PoseSelectors |
| PoseSelectorFactory.fwd.hh | |
| PoseSelectorFactory.hh | |
| RosettaScriptsParser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| RosettaScriptsParser.hh | Header file for Parser class, part of August 2008 job distributor |
| SavePoseMover.cc | |
| SavePoseMover.fwd.hh | |
| SavePoseMover.hh | |
| SavePoseMoverCreator.hh | This class will create instances of Mover SavePoseMover for the MoverFactory |
| util.cc | Utility functions useful in RosettaScripts |
| util.hh | Utility functions useful in RosettaScripts |
| ► rotamer_recovery | |
| RotamerRecovery.cc | |
| RotamerRecovery.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RotamerRecovery.hh | |
| RotamerRecoveryCreator.cc | Creator classes for components of the RotamerRecovery framework |
| RotamerRecoveryCreator.fwd.hh | Forward Header for base class for Rotamer Recovery Creators for the RotamerRecovery load-time factory registration scheme |
| RotamerRecoveryCreator.hh | Base class for RotamerRecoveryCreators for the RotamerRecovery load-time factory registration scheme |
| RotamerRecoveryFactory.cc | Factory for creating RotamerRecoverys objects |
| RotamerRecoveryFactory.fwd.hh | Report atom-atom pair geometry and scores to rotamer_recovery Statistics Scientific Benchmark |
| RotamerRecoveryFactory.hh | Factory for creating RotamerRecovery objects |
| RotamerRecoveryMover.cc | A wrapper that measures how similar the rotamers are between before and after running the child mover |
| RotamerRecoveryMover.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RotamerRecoveryMover.hh | A wrapper that measures how similar the rotamers are between before and after running the child mover |
| RotamerRecoveryMoverCreator.hh | This class will create instances of Mover ConstraintSetMover for the MoverFactory |
| RRComparer.cc | |
| RRComparer.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RRComparer.hh | |
| RRComparerAutomorphicRMSD.cc | |
| RRComparerAutomorphicRMSD.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure by measuing the minimum root mean squared deviation of sidechain atoms for all chemical atomorphic forms |
| RRComparerAutomorphicRMSD.hh | |
| RRComparerElecDensDiff.cc | |
| RRComparerElecDensDiff.fwd.hh | Measure rotamer recovery by change in sidechain electron density correlation |
| RRComparerElecDensDiff.hh | |
| RRProtocol.cc | |
| RRProtocol.fwd.hh | Manage how the rotamer recovery test should be preformed |
| RRProtocol.hh | |
| RRProtocolMinPack.cc | |
| RRProtocolMinPack.fwd.hh | Preform the rotamer recovery test by minimizing each residue in a fixed context |
| RRProtocolMinPack.hh | |
| RRProtocolMover.cc | Preform the rotamer recovery after applying mover |
| RRProtocolMover.fwd.hh | Preform the rotamer recovery after applying mover |
| RRProtocolMover.hh | Preform the rotamer recovery after applying mover |
| RRProtocolPackRotamers.cc | |
| RRProtocolPackRotamers.fwd.hh | Preform the rotamer recovery test using the pack_rotamers discrete optimization algorithm |
| RRProtocolPackRotamers.hh | |
| RRProtocolReferenceStructure.cc | Preform the rotamer recovery against a reference structure |
| RRProtocolReferenceStructure.fwd.hh | Preform the rotamer recovery after applying mover |
| RRProtocolReferenceStructure.hh | Preform the rotamer recovery against a reference structure |
| RRProtocolRelax.cc | Perform the rotamer recovery test using the FastRelax protocol |
| RRProtocolRelax.fwd.hh | Perform the rotamer recovery test using the FastRelax protocol |
| RRProtocolRelax.hh | |
| RRProtocolRotamerTrials.cc | |
| RRProtocolRotamerTrials.fwd.hh | Preform the rotamer recovery test by determining the lowest energy (discrete) rotamer for each residue in a fixed context |
| RRProtocolRotamerTrials.hh | |
| RRProtocolRTMin.cc | |
| RRProtocolRTMin.fwd.hh | Preform the rotamer recovery test by minimizing each residue in a fixed context |
| RRProtocolRTMin.hh | |
| RRReporter.cc | |
| RRReporter.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RRReporter.hh | |
| RRReporterHuman.cc | |
| RRReporterHuman.fwd.hh | Report how well rosetta is a recovering the conformation of an experimentally validated structure in a human readable format |
| RRReporterHuman.hh | |
| RRReporterSQLite.cc | |
| RRReporterSQLite.fwd.hh | Report Rotamer Recovery to an SQLite database |
| RRReporterSQLite.hh | |
| ► RotamerDump | |
| RotamerDumpMover.cc | |
| RotamerDumpMover.fwd.hh | |
| RotamerDumpMover.hh | |
| ► rpc | |
| rpc.cc | |
| rpc.fwd.hh | JSON_RPC base classes |
| rpc.hh | |
| ► sasa_scores | |
| sasapack.cc | Some simple examples of how to use basic functionality + some DNA functionality |
| sasapack.hh | Sasapack and other scores that are normalized by residue sasa |
| ► scoring | |
| ► methods | |
| ► pcs | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcs2 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| GridSearchIteratorCA.cc | |
| GridSearchIteratorCA.fwd.hh | |
| GridSearchIteratorCA.hh | |
| PcsDataCenter.cc | |
| PcsDataCenter.fwd.hh | |
| PcsDataCenter.hh | Hold the PCS data on which the SVD will be applyed |
| PcsDataCenterManager.cc | |
| PcsDataCenterManager.fwd.hh | |
| PcsDataCenterManager.hh | |
| PcsDataCenterManagerSingleton.cc | |
| PcsDataCenterManagerSingleton.fwd.hh | |
| PcsDataCenterManagerSingleton.hh | |
| PcsDataLanthanide.cc | |
| PcsDataLanthanide.fwd.hh | |
| PcsDataLanthanide.hh | |
| PcsEnergy.cc | |
| PcsEnergy.fwd.hh | |
| PcsEnergy.hh | |
| PcsEnergyCreator.hh | Declaration for the class that connects PcsEnergyCreator with the ScoringManager |
| PcsEnergyParameter.cc | |
| PcsEnergyParameter.fwd.hh | |
| PcsEnergyParameter.hh | |
| PcsEnergyParameterManager.cc | |
| PcsEnergyParameterManager.fwd.hh | |
| PcsEnergyParameterManager.hh | |
| PcsGridSearchParameter.cc | |
| PcsGridSearchParameter.fwd.hh | |
| PcsGridSearchParameter.hh | |
| PcsGridSearchParameterManager.cc | |
| PcsGridSearchParameterManager.fwd.hh | |
| PcsGridSearchParameterManager.hh | |
| PcsInputCenter.cc | |
| PcsInputCenter.fwd.hh | Christophe Schmitz |
| PcsInputCenter.hh | This class hold the information for each paramagnetic center Multiple data set with different lanthanide can be measured for each paramagnetic center |
| PcsInputCenterManager.cc | Singleton that hold everything about the input PCS This avoid multiple reading of the input file |
| PcsInputCenterManager.fwd.hh | Christophe Schmitz |
| PcsInputCenterManager.hh | Singleton that hold everything about the input PCS This avoid multiple reading of the input files |
| PcsInputFile.cc | Read all input from a .npc input file, and hold the data in the class One file per lanthanide data |
| PcsInputFile.fwd.hh | Read all input from a .npc input file, and hold the data in the class |
| PcsInputFile.hh | Read all input from a .npc input file, and hold the data in the class. One file per lanthanide data |
| PcsInputLine.cc | |
| PcsInputLine.fwd.hh | Class that hold a line data of the input file |
| PcsInputLine.hh | Class that hold a line data of the input file |
| PcsTensor.cc | Hold chi-tensor information of PCS |
| PcsTensor.fwd.hh | |
| PcsTensor.hh | Hold chi-tensor information of PCS |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| TensorsOptimizerFix.cc | |
| TensorsOptimizerFix.fwd.hh | |
| TensorsOptimizerFix.hh | |
| TensorsOptimizerSvd.cc | |
| TensorsOptimizerSvd.fwd.hh | |
| TensorsOptimizerSvd.hh | |
| ► pcsTs1 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs2 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs3 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs4 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► saxs | |
| PDDFEnergy.cc | "Energy" based on a similarity of theoretical PDDF (pairwise distance distribution function) |
| PDDFEnergy.fwd.hh | Forward declaration of a PDDF energy term |
| PDDFEnergy.hh | "Energy" based on a similarity of theoretical PDDF (pairwise distance distribution function) |
| PDDFEnergyCreator.hh | Declaration for the class that connects PDDFEnergyCreator with the ScoringManager |
| EnsembleEnergy.cc | Function to subtract out individual reference energies during ensemble docking |
| EnsembleEnergy.hh | Function to constrain particular residues to an interface during docking |
| EnsembleEnergyCreator.hh | Declaration for the class that connects EnsembleEnergy with the ScoringManager |
| InterchainEnvEnergy.cc | Statistically derived rotamer pair potentials |
| InterchainEnvEnergy.hh | Statistically derived rotamer pair potentials |
| InterchainEnvEnergyCreator.hh | Declaration for the class that connects InterchainEnvEnergy with the ScoringManager |
| InterchainPairEnergy.cc | Statistically derived rotamer pair potentials |
| InterchainPairEnergy.hh | Statistically derived rotamer pair potentials |
| InterchainPairEnergyCreator.hh | Declaration for the class that connects InterchainPairEnergy with the ScoringManager |
| ResidualDipolarCouplingEnergyRigidSegments.cc | RDC energy - comparing experimental RDC values to calculated values |
| ResidualDipolarCouplingEnergyRigidSegments.fwd.hh | |
| ResidualDipolarCouplingEnergyRigidSegments.hh | RDC energy - comparing experimental RDC values to calculated values |
| ResidualDipolarCouplingEnergyRigidSegmentsCreator.hh | Declaration for the class that connects ResidualDipolarCouplingEnergy with the ScoringManager |
| SpecialRotamerEnergy.cc | Adds a bonus to any rotamer that is flagged |
| SpecialRotamerEnergy.fwd.hh | Adds a bonus to any rotamer that is flagged |
| SpecialRotamerEnergy.hh | Adds a bonus to any rotamer that is flagged |
| SpecialRotamerEnergyCreator.hh | Declaration for the class that connects SpecialRotamerEnergy with the ScoringManager |
| ImplicitFastClashCheck.cc | Does implicit fast clash checking WRT the provided pose |
| ImplicitFastClashCheck.fwd.hh | Does implicit fast clash checking WRT the provided pose |
| ImplicitFastClashCheck.hh | Does implicit fast clash checking WRT the provided pose |
| InterchainPotential.cc | Statistically derived rotamer pair potentials |
| InterchainPotential.fwd.hh | Statistically derived rotamer pair potentials |
| InterchainPotential.hh | Statistically derived rotamer pair potentials |
| Interface.cc | Following information: calculate the interface between the two (or other?) partners set the packer task to only pack the interface |
| Interface.fwd.hh | |
| Interface.hh | Following information: calculate the interface between the two (or other?) partners set the packer task to only pack the interface |
| InterfaceInfo.cc | Statistically derived rotamer pair potentials |
| InterfaceInfo.fwd.hh | Statistically derived rotamer pair potentials |
| InterfaceInfo.hh | Statistically derived rotamer pair potentials |
| ResidualDipolarCouplingRigidSegments.cc | Uses NMR RDC for scoring |
| ResidualDipolarCouplingRigidSegments.fwd.hh | |
| ResidualDipolarCouplingRigidSegments.hh | Creates, stores and manages a list of individual RDC objects for Rigid Segment-based RDC scoring |
| ► seeded_abinitio | |
| CAcstGenerator.cc | |
| CAcstGenerator.hh | |
| CAcstGeneratorCreator.hh | |
| CloseFold.cc | |
| CloseFold.hh | |
| CloseFoldCreator.hh | |
| CoordinateCst.cc | Allows to add coordinate constraints to the pose based on parsed spans or residues residues specified are parsed at runtime not at parse time, so it can be used somewhat used with length changes currently it only adds CA constraints, but hopefully at some time point others too |
| CoordinateCst.hh | |
| CoordinateCstCreator.hh | |
| DefineMovableLoops.cc | Specific to seeded abinitio protocol this class finds loops after seeded abinitio that should be closed |
| DefineMovableLoops.hh | |
| DefineMovableLoopsCreator.hh | |
| GrowPeptides.cc | Different ways of growing peptide sequences |
| GrowPeptides.hh | |
| GrowPeptidesCreator.hh | |
| SeededAbinitio_util.cc | |
| SeededAbinitio_util.hh | |
| SeedFoldTree.cc | |
| SeedFoldTree.fwd.hh | |
| SeedFoldTree.hh | |
| SeedFoldTreeCreator.hh | |
| SeedSetupMover.cc | Mover to set up packer task and movemap for seededabinitio |
| SeedSetupMover.hh | |
| SeedSetupMoverCreator.hh | |
| SegmentHybridizer.cc | Repurposing logic and some functions from CartesianHybridze protocols for segment insertions and chain closure |
| SegmentHybridizer.hh | Repurposing logic and some functions from CartesianHybridze protocols for segment insertions and chain closure |
| SegmentHybridizerCreator.hh | Declaration of the MoverCreator class for the SegmentHybridizer |
| SwapSegment.cc | |
| SwapSegment.hh | |
| SwapSegmentCreator.hh | |
| util.cc | Utility functions useful in Seeded Abinitio |
| util.hh | Utility functions useful in Seeded Abinitio |
| ► sic_dock | |
| ► scores | |
| MotifHashRigidScore.cc | |
| MotifHashRigidScore.fwd.hh | |
| MotifHashRigidScore.hh | |
| TrisBpyScore.cc | |
| TrisBpyScore.fwd.hh | |
| TrisBpyScore.hh | |
| designability_score.cc | |
| designability_score.hh | |
| loophash_util.cc | |
| loophash_util.hh | |
| read_biounit.cc | |
| read_biounit.hh | |
| RigidScore.cc | |
| RigidScore.fwd.hh | |
| RigidScore.hh | |
| Rose.cc | |
| Rose.fwd.hh | |
| Rose.hh | |
| SICFast.cc | |
| SICFast.fwd.hh | |
| SICFast.hh | |
| types.hh | |
| util.cc | |
| util.hh | |
| xyzStripeHashPoseWithMeta.fwd.hh | |
| xyzStripeHashPoseWithMeta.hh | |
| ► simple_filters | |
| AbinitioBaseFilter.cc | Header file for Filters.cc |
| AbinitioBaseFilter.hh | Header file for AbinitioBaseFilter.cc |
| AlaScan.cc | |
| AlaScan.fwd.hh | |
| AlaScan.hh | Definition of filter class AlsScan |
| AlaScanCreator.hh | FilterCreators for the AlaScanCreator |
| AngleToVectorFilter.cc | |
| AngleToVectorFilter.fwd.hh | |
| AngleToVectorFilter.hh | |
| AngleToVectorFilterCreator.hh | FilterCreators for the AngleToVectorFilter |
| AtomicContactFilter.cc | Filters for interfaces which could form a disulfide bond between docking partners |
| AtomicContactFilter.hh | Filters for interfaces which could form a disulfide bond between docking partners |
| AtomicContactFilterCreator.hh | FilterCreator for the AtomicContactFilter |
| AtomicDistanceFilter.cc | Filter for looking at specific atom distances |
| AtomicDistanceFilter.hh | Filter for looking at specific atom distances |
| AtomicDistanceFilterCreator.hh | FilterCreator for the AtomicDistanceFilter |
| AveragePathLengthFilter.cc | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilter.fwd.hh | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilter.hh | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilterCreator.hh | FilterCreators for the AveragePathLengthFilter |
| BatchNrEvaluator.cc | PoseEvaluator |
| BatchNrEvaluator.hh | |
| BuriedUnsatHbondFilter.cc | |
| BuriedUnsatHbondFilter.fwd.hh | |
| BuriedUnsatHbondFilter.hh | Definition of filter class BuriedUnsatHbondFilter |
| BuriedUnsatHbondFilterCreator.hh | FilterCreators for the BuriedUnsatHbondFilterCreator |
| CamShiftEvaluator.cc | PoseEvaluator |
| CamShiftEvaluator.hh | |
| CamShiftEvaluatorCreator.cc | Header for CamShiftEvaluatorCreator |
| CamShiftEvaluatorCreator.hh | Header for CamShiftEvaluatorCreator |
| ChiWellRmsdEvaluator.cc | PoseEvaluator |
| ChiWellRmsdEvaluator.hh | Initialization protocols for relax |
| ChiWellRmsdEvaluatorCreator.cc | Header for ChiWellRmsdEvaluatorCreator |
| ChiWellRmsdEvaluatorCreator.hh | Header for ChiWellRmsdEvaluatorCreator |
| COFilter.cc | Runs reject or accept filters on pose |
| COFilter.hh | Header file for SheetCOFilter class |
| ConservedPosMutationFilter.cc | |
| ConservedPosMutationFilter.fwd.hh | |
| ConservedPosMutationFilter.hh | Header file for ConservedPosMutationFitler class |
| ConservedPosMutationFilterCreator.hh | FilterCreator for the ConservedPosMutationFilter |
| ConstraintScoreCutoffFilter.cc | |
| ConstraintScoreCutoffFilter.fwd.hh | |
| ConstraintScoreCutoffFilter.hh | Header file for ConstraintScoreCutoffFitler class |
| ConstraintScoreCutoffFilterCreator.hh | FilterCreator for the ConstraintScoreCutoffFilter |
| ContactMapEvaluator.cc | |
| ContactMapEvaluator.hh | |
| ContactMapEvaluatorCreator.cc | Header for ContactMapEvaluatorCreator |
| ContactMapEvaluatorCreator.hh | Header for ContactMapEvaluatorCreator |
| DdgFilter.cc | |
| DdgFilter.fwd.hh | |
| DdgFilter.hh | Definition of filter class DdgFilter |
| DdgFilterCreator.hh | FilterCreators for the DdgFilterCreator |
| DdGScan.cc | |
| DdGScan.fwd.hh | |
| DdGScan.hh | Definition of filter class DdGScan |
| DdGScanCreator.hh | FilterCreators for the DdGScanCreator |
| DeltaFilter.cc | |
| DeltaFilter.fwd.hh | Forward declaration for DeltaFilter |
| DeltaFilter.hh | Reports the average degree of connectivity of interface residues |
| DeltaFilterCreator.hh | FilterCreators for the DeltaFilter |
| DisulfideEntropyFilter.cc | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilter.fwd.hh | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilter.hh | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilterCreator.hh | FilterCreators for the DisulfideEntropyFilter |
| DomainInterfaceFilter.cc | Implementation of DomainInterfaceFilter which checks whether a defined region of a protein is part of an interface with a pre-defined other domain of the protein |
| DomainInterfaceFilter.fwd.hh | Forward declaration for DomainInterfaceFilter which checks if a query region is part of an an interface with a pre-defined other domain of a protein |
| DomainInterfaceFilter.hh | Header file for DomainInterfaceFilter which checks whether a defined region of a protein is buried in an interface by evaluating the number of non-water neighbors of all residues |
| EnergyPerResidueFilter.cc | |
| EnergyPerResidueFilter.fwd.hh | |
| EnergyPerResidueFilter.hh | Definition of filter class EnergyPerResidueFilter |
| EnergyPerResidueFilterCreator.hh | FilterCreators for the EnergyPerResidueFilterCreator |
| EvaluatedTrialMover.cc | PoseEvaluator |
| EvaluatedTrialMover.hh | |
| ExpiryFilter.cc | |
| ExpiryFilter.fwd.hh | |
| ExpiryFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| ExpiryFilterCreator.hh | FilterCreators for the ExpiryFilter |
| ExternalEvaluator.cc | PoseEvaluator |
| ExternalEvaluator.hh | |
| ExtraScoreEvaluatorCreator.cc | Header for ExtraScoreEvaluatorCreator |
| ExtraScoreEvaluatorCreator.hh | Header for ExtraScoreEvaluatorCreator |
| FileExistFilter.cc | |
| FileExistFilter.fwd.hh | |
| FileExistFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| FileExistFilterCreator.hh | FilterCreators for the FileExistFilter |
| FileRemoveFilter.cc | |
| FileRemoveFilter.fwd.hh | |
| FileRemoveFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| FileRemoveFilterCreator.hh | FilterCreators for the FileRemoveFilter |
| GeometryFilter.cc | |
| GeometryFilter.fwd.hh | |
| GeometryFilter.hh | Definition of filter class GeometryFilter |
| GeometryFilterCreator.hh | FilterCreators for the GeometryFilterCreator |
| HolesFilter.cc | Filter structures by will's hole value |
| HolesFilter.fwd.hh | Filter structures by will's hole score |
| HolesFilter.hh | Header file for HolesFilter class |
| HolesFilterCreator.hh | FilterCreator for the HolesFilter |
| InterfaceBindingEnergyDensityFilter.cc | Implementation of the binding-energy-density filter |
| InterfaceBindingEnergyDensityFilter.fwd.hh | Forward declaration and typedefs for InterfaceBindingEnergyDensityFilter |
| InterfaceBindingEnergyDensityFilter.hh | Filter class for looking at the dGbind/dSASA ratio |
| InterfaceBindingEnergyDensityFilterCreator.hh | FilterCreators for the InterfaceBindingEnergyDensityFilterCreator |
| InterfaceSasaFilter.cc | |
| InterfaceSasaFilter.fwd.hh | |
| InterfaceSasaFilter.hh | Definition of filter class InterfaceSasaFilter |
| InterfaceSasaFilterCreator.hh | FilterCreators for the InterfaceSasaFilterCreator |
| InterRepeatContactFilter.cc | Filter structures by InterRepeatContacts |
| InterRepeatContactFilter.fwd.hh | Filter structures by Inter Repeat Contacts |
| InterRepeatContactFilter.hh | Filter structures by InterRepeatContacts |
| InterRepeatContactFilterCreator.hh | FilterCreator for the InterRepeatContact |
| IntraRepeatContactFilter.cc | Filter structures by IntraRepeatContacts |
| IntraRepeatContactFilter.fwd.hh | Filter structures by Intra Repeat Contacts |
| IntraRepeatContactFilter.hh | Filter structures by IntraRepeatContacts |
| IntraRepeatContactFilterCreator.hh | FilterCreator for the IntraRepeatContact |
| JScoreEvaluator.cc | |
| JScoreEvaluator.hh | |
| JScoreEvaluatorCreator.cc | Header for JScoreEvaluatorCreator |
| JScoreEvaluatorCreator.hh | Header for JScoreEvaluatorCreator |
| JumpEvaluator.cc | PoseEvaluator |
| JumpEvaluator.hh | |
| JumpNrEvaluatorCreator.cc | Header for JumpNrEvaluatorCreator |
| JumpNrEvaluatorCreator.hh | Header for JumpNrEvaluatorCreator |
| MotifScoreFilter.cc | Scores poses using will's motifScore |
| MotifScoreFilter.fwd.hh | Dumps the motif score to the score file |
| MotifScoreFilter.hh | Filter for MotifScore |
| MotifScoreFilterCreator.hh | FilterCreator for MotifScore |
| MultipleSigmoidsFilter.cc | |
| MultipleSigmoidsFilter.fwd.hh | |
| MultipleSigmoidsFilter.hh | Computes a filter's value on a pose that is modified from one that is read from disk. Useful for computing values for the same sequence across many structures |
| MultipleSigmoidsFilterCreator.hh | FilterCreators for the MultipleSigmoidsFilter |
| MutationsFilter.cc | |
| MutationsFilter.fwd.hh | Forward declaration for MutationsFilter |
| MutationsFilter.hh | A filter to return the number of mutated positions within a given set of designable resdues |
| MutationsFilterCreator.hh | FilterCreators for the MutationsFilter |
| NativeEvaluatorCreator.cc | Header for NativeEvaluatorCreator |
| NativeEvaluatorCreator.hh | Header for NativeEvaluatorCreator |
| NeighborTypeFilter.cc | |
| NeighborTypeFilter.fwd.hh | |
| NeighborTypeFilter.hh | Definition of filter class InterfaceSasaFilter |
| NeighborTypeFilterCreator.hh | FilterCreators for the NeighborTypeFilterCreator |
| NetChargeFilter.cc | |
| NetChargeFilter.fwd.hh | |
| NetChargeFilter.hh | Definition of filter class NetChargeFilter |
| NetChargeFilterCreator.hh | FilterCreators for the NetChargeFilterCreator |
| NMerPSSMEnergyFilter.cc | |
| NMerPSSMEnergyFilter.fwd.hh | |
| NMerPSSMEnergyFilter.hh | Definition of filter class NMerPSSMEnergyFilter |
| NMerPSSMEnergyFilterCreator.hh | FilterCreators for the NMerPSSMEnergyFilter |
| NMerSVMEnergyFilter.cc | |
| NMerSVMEnergyFilter.fwd.hh | |
| NMerSVMEnergyFilter.hh | Definition of filter class NMerSVMEnergyFilter |
| NMerSVMEnergyFilterCreator.hh | FilterCreators for the NMerSVMEnergyFilter |
| NonSequentialNeighborsFilter.cc | |
| NonSequentialNeighborsFilter.fwd.hh | |
| NonSequentialNeighborsFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| NonSequentialNeighborsFilterCreator.hh | FilterCreators for the NonSequentialNeighborsFilter |
| OperatorFilter.cc | |
| OperatorFilter.fwd.hh | |
| OperatorFilter.hh | |
| OperatorFilterCreator.hh | FilterCreators for the OperatorFilter |
| PackerNeighborGraphFilter.cc | |
| PackerNeighborGraphFilter.hh | Header file for packer neighbor graph based filter |
| PackStatFilter.cc | Filter structures by packstat score |
| PackStatFilter.fwd.hh | |
| PackStatFilter.hh | Header file for PackStatFilter class |
| PackStatFilterCreator.hh | FilterCreator for the PackStatFilter |
| PalesEvaluator.cc | PoseEvaluator |
| PalesEvaluator.hh | |
| PalesEvaluatorCreator.cc | Header for PalesEvaluatorCreator |
| PalesEvaluatorCreator.hh | Header for PalesEvaluatorCreator |
| PDDFScoreFilter.cc | Runs reject or accept filters on pose |
| PDDFScoreFilter.fwd.hh | Forward declaration for PDDFScoreFilter |
| PDDFScoreFilter.hh | Header file for PDDFScoreFilter class |
| PoolEvaluatorCreator.cc | Header for PoolEvaluatorCreator |
| PoolEvaluatorCreator.hh | Header for PoolEvaluatorCreator |
| PoseCommentFilter.cc | |
| PoseCommentFilter.fwd.hh | |
| PoseCommentFilter.hh | |
| PoseCommentFilterCreator.hh | FilterCreators for the PoseCommentFilter |
| PoseInfoFilter.cc | Filter for looking at specific atom distances |
| PoseInfoFilter.hh | Filter for outputing information about the pose |
| PoseInfoFilterCreator.hh | FilterCreator for the PoseInfoFilter |
| PoseMetricEvaluator.hh | |
| PredictedBurialEvaluator.cc | |
| PredictedBurialEvaluator.hh | |
| PredictedBurialFnEvaluatorCreator.cc | Header for PredictedBurialFnEvaluatorCreator |
| PredictedBurialFnEvaluatorCreator.hh | Header for PredictedBurialFnEvaluatorCreator |
| RangeFilter.cc | |
| RangeFilter.fwd.hh | |
| RangeFilter.hh | Range filter evaluates if the return value of a particular filter is between a specific range |
| RangeFilterCreator.hh | FilterCreator for the RangeFilter |
| RDC_Evaluator.cc | PoseEvaluator |
| RDC_Evaluator.fwd.hh | |
| RDC_Evaluator.hh | Initialization protocols for relax |
| RdcEvaluatorCreator.cc | Header for RdcEvaluatorCreator |
| RdcEvaluatorCreator.hh | Header for RdcEvaluatorCreator |
| RdcSelectEvaluatorCreator.cc | Header for RdcSelectEvaluatorCreator |
| RdcSelectEvaluatorCreator.hh | Header for RdcSelectEvaluatorCreator |
| RdcTargetEvaluatorCreator.cc | Header for RdcTargetEvaluatorCreator |
| RdcTargetEvaluatorCreator.hh | Header for RdcTargetEvaluatorCreator |
| RelativePoseFilter.cc | |
| RelativePoseFilter.fwd.hh | Forward declaration for RelativePoseFilter |
| RelativePoseFilter.hh | Computes a filter's value on a pose that is modified from one that is read from disk. Useful for computing values for the same sequence across many structures |
| RelativePoseFilterCreator.hh | FilterCreators for the RelativePoseFilter |
| RepeatParameterFilter.cc | Can filter a pose for the rise, run and omega. Many of the functions have been stolen from RepeatGlobalFrame but made const to work with filter obejcts |
| RepeatParameterFilter.fwd.hh | Forward declaration for RepeatParameterFilter |
| RepeatParameterFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| RepeatParameterFilterCreator.hh | FilterCreators for the RepeatPararmeterFilter |
| ReportFilter.cc | |
| ReportFilter.fwd.hh | |
| ReportFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| ReportFilterCreator.hh | FilterCreators for the ReportFilter |
| ResidueBurialFilter.cc | |
| ResidueBurialFilter.fwd.hh | |
| ResidueBurialFilter.hh | Definition of filter class ResidueBurialFilter |
| ResidueBurialFilterCreator.hh | FilterCreator for the ResidueBurialFilter |
| ResidueCountFilter.cc | Filter on the total number of residues in the structure |
| ResidueCountFilter.fwd.hh | Filter on the total number of residues in the structure |
| ResidueCountFilter.hh | Filter on the total number of residues in the structure |
| ResidueCountFilterCreator.hh | FilterCreators for the ResidueCountFilter |
| ResidueDistanceFilter.cc | |
| ResidueDistanceFilter.fwd.hh | |
| ResidueDistanceFilter.hh | Definition of filter class ResidueDistanceFilter |
| ResidueDistanceFilterCreator.hh | FilterCreator for the ResidueDistanceFilter |
| ResidueIEFilter.cc | |
| ResidueIEFilter.fwd.hh | |
| ResidueIEFilter.hh | Definition of filter class ResidueIEFilter |
| ResidueIEFilterCreator.hh | FilterCreators for the ResidueIEFilterCreator |
| ResidueSetChainEnergyFilter.cc | |
| ResidueSetChainEnergyFilter.fwd.hh | |
| ResidueSetChainEnergyFilter.hh | Definition of filter class ResidueSetChainEnergyFilter |
| ResidueSetChainEnergyFilterCreator.hh | FilterCreators for the ResidueSetChainEnergyFilter |
| ResiduesInInterfaceFilter.cc | |
| ResiduesInInterfaceFilter.fwd.hh | Forward declaration for RotamerBoltzmannWeightFilter |
| ResiduesInInterfaceFilter.hh | Reports to Tracer which residues are designable in a taskfactory |
| ResiduesInInterfaceFilterCreator.hh | FilterCreators for the ResiduesInInterfaceFilter |
| RGFilter.cc | Runs reject or accept filters on pose |
| RGFilter.hh | Header file for SheetRGFilter class |
| RmsdEvaluator.cc | PoseEvaluator |
| RmsdEvaluator.hh | Initialization protocols for relax |
| RmsdEvaluatorCreator.cc | Header for RmsdEvaluatorCreator |
| RmsdEvaluatorCreator.hh | Header for RmsdEvaluatorCreator |
| RmsdTargetEvaluatorCreator.cc | Header for RmsdTargetEvaluatorCreator |
| RmsdTargetEvaluatorCreator.hh | Header for RmsdTargetEvaluatorCreator |
| RotamerBoltzmannWeight.cc | |
| RotamerBoltzmannWeight.fwd.hh | Forward declaration for RotamerBoltzmannWeightFilter |
| RotamerBoltzmannWeight.hh | Reports to Tracer which residues are designable in a taskfactory |
| RotamerBoltzmannWeightFilterCreator.hh | FilterCreators for the RotamerBoltzmannWeightFilter |
| SavePoseConstraintToFileFilter.cc | Filter for looking at specific atom distances |
| SavePoseConstraintToFileFilter.hh | Filter for outputing information about the pose |
| SavePoseConstraintToFileFilterCreator.hh | FilterCreator for the SavePoseConstraintToFileFilter |
| SaveResfileToDiskFilter.cc | Outputs a resfile based on a given set of taskoperations |
| SaveResfileToDiskFilter.fwd.hh | |
| SaveResfileToDiskFilter.hh | Header file for SaveResfileToDiskFilter class |
| SaveResfileToDiskFilterCreator.hh | FilterCreator for the SaveResfileToDiskFilter |
| SAXSScoreFilter.cc | Runs reject or accept filters on pose |
| SAXSScoreFilter.fwd.hh | Forward declaration for SAXSScoreFilter |
| SAXSScoreFilter.hh | Header file for SAXSScoreFilter class |
| ScoreCutoffFilter.cc | |
| ScoreCutoffFilter.fwd.hh | |
| ScoreCutoffFilter.hh | Header file for ScoreCutoffFitler class |
| ScoreCutoffFilterCreator.hh | FilterCreator for the ScoreCutoffFilter |
| ScoreEvaluator.cc | Initialization protocols for relax |
| ScoreEvaluator.hh | Initialization protocols for relax |
| ScoreTypeFilter.cc | |
| ScoreTypeFilter.fwd.hh | |
| ScoreTypeFilter.hh | Definition of filter class ScoreTypeFilter |
| ScoreTypeFilterCreator.hh | FilterCreators for the ScoreTypeFilter |
| ShapeComplementarityFilter.cc | Filter structures by shape complementarity and/or interface area |
| ShapeComplementarityFilter.fwd.hh | |
| ShapeComplementarityFilter.hh | Header file for ShapeComplementarityFilter class |
| ShapeComplementarityFilterCreator.hh | FilterCreator for the ShapeComplementarityFilter |
| SheetFilter.cc | Runs reject or accept filters on pose |
| SheetFilter.hh | Header file for SheetSheetFilter class |
| SidechainRmsdFilter.cc | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilter.fwd.hh | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilter.hh | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilterCreator.hh | A filter based on automorphic sidechain RMSD |
| SigmoidFilter.cc | |
| SigmoidFilter.fwd.hh | |
| SigmoidFilter.hh | |
| SigmoidFilterCreator.hh | FilterCreators for the SigmoidFilter |
| SSMotifFinderFilter.cc | |
| SSMotifFinderFilter.fwd.hh | |
| SSMotifFinderFilter.hh | |
| SSMotifFinderFilterCreator.hh | FilterCreators for the SSMotifFinderFilter |
| StemFinderFilter.cc | |
| StemFinderFilter.fwd.hh | |
| StemFinderFilter.hh | |
| StemFinderFilterCreator.hh | FilterCreators for the StemFinderFilter |
| StructuralSimilarityEvaluator.cc | |
| StructuralSimilarityEvaluator.fwd.hh | Forward declaration for StructuralSimilarityEvaluator class |
| StructuralSimilarityEvaluator.hh | |
| StructureSimilarityEvaluatorCreator.cc | Header for StructureSimilarityEvaluatorCreator |
| StructureSimilarityEvaluatorCreator.hh | Header for StructureSimilarityEvaluatorCreator |
| SymmetricMotifFilter.cc | Position-independent RMS filter evaluating how close a set of interfaces is to symmetric |
| SymmetricMotifFilter.hh | Position-independent RMS filter evaluating how close a set of interfaces is to symmetric |
| SymmetricMotifFilterCreator.hh | Position-independent RMS filter evaluating how close a set of interfaces is to symmetric |
| TaskAwareSASAFilter.cc | Calculates SASA for a set of residues defined by TaskOperations |
| TaskAwareSASAFilter.fwd.hh | |
| TaskAwareSASAFilter.hh | Header file for TaskAwareSASAFilter class |
| TaskAwareSASAFilterCreator.hh | FilterCreator for the TaskAwareSASAFilter |
| TaskAwareScoreTypeFilter.cc | Formerly devel/matdes/AverageInterfaceEnergyFilter. Calculates/filters based on a particular score type over the set of packable residues specified by the user-provided task operations. Can be calculate in either the bound or unbound state (a jump or sym_dof_names must be provided to create the unbound pose). Can operate in 1 of 3 modes: 1) if mode=total then compute function returns the total score over all packable residues and the apply function returns true if the total score is less than or equal to the user-specified threshold (false otherwise), 2) if mode=average then the compute function returns the average score over all packable residues and the apply function returns true if the average score is less than or equal to the user-specified threshold (false otherwise), and 3) if mode=individual then the compute function returns the number of individual residues that do not pass the user-specified score type threshold and the apply function returns true if all residues passed the user-specified threshold (false otherwise) |
| TaskAwareScoreTypeFilter.fwd.hh | Forward declaration for TaskAwareScoreTypeFilter |
| TaskAwareScoreTypeFilter.hh | Header file for TaskAwareScoreTypeFilter |
| TaskAwareScoreTypeFilterCreator.hh | FilterCreators for the TaskAwareScoreTypeFilter |
| TerminusDistanceFilter.cc | |
| TerminusDistanceFilter.fwd.hh | |
| TerminusDistanceFilter.hh | Definition of filter class TerminusDistanceFilter |
| TerminusDistanceFilterCreator.hh | FilterCreators for the TerminusDistanceFilterCreator |
| TotalSasaFilter.cc | |
| TotalSasaFilter.fwd.hh | |
| TotalSasaFilter.hh | Definition of filter class TotalSasaFilter |
| TotalSasaFilterCreator.hh | FilterCreators for the TotalSasaFilterCreator |
| ► simple_moves | |
| ► asym_fold_and_dock | |
| AsymFoldandDockMoveRbJumpMover.cc | |
| AsymFoldandDockMoveRbJumpMover.fwd.hh | |
| AsymFoldandDockMoveRbJumpMover.hh | |
| AsymFoldandDockRbTrialMover.cc | |
| AsymFoldandDockRbTrialMover.fwd.hh | |
| AsymFoldandDockRbTrialMover.hh | |
| ► bin_transitions | |
| InitializeByBins.cc | This mover takes a stretch of backbone and initializes its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| InitializeByBins.fwd.hh | Fwd declarations for the InitializeByBins mover. This mover takes a stretch of backbone and initializes its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| InitializeByBins.hh | Headers for the InitializeByBins mover. This mover takes a stretch of backbone and initializes its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| InitializeByBinsCreator.hh | This class will create instances of protocols::moves::Mover InitializeByBins for the protocols::moves::MoverFactory |
| PerturbByBins.cc | This mover takes a stretch of backbone and perturbs its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| PerturbByBins.fwd.hh | Fwd declarations for the PerturbByBins mover. This mover takes a stretch of backbone and perturbs its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| PerturbByBins.hh | Headers for the PerturbByBins mover. This mover takes a stretch of backbone and perturbs its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| PerturbByBinsCreator.hh | This class will create instances of protocols::moves::Mover PerturbByBins for the protocols::moves::MoverFactory |
| ► chiral | |
| ChiralMover.cc | ChiralMover methods implemented |
| ChiralMover.fwd.hh | ChiralMover forward declarations header |
| ChiralMover.hh | |
| ► hbs | |
| HbsPatcher.cc | HbsPatcher methods implemented |
| HbsPatcher.fwd.hh | HbsPatcher forward declarations header |
| HbsPatcher.hh | |
| ► oop | |
| OopMover.cc | OopMover methods implemented |
| OopMover.fwd.hh | OopMover forward declarations header |
| OopMover.hh | |
| OopPatcher.cc | OopPatcher methods implemented |
| OopPatcher.fwd.hh | OopPatcher forward declarations header |
| OopPatcher.hh | |
| OopPuckMover.cc | OopPuckMover methods implemented |
| OopPuckMover.fwd.hh | OopPuckMover forward declarations header |
| OopPuckMover.hh | |
| OopRandomPuckMover.cc | OopRandomPuckMover methods implemented |
| OopRandomPuckMover.fwd.hh | OopRandomPuckMover forward declarations header |
| OopRandomPuckMover.hh | |
| OopRandomSmallMover.cc | OopRandomSmallMover methods implemented |
| OopRandomSmallMover.fwd.hh | OopRandomSmallMover forward declarations header |
| OopRandomSmallMover.hh | |
| ► rational_mc | |
| RationalMonteCarlo.cc | |
| RationalMonteCarlo.fwd.hh | |
| RationalMonteCarlo.hh | |
| ► sidechain_moves | |
| JumpRotamerSidechainMover.cc | Implementation of JumpRotamerSidechainMover class and functions |
| JumpRotamerSidechainMover.fwd.hh | |
| JumpRotamerSidechainMover.hh | Definition of JumpRotamerSidechainMover class and functions |
| JumpRotamerSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover JumpRotamerSidechainMover for the protocols::moves::MoverFactory |
| PerturbChiSidechainMover.cc | Implementation of PerturbChiSidechainMover class and functions |
| PerturbChiSidechainMover.fwd.hh | |
| PerturbChiSidechainMover.hh | Definition of PerturbChiSidechainMover class and functions |
| PerturbChiSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover PerturbChiSidechainMover for the protocols::moves::MoverFactory |
| PerturbRotamerSidechainMover.cc | Implementation of PerturbRotamerSidechainMover class and functions |
| PerturbRotamerSidechainMover.fwd.hh | |
| PerturbRotamerSidechainMover.hh | Definition of PerturbRotamerSidechainMover class and functions |
| PerturbRotamerSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover PerturbRotamerSidechainMover for the protocols::moves::MoverFactory |
| SetChiMover.cc | A mover to change one chi angle |
| SetChiMover.fwd.hh | A mover to change one chi angle |
| SetChiMover.hh | A mover to change one chi angle |
| SetChiMoverCreator.hh | A mover to change one chi angle |
| SidechainMCMover.cc | Implementation of SidechainMCMover class and functions |
| SidechainMCMover.fwd.hh | |
| SidechainMCMover.hh | Definition of SidechainMCMover class and functions |
| SidechainMCMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMCMover for the protocols::moves::MoverFactory |
| SidechainMover.cc | Implementation of SidechainMover class and functions |
| SidechainMover.fwd.hh | |
| SidechainMover.hh | Definition of SidechainMover class and functions |
| SidechainMoverBase.cc | Implementation of SidechainMoverBase class and functions |
| SidechainMoverBase.fwd.hh | |
| SidechainMoverBase.hh | Definition of SidechainMoverBase class and functions |
| SidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMover for the protocols::moves::MoverFactory |
| ► symmetry | |
| DetectSymmetryMover.cc | Automatical detection and setup of the symmetry machinery from an assymetric pose made of symmetric chains. Only works with cyclic simmetries |
| DetectSymmetryMover.fwd.hh | |
| DetectSymmetryMover.hh | Automatical detection and setup of the symmetry machinery from an asymetric pose made of symmetric chains. Only works with cyclic simmetries |
| DetectSymmetryMoverCreator.hh | |
| SetupForSymmetryMover.cc | |
| SetupForSymmetryMover.fwd.hh | |
| SetupForSymmetryMover.hh | |
| SetupForSymmetryMoverCreator.hh | |
| SetupNCSMover.cc | Sets up NCS restraints |
| SetupNCSMover.fwd.hh | Sets up NCS restraints |
| SetupNCSMover.hh | Sets up NCS restraints |
| SetupNCSMoverCreator.hh | Protocols::moves::MoverCreator for SetupNCSMover |
| SymDockingInitialPerturbation.cc | Initial position functions |
| SymDockingInitialPerturbation.hh | |
| SymmetricRMSMover.cc | |
| SymmetricRMSMover.fwd.hh | |
| SymmetricRMSMover.hh | |
| SymMinMover.cc | |
| SymMinMover.fwd.hh | MinMover forward declarations header |
| SymMinMover.hh | |
| SymMinMoverCreator.hh | |
| SymPackRotamersMover.cc | |
| SymPackRotamersMover.fwd.hh | |
| SymPackRotamersMover.hh | |
| SymPackRotamersMoverCreator.hh | |
| SymRotamerTrialsMover.cc | |
| SymRotamerTrialsMover.fwd.hh | |
| SymRotamerTrialsMover.hh | |
| SymRotamerTrialsMoverCreator.hh | |
| SymShakeStructureMover.cc | |
| SymShakeStructureMover.fwd.hh | |
| SymShakeStructureMover.hh | |
| TaskAwareSymMinMover.cc | |
| TaskAwareSymMinMover.fwd.hh | |
| TaskAwareSymMinMover.hh | Minimize only those residues specified by a set of TaskOperations in a symmetric pose |
| TaskAwareSymMinMoverCreator.hh | |
| AddCavitiesMover.cc | |
| AddCavitiesMover.hh | |
| AddChainMover.cc | |
| AddChainMover.fwd.hh | Add chain to an existing pose (as a new chain) |
| AddChainMover.hh | Switch the chain order |
| AddChainMoverCreator.hh | |
| AddConstraintsToCurrentConformationMover.cc | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMover.hh | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMoverCreator.hh | |
| AddJobPairData.cc | A really simple mover that takes some data in through xml and appends it to the pose |
| AddJobPairData.fwd.hh | Forward Header file for the AddJobPairData Mover |
| AddJobPairData.hh | Header file for the AddJobPairData Mover |
| AddJobPairDataCreator.hh | MoverCreator definitions for the AddJobPairData mover |
| AlignChainMover.cc | |
| AlignChainMover.fwd.hh | |
| AlignChainMover.hh | Switch the chain order |
| AlignChainMoverCreator.hh | |
| BackboneMover.cc | Method definitions for SmallMover and ShearMover |
| BackboneMover.fwd.hh | BackboneMover forward declarations header |
| BackboneMover.hh | Declarations and simple accessor/mutator definitions for SmallMover and ShearMover |
| BackboneMoverCreator.hh | This class will create instances of protocols::moves::Movers SmallMover and ShearMover for the protocols::moves::MoverFactory |
| BBConRotMover.cc | |
| BBConRotMover.fwd.hh | |
| BBConRotMover.hh | |
| BBGaussianMover.cc | Gaussian Perturbation to backbone |
| BBGaussianMover.fwd.hh | Gaussian Perturbation to backbone |
| BBGaussianMover.hh | Gaussian Perturbation to backbone |
| BBGaussianMoverCreator.hh | |
| BoltzmannRotamerMover.cc | Implementation of BoltzmannRotamerMover class and functions |
| BoltzmannRotamerMover.fwd.hh | |
| BoltzmannRotamerMover.hh | Definition of BoltzmannRotamerMover class and functions |
| BoltzmannRotamerMoverCreator.hh | This class will create instances of protocols::moves::Mover BoltzmannRotamerMover for the protocols::moves::MoverFactory |
| ChainSplitMover.cc | ChainSplitMover splits a pose into two chains given a cutpoint |
| ChainSplitMover.fwd.hh | Forward declaration of ChainSplitMover which splits a pose into two chains at a given cutpoint |
| ChainSplitMover.hh | Declaration of ChainSplitMover which splits a pose into two chains at a given cutpoint |
| ChangeAndResetFoldTreeMover.cc | |
| ChangeAndResetFoldTreeMover.fwd.hh | |
| ChangeAndResetFoldTreeMover.hh | Basic Mover used for setting up atomic protocols |
| ChangeAndResetFoldTreeMoverCreator.hh | |
| ClearConstraintsMover.cc | Add constraints to the current pose conformation |
| ClearConstraintsMover.hh | Add constraints to the current pose conformation |
| ClearConstraintsMoverCreator.hh | |
| CombinePoseMover.cc | |
| CombinePoseMover.fwd.hh | |
| CombinePoseMover.hh | |
| ConsensusDesignMover.cc | Cc file for ConsensusDesignMover |
| ConsensusDesignMover.fwd.hh | Fwd.hh file for ConsensusDesignMover |
| ConsensusDesignMover.hh | Header file for ConsensusDesignMover |
| ConsensusDesignMoverCreator.hh | |
| ConstrainToIdealMover.cc | Adds to your pose constraints suitable for idealization of bond lengths and angles |
| ConstrainToIdealMover.fwd.hh | ConstrainToIdealMover forward declarations header |
| ConstrainToIdealMover.hh | Adds to your pose constraints suitable for idealization of bond lengths and angles |
| ConstraintSetMover.cc | Assigns a ConstraintSet to a pose. Reads and creats ConstraintSet from file via command line option -constraints::cst_file, unless a ConstraintSet is supplied via the constructor or the constraint_set() method |
| ConstraintSetMover.fwd.hh | |
| ConstraintSetMover.hh | Assigns a ConstraintSet to a pose. Reads and creats ConstraintSet from file via command line option -constraints::cst_file, unless a ConstraintSet is supplied via the constructor or the constraint_set() method |
| ConstraintSetMoverCreator.hh | |
| ContingentAcceptMover.cc | |
| ContingentAcceptMover.fwd.hh | Switch the chain order |
| ContingentAcceptMover.hh | Switch the chain order |
| ContingentAcceptMoverCreator.hh | |
| CopyDofMover.cc | |
| CopyDofMover.fwd.hh | |
| CopyDofMover.hh | |
| CoupledMover.cc | Implementation of CoupledMover class and functions |
| CoupledMover.fwd.hh | |
| CoupledMover.hh | Definition of CoupledMover class and functions |
| CoupledMoverCreator.hh | This class will create instances of protocols::moves::Mover CoupledMover for the protocols::moves::MoverFactory |
| CutChainMover.cc | |
| CutChainMover.fwd.hh | ForceDisulfidesMover forward declarations header |
| CutChainMover.hh | |
| CutChainMoverCreator.hh | |
| CyclizationMover.cc | Implimentation file for CyclizationMover |
| CyclizationMover.fwd.hh | Forward header file for CyclizationMover |
| CyclizationMover.hh | Header file for CyclizationMover |
| ddG.cc | Implementation of the ddG class for computing interface delta dGs |
| ddG.fwd.hh | Forward declarations for ddG |
| ddG.hh | Calculate interface ddg |
| ddGCreator.hh | Declaration of the ddGCreator class for the ddG mover |
| DesignRepackMover.cc | |
| DesignRepackMover.fwd.hh | Forward declations for DesignRepackMover |
| DesignRepackMover.hh | |
| DisulfideInsertionMover.cc | Mover that closes a receptor bound peptide by an added disulfide bond |
| DisulfideInsertionMover.fwd.hh | Forward header file for DisulfideInsertionMover |
| DisulfideInsertionMover.hh | Header file for DisulfideInsertionMover |
| DME_FilterMover.cc | Performs a move and accepts it according to Monte Carlo accept/reject criterion |
| DME_FilterMover.hh | Performs a move and accepts it according to Monte Carlo accept/reject criterion |
| DOFHistogramRecorder.cc | |
| DOFHistogramRecorder.fwd.hh | Forward declarations for class DOFHistogramRecorder |
| DOFHistogramRecorder.hh | |
| DumpPdb.cc | |
| DumpPdb.hh | |
| DumpPdbCreator.hh | Declaration of the MoverCreator class for the DumpPdb |
| ExtendedPoseMover.cc | |
| ExtendedPoseMover.fwd.hh | |
| ExtendedPoseMover.hh | |
| ExtendedPoseMoverCreator.cc | |
| ExtendedPoseMoverCreator.hh | |
| FavorSequenceProfile.cc | Add a SequenceProfileConstraint to a pose |
| FavorSequenceProfile.hh | Add a SequenceProfileConstraint to a pose |
| FavorSequenceProfileCreator.hh | Declaration of the protocols::moves::MoverCreator class for the FavorSequenceProfile |
| FavorSymmetricSequence.cc | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequence.fwd.hh | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequence.hh | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequenceCreator.hh | Apply constraints to enforce a symmetric sequence |
| FindConsensusSequence.cc | Takes in multiple poses from the MSDJobDistributor and finds the consensus sequence that optimizes energy of all input poses |
| FindConsensusSequence.fwd.hh | Finds the consensus sequence that optimizes energy of all input poses |
| FindConsensusSequence.hh | Takes in multiple poses from the MSDJobDistributor and finds the consensus sequence that optimizes energy of all input poses |
| FindConsensusSequenceCreator.hh | Multistate design mover used for constrained MSD application |
| ForceDisulfidesMover.cc | |
| ForceDisulfidesMover.fwd.hh | ForceDisulfidesMover forward declarations header |
| ForceDisulfidesMover.hh | |
| ForceDisulfidesMoverCreator.hh | |
| FragmentMover.cc | |
| FragmentMover.fwd.hh | Set of fragments for a certain alignment frame |
| FragmentMover.hh | Set of fragments |
| GenericMonteCarloMover.cc | Perform a given mover and sample structures by MonteCarlo |
| GenericMonteCarloMover.fwd.hh | |
| GenericMonteCarloMover.hh | Perform a given mover and sample structures by MonteCarlo |
| GenericMonteCarloMoverCreator.hh | |
| GreenPacker.cc | Packing mover that makes extensive reuse of rotamer pair energies class definition |
| GreenPacker.fwd.hh | Packing mover that makes extensive reuse of rotamer pair energies class forward declaration |
| GreenPacker.hh | Packing mover that makes extensive reuse of rotamer pair energies class declaration |
| GunnCost.cc | |
| GunnCost.hh | |
| LoadPDBMover.cc | Simple mover that loads a pdb from file and replaces the current pdb with it. Useful for checkpointing |
| LoadPDBMover.fwd.hh | Switch the chain order |
| LoadPDBMover.hh | Switch the chain order |
| LoadPDBMoverCreator.hh | |
| LoadUnboundRotMover.cc | LoadUnboundRotMover methods implemented |
| LoadUnboundRotMover.fwd.hh | |
| LoadUnboundRotMover.hh | |
| LoadUnboundRotMoverCreator.hh | |
| MakePolyXMover.cc | Convert pose to poly XXX: any amino acid, default poly Ala |
| MakePolyXMover.fwd.hh | Convert pose to poly XXX: any amino acid, default poly Ala |
| MakePolyXMover.hh | Header file of MakePolyXMover.cc |
| MakePolyXMoverCreator.hh | This class will create instances of protocols::moves::Mover MakePolyXMover for the protocols::moves::MoverFactory |
| MembraneTopology.cc | |
| MembraneTopology.fwd.hh | |
| MembraneTopology.hh | |
| MembraneTopologyCreator.hh | |
| MinMover.cc | Method definitions for MinMover |
| MinMover.fwd.hh | MinMover forward declarations header |
| MinMover.hh | Class definition for MinMover |
| MinMoverCreator.hh | |
| MinPackMover.cc | Implementation of the MinPackMover class; a wrapper class for invoking core::pack::min_pack |
| MinPackMover.fwd.hh | Forward declaration of the mover class to both pack and minimize rotamers |
| MinPackMover.hh | Protocols::moves::Mover class to invoke core::pack::min_pack |
| MinPackMoverCreator.hh | This class will create instances of protocols::moves::Mover MinPackMover for the protocols::moves::MoverFactory |
| MissingDensityToJumpMover.cc | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| MissingDensityToJumpMover.fwd.hh | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| MissingDensityToJumpMover.hh | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| ModifyVariantTypeMover.cc | Modify variant type to residues |
| ModifyVariantTypeMover.fwd.hh | |
| ModifyVariantTypeMover.hh | |
| ModifyVariantTypeMoverCreator.hh | |
| MonteCarloRecover.cc | |
| MonteCarloRecover.fwd.hh | |
| MonteCarloRecover.hh | |
| MonteCarloRecoverCreator.hh | |
| MonteCarloReset.cc | |
| MonteCarloReset.fwd.hh | |
| MonteCarloReset.hh | Perform a given mover and sample structures by MonteCarlo |
| MonteCarloResetCreator.hh | |
| MonteCarloTest.cc | |
| MonteCarloTest.fwd.hh | |
| MonteCarloTest.hh | Perform a given mover and sample structures by MonteCarlo |
| MonteCarloTestCreator.hh | |
| MSDMover.cc | Multistate design mover used for restrained multistate design |
| MSDMover.fwd.hh | Multistate design mover used for constrained MSD application |
| MSDMover.hh | Multistate design mover used for restrained multistate design |
| MSDMoverCreator.hh | Multistate design mover used for constrained MSD application |
| MutateResidue.cc | |
| MutateResidue.fwd.hh | |
| MutateResidue.hh | |
| MutateResidueCreator.hh | |
| O2M_MutateMover.cc | Mover that takes a single starting structure and some task ops, and produces every single possible point mutation DOES NOT WORK WITH ROSETTASCRIPTS |
| O2M_MutateMover.fwd.hh | O2M_MutateMover forward declarations header |
| O2M_MutateMover.hh | Mover that takes a starting structure and some task ops, and produces every single possible point mutation DOES NOT WORK WITH ROSETTASCRIPTS |
| PackRotamersMover.cc | |
| PackRotamersMover.fwd.hh | |
| PackRotamersMover.hh | |
| PackRotamersMoverCreator.hh | |
| PackRotamersMoverLazy.cc | |
| PackRotamersMoverLazy.fwd.hh | |
| PackRotamersMoverLazy.hh | |
| PackRotamersMoverLazyCreator.hh | |
| PDBReloadMover.cc | |
| PDBReloadMover.fwd.hh | PDBReloadMover forward declarations header |
| PDBReloadMover.hh | |
| PDBReloadMoverCreator.hh | |
| PeptideStapleMover.cc | Peptide Staples are covalent links between i/i+[4,7] residues in a helix. Applying a PeptideStapleMover creates one of these links |
| PeptideStapleMover.fwd.hh | Forward header for PeptideStapleMover |
| PeptideStapleMover.hh | Definition of classes for placing peptide staples in the pose |
| ProlineFixMover.cc | |
| ProlineFixMover.fwd.hh | |
| ProlineFixMover.hh | |
| PSSM2BfactorMover.cc | |
| PSSM2BfactorMover.fwd.hh | Switch the chain order |
| PSSM2BfactorMover.hh | |
| PSSM2BfactorMoverCreator.hh | |
| RandomOmegaFlipMover.cc | RandomOmegaFlipMover methods implemented |
| RandomOmegaFlipMover.fwd.hh | RandomOmegaFlipMover forward declarations header |
| RandomOmegaFlipMover.hh | RandomOmegaFlipMover class declaration file |
| RandomOmegaFlipMoverCreator.hh | This class will create instances of RandomOmegaFlipMover for the MoverFactory |
| RandomTorsionMover.cc | RandomTorsionMover methods implemented |
| RandomTorsionMover.fwd.hh | RandomTorsionMover forward declarations header |
| RandomTorsionMover.hh | RandomTorsionMover class declaration file |
| RandomTorsionMoverCreator.hh | This class will create instances of RandomTorsionMover for the MoverFactory |
| RepackSidechainsMover.cc | |
| RepackSidechainsMover.fwd.hh | |
| RepackSidechainsMover.hh | |
| RepackSidechainsMoverCreator.hh | |
| RepeatPropagationMover.cc | Can repeat both a symmetric, non symmetric & broken pose |
| RepeatPropagationMover.fwd.hh | |
| RepeatPropagationMover.hh | Can repeat both a symmetric and non symmetric protein. Modifies the pose |
| RepeatPropagationMoverCreator.hh | |
| ReportEffectivePKA.cc | |
| ReportEffectivePKA.hh | |
| ReportEffectivePKACreator.hh | This class will create instances of Mover ReportEffectivePKA for the MoverFactory |
| RepulsiveOnlyMover.cc | Calculate repulsive energy only for certain residues |
| RepulsiveOnlyMover.fwd.hh | |
| RepulsiveOnlyMover.hh | |
| ResetBaselineMover.cc | |
| ResetBaselineMover.fwd.hh | Switch the chain order |
| ResetBaselineMover.hh | Switch the chain order |
| ResetBaselineMoverCreator.hh | |
| ResidueTypeConstraintMover.cc | Assigns a ResidueTypeConstraint to a pose |
| ResidueTypeConstraintMover.fwd.hh | |
| ResidueTypeConstraintMover.hh | Assigns a ResidueTypeConstraint to a pose |
| ResidueTypeConstraintMoverCreator.hh | This class will create instances of protocols::moves::Mover ResidueTypeConstraintMover for the protocols::moves::MoverFactory |
| ResTypeFragmentMover.cc | |
| ResTypeFragmentMover.fwd.hh | |
| ResTypeFragmentMover.hh | |
| ReturnSidechainMover.cc | ReturnSidechainMover methods implemented |
| ReturnSidechainMover.fwd.hh | ReturnSidechainMover forward declarations header |
| ReturnSidechainMover.hh | Protocols::moves::Mover to "return" proper sidechains to a pose that was temporarily in centroid mode (can be used for any sidechain copying) |
| RingConformationMover.cc | Method definitions for RingConformationMover |
| RingConformationMover.fwd.hh | Forward declarations for RingConformationMover |
| RingConformationMover.hh | Declarations and simple accessor/mutator definitions for RingConformationMover |
| RotamerizeMover.cc | Definitions of class methods for RotamerizeMover |
| RotamerizeMover.fwd.hh | Forward declarations for rotamerizing |
| RotamerizeMover.hh | Class declaration for RotamerizeMover |
| RotamerTrialsMinMover.cc | Protocols::moves::Mover for Rotamer-Trials with Minimization (based on RotamerTrialsMover) |
| RotamerTrialsMinMover.fwd.hh | |
| RotamerTrialsMinMover.hh | Wrapper mover for Rotamer-Trials with Minimization (based on RotamerTrialsMover) |
| RotamerTrialsMinMoverCreator.hh | This class will create instances of RotamerTrialsMinMover for the protocols::moves::MoverFactory |
| RotamerTrialsMover.cc | |
| RotamerTrialsMover.fwd.hh | |
| RotamerTrialsMover.hh | |
| RotamerTrialsMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMCMover for the protocols::moves::MoverFactory |
| SaneMinMover.cc | |
| SaneMinMover.fwd.hh | MinMover forward declarations header |
| SaneMinMover.hh | |
| SaneMinMoverCreator.hh | |
| ScoreMover.cc | |
| ScoreMover.fwd.hh | ScoreMover forward declarations header |
| ScoreMover.hh | |
| ScoreMoverCreator.hh | |
| SequenceProfileMover.cc | Moverization of code that was embedded in the parser |
| SequenceProfileMover.fwd.hh | BS mover to get around a stupid "mover" that was embedded in the parser |
| SequenceProfileMover.hh | BS mover to get around a stupid "mover" that was embedded in the parser |
| SequenceProfileMoverCreator.hh | |
| SetReturningPackRotamersMover.cc | A pack mover which returns not just the best packer solution, but all nloop solutions |
| SetReturningPackRotamersMover.fwd.hh | |
| SetReturningPackRotamersMover.hh | A PackRotamers mover which returns a set of packed poses for when ndruns/nloop is in use |
| SetTorsion.cc | |
| SetTorsion.fwd.hh | |
| SetTorsion.hh | |
| SetTorsionCreator.hh | |
| ShakeStructureMover.cc | |
| ShakeStructureMover.fwd.hh | |
| ShakeStructureMover.hh | |
| ShortBackrubMover.cc | Implementation of ShortBackrubMover class and functions |
| ShortBackrubMover.fwd.hh | |
| ShortBackrubMover.hh | Definition of ShortBackrubMover class and functions |
| ShortBackrubMoverCreator.hh | This class will create instances of protocols::moves::Mover ShortBackrubMover for the protocols::moves::MoverFactory |
| SmoothFragmentMover.cc | |
| SmoothFragmentMover.fwd.hh | |
| SmoothFragmentMover.hh | |
| SuperimposeMover.cc | |
| SuperimposeMover.fwd.hh | SuperimposeMover forward declarations header |
| SuperimposeMover.hh | |
| SuperimposeMoverCreator.hh | |
| SwitchChainOrderMover.cc | |
| SwitchChainOrderMover.fwd.hh | Switch the chain order |
| SwitchChainOrderMover.hh | Switch the chain order |
| SwitchChainOrderMoverCreator.hh | |
| SwitchResidueTypeSetMover.cc | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMover.fwd.hh | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMover.hh | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMoverCreator.hh | |
| SymmetricFragmentMover.cc | |
| SymmetricFragmentMover.fwd.hh | Set of fragments for a certain alignment frame |
| SymmetricFragmentMover.hh | Set of fragments |
| TailsScoreMover.cc | |
| TailsScoreMover.hh | |
| TaskAwareMinMover.cc | TaskAwareMinMover methods implemented |
| TaskAwareMinMover.fwd.hh | TaskAwareMinMover forward declarations header |
| TaskAwareMinMover.hh | MinMover which updates MoveMap to mirror PackerTask |
| TaskAwareMinMoverCreator.hh | |
| TorsionDOFMover.cc | TorsionDOFMover methods implemented |
| TorsionDOFMover.fwd.hh | TorsionDOFMover forward declarations header |
| TorsionDOFMover.hh | TorsionDOFMover header |
| TorsionSetMover.cc | |
| TorsionSetMover.fwd.hh | |
| TorsionSetMover.hh | |
| Tumble.cc | Add constraints to the current pose conformation |
| Tumble.hh | |
| TumbleCreator.hh | Declaration of the MoverCreator class for the Tumble |
| UniformPositionMover.cc | Apply a uniform (deterministic move) to a given position |
| UniformPositionMover.fwd.hh | Apply a uniform (deterministic move) to a given position |
| UniformPositionMover.hh | Apply a uniform (deterministic move) to a given position |
| VirtualRootMover.cc | Manipulate virtual roots on poses. This is a seperate mover mainly to be RosettaScriptable |
| VirtualRootMover.fwd.hh | VirtualRootMover forward declarations header |
| VirtualRootMover.hh | Manipulate virtual roots on poses |
| VirtualRootMoverCreator.hh | |
| WobbleMover.cc | |
| WobbleMover.hh | |
| ► sparta | |
| ANN.cc | |
| ANN.hh | |
| ChemicalShiftEvaluator.cc | PoseEvaluator |
| ChemicalShiftEvaluator.hh | |
| ChemicalShiftEvaluatorCreator.cc | Header for ChemicalShiftsEvaluatorCreator |
| ChemicalShiftEvaluatorCreator.hh | Header for ChemicalShiftsEvaluatorCreator |
| constants.hh | |
| GDB.cc | |
| GDB.hh | |
| main.cc | |
| PDB.cc | |
| PDB.hh | |
| Sparta.cc | |
| Sparta.hh | |
| SpartaUtil.cc | |
| SpartaUtil.hh | |
| util.cc | |
| util.hh | |
| ► ss_prediction | |
| SS_predictor.cc | A simple svm based secondary structure predictor |
| SS_predictor.fwd.hh | SS_predictor forward header |
| SS_predictor.hh | |
| ► star | |
| Extender.cc | |
| Extender.hh | |
| StarAbinitio.cc | |
| StarAbinitio.fwd.hh | |
| StarAbinitio.hh | |
| StarAbinitioMain.cc | |
| StarAbinitioMain.hh | |
| util.cc | |
| util.hh | |
| ► stepwise | |
| ► legacy | |
| ► modeler | |
| ► protein | |
| StepWiseProteinMinimizer.cc | Not particularly fancy, just minimizes a list of poses |
| StepWiseProteinMinimizer.fwd.hh | |
| StepWiseProteinMinimizer.hh | |
| StepWiseProteinPoseSetup.cc | Sets up pose and job parameters for protein or RNA stepwise building |
| StepWiseProteinPoseSetup.fwd.hh | Various OPS for various classes |
| StepWiseProteinPoseSetup.hh | |
| util.cc | Few functions used by several StepWiseProteinAnsatz classes |
| util.hh | |
| ► rna | |
| RNA_AnalyticLoopCloser.cc | Protocols that are specific to RNA_AnalyticLoopCloser |
| RNA_AnalyticLoopCloser.fwd.hh | Pose forward declarations header |
| RNA_AnalyticLoopCloser.hh | |
| StepWiseRNA_Clusterer.cc | |
| StepWiseRNA_Clusterer.hh | |
| StepWiseRNA_Minimizer.cc | Not particularly fancy, just minimizes a list of poses |
| StepWiseRNA_Minimizer.fwd.hh | |
| StepWiseRNA_Minimizer.hh | |
| StepWiseRNA_PoseSelection.cc | |
| StepWiseRNA_PoseSelection.fwd.hh | |
| StepWiseRNA_PoseSelection.hh | |
| StepWiseRNA_PoseSetup.cc | Sets up pose and job parameters for RNA stepwise building |
| StepWiseRNA_PoseSetup.fwd.hh | |
| StepWiseRNA_PoseSetup.hh | |
| StepWiseRNA_PoseSetupFromCommandLine.cc | |
| StepWiseRNA_PoseSetupFromCommandLine.hh | |
| StepWiseRNA_WorkingParametersSetup.cc | Sets up pose and job parameters for RNA stepwise building |
| StepWiseRNA_WorkingParametersSetup.hh | |
| util.cc | |
| util.fwd.hh | |
| util.hh | |
| ► screener | |
| ProteinAtrRepScreener.cc | |
| ProteinAtrRepScreener.fwd.hh | |
| ProteinAtrRepScreener.hh | |
| RNA_AtrRepScreener.cc | |
| RNA_AtrRepScreener.fwd.hh | |
| RNA_AtrRepScreener.hh | |
| SimplePoseSelection.cc | |
| SimplePoseSelection.fwd.hh | |
| SimplePoseSelection.hh | |
| SimpleRMSD_Screener.cc | |
| SimpleRMSD_Screener.fwd.hh | |
| SimpleRMSD_Screener.hh | |
| ► modeler | |
| ► align | |
| StepWiseClusterer.cc | |
| StepWiseClusterer.fwd.hh | |
| StepWiseClusterer.hh | |
| StepWiseLegacyClusterer.cc | Not particularly fancy, just filters a list of poses |
| StepWiseLegacyClusterer.fwd.hh | Various OPS for various classes |
| StepWiseLegacyClusterer.hh | |
| StepWiseLegacyClustererSilentBased.cc | Not particularly fancy, just filters a list of poses |
| StepWiseLegacyClustererSilentBased.fwd.hh | Various OPS for various classes |
| StepWiseLegacyClustererSilentBased.hh | |
| StepWisePoseAligner.cc | |
| StepWisePoseAligner.fwd.hh | |
| StepWisePoseAligner.hh | |
| util.cc | |
| util.hh | |
| ► movemap | |
| util.cc | |
| util.hh | |
| ► options | |
| StepWiseBasicModelerOptions.cc | |
| StepWiseBasicModelerOptions.fwd.hh | |
| StepWiseBasicModelerOptions.hh | |
| StepWiseModelerOptions.cc | |
| StepWiseModelerOptions.fwd.hh | |
| StepWiseModelerOptions.hh | |
| StepWiseProteinModelerOptions.cc | |
| StepWiseProteinModelerOptions.fwd.hh | |
| StepWiseProteinModelerOptions.hh | |
| StepWiseRNA_ModelerOptions.cc | |
| StepWiseRNA_ModelerOptions.fwd.hh | |
| StepWiseRNA_ModelerOptions.hh | |
| ► packer | |
| SideChainCopier.cc | |
| SideChainCopier.fwd.hh | |
| SideChainCopier.hh | |
| StepWiseMasterPacker.cc | |
| StepWiseMasterPacker.fwd.hh | |
| StepWiseMasterPacker.hh | |
| StepWisePacker.cc | Not particularly fancy, just minimizes a list of poses |
| StepWisePacker.fwd.hh | |
| StepWisePacker.hh | |
| util.cc | |
| util.hh | |
| ► polar_hydrogens | |
| PolarHydrogenPacker.cc | |
| PolarHydrogenPacker.fwd.hh | |
| PolarHydrogenPacker.hh | |
| util.cc | |
| util.hh | |
| ► precomputed | |
| PrecomputedLibraryMover.cc | |
| PrecomputedLibraryMover.fwd.hh | |
| PrecomputedLibraryMover.hh | |
| ► protein | |
| ► checker | |
| ProteinAtrRepChecker.cc | |
| ProteinAtrRepChecker.fwd.hh | |
| ProteinAtrRepChecker.hh | |
| ► loop_close | |
| StepWiseProteinCCD_Closer.cc | Makes a list of (phi, psi, omega) at moving_residues that could be useful for full-atom packing |
| StepWiseProteinCCD_Closer.fwd.hh | |
| StepWiseProteinCCD_Closer.hh | |
| StepWiseProteinCCD_MultiPoseCloser.cc | |
| StepWiseProteinCCD_MultiPoseCloser.fwd.hh | |
| StepWiseProteinCCD_MultiPoseCloser.hh | |
| StepWiseProteinKIC_LoopBridger.cc | Makes a list of (phi, psi, omega) at moving_residues that could be useful for full-atom packing |
| StepWiseProteinKIC_LoopBridger.hh | |
| util.cc | |
| util.hh | |
| InputStreamWithResidueInfo.cc | Sets up pose and job parameters for protein or RNA stepwise building |
| InputStreamWithResidueInfo.fwd.hh | Various OPS for various classes |
| InputStreamWithResidueInfo.hh | |
| MainChainTorsionSet.cc | Few functions used by several StepWiseProteinAnsatz classes |
| MainChainTorsionSet.hh | |
| StepWiseProteinBackboneSampler.cc | Makes a list of (phi, psi, omega) at moving_residues that could be useful for full-atom packing |
| StepWiseProteinBackboneSampler.hh | |
| util.cc | Few functions used by several StepWiseProteinAnsatz classes |
| util.hh | |
| ► rna | |
| ► bulge | |
| BulgeApplyMover.cc | |
| BulgeApplyMover.fwd.hh | |
| BulgeApplyMover.hh | |
| BulgeUnApplyMover.cc | |
| BulgeUnApplyMover.fwd.hh | |
| BulgeUnApplyMover.hh | |
| util.cc | |
| util.hh | |
| ► checker | |
| RNA_AtrRepChecker.cc | |
| RNA_AtrRepChecker.fwd.hh | |
| RNA_AtrRepChecker.hh | |
| RNA_BaseCentroidChecker.cc | Parameters to be passed between different modules of stepwise RNA building |
| RNA_BaseCentroidChecker.fwd.hh | Various OPS for various classes |
| RNA_BaseCentroidChecker.hh | |
| RNA_ChainClosableGeometryChecker.cc | |
| RNA_ChainClosableGeometryChecker.fwd.hh | |
| RNA_ChainClosableGeometryChecker.hh | |
| RNA_ChainClosureChecker.cc | |
| RNA_ChainClosureChecker.fwd.hh | |
| RNA_ChainClosureChecker.hh | |
| RNA_VDW_BinChecker.cc | Very fast version of VWD repulsion screening |
| RNA_VDW_BinChecker.fwd.hh | Various OPS for various classes |
| RNA_VDW_BinChecker.hh | |
| ► helix | |
| RNA_HelixAssembler.cc | Protocols that are specific to RNA_HelixAssembler |
| RNA_HelixAssembler.fwd.hh | Pose forward declarations header |
| RNA_HelixAssembler.hh | |
| ► o2prime | |
| O2PrimePacker.cc | |
| O2PrimePacker.fwd.hh | |
| O2PrimePacker.hh | |
| ► phosphate | |
| MultiPhosphateSampler.cc | |
| MultiPhosphateSampler.fwd.hh | |
| MultiPhosphateSampler.hh | |
| PhosphateMove.cc | |
| PhosphateMove.fwd.hh | |
| PhosphateMove.hh | |
| PhosphateMover.cc | |
| PhosphateMover.fwd.hh | |
| PhosphateMover.hh | |
| util.cc | |
| util.hh | |
| ► rigid_body | |
| FloatingBaseClasses.hh | |
| util.cc | Not particularly fancy, just minimizes a list of poses |
| util.hh | |
| ► sugar | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator.cc | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator.fwd.hh | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator.hh | |
| StepWiseRNA_VirtualSugarSampler.cc | |
| StepWiseRNA_VirtualSugarSampler.hh | |
| StepWiseRNA_VirtualSugarSamplerFromStringList.cc | |
| StepWiseRNA_VirtualSugarSamplerFromStringList.fwd.hh | |
| StepWiseRNA_VirtualSugarSamplerFromStringList.hh | |
| SugarInstantiateMover.cc | |
| SugarInstantiateMover.fwd.hh | |
| SugarInstantiateMover.hh | |
| SugarModeling.cc | |
| SugarModeling.fwd.hh | |
| SugarModeling.hh | |
| SugarVirtualizeMover.cc | |
| SugarVirtualizeMover.fwd.hh | |
| SugarVirtualizeMover.hh | |
| util.cc | |
| util.hh | |
| StepWiseRNA_Classes.hh | |
| StepWiseRNA_CombineLongLoopFilterer.cc | Sets up pose and job parameters for RNA stepwise building |
| StepWiseRNA_CombineLongLoopFilterer.fwd.hh | |
| StepWiseRNA_CombineLongLoopFilterer.hh | |
| StepWiseRNA_OutputData.cc | Output silent_file_data functions for Stepwise Assembly RNA |
| StepWiseRNA_OutputData.hh | |
| StepWiseRNA_ResidueInfo.cc | Function used by the residue_info data structure |
| StepWiseRNA_ResidueInfo.hh | |
| util.cc | Util functions for Stepwise Assembly RNA |
| util.hh | |
| ► working_parameters | |
| StepWiseBasicWorkingParameters.cc | |
| StepWiseBasicWorkingParameters.fwd.hh | |
| StepWiseBasicWorkingParameters.hh | |
| StepWiseWorkingParameters.cc | |
| StepWiseWorkingParameters.fwd.hh | |
| StepWiseWorkingParameters.hh | |
| util.cc | |
| util.hh | |
| constraint_util.cc | |
| constraint_util.hh | |
| file_util.cc | |
| file_util.hh | |
| output_util.cc | |
| output_util.hh | |
| scoring_util.cc | |
| scoring_util.hh | |
| StepWiseConnectionSampler.cc | |
| StepWiseConnectionSampler.fwd.hh | |
| StepWiseConnectionSampler.hh | |
| StepWiseMinimizer.cc | |
| StepWiseMinimizer.fwd.hh | |
| StepWiseMinimizer.hh | |
| StepWiseModeler.cc | |
| StepWiseModeler.fwd.hh | |
| StepWiseModeler.hh | |
| util.cc | Not particularly fancy, just minimizes a list of poses |
| util.hh | |
| ► monte_carlo | |
| ► mover | |
| AddMover.cc | Adds an RNA residue from a chain terminus |
| AddMover.fwd.hh | Various suite/nucleoside moves |
| AddMover.hh | |
| AddOrDeleteMover.cc | AddOrDeletes an RNA residue from a chain terminus |
| AddOrDeleteMover.fwd.hh | Various suite/nucleoside moves |
| AddOrDeleteMover.hh | |
| DeleteMover.cc | Deletes an RNA residue from a chain terminus |
| DeleteMover.fwd.hh | Various suite/nucleoside moves |
| DeleteMover.hh | |
| FromScratchMover.cc | |
| FromScratchMover.fwd.hh | |
| FromScratchMover.hh | |
| ResampleMover.cc | |
| ResampleMover.fwd.hh | |
| ResampleMover.hh | |
| TransientCutpointHandler.cc | |
| TransientCutpointHandler.fwd.hh | |
| TransientCutpointHandler.hh | |
| ► options | |
| StepWiseMonteCarloOptions.cc | |
| StepWiseMonteCarloOptions.fwd.hh | |
| StepWiseMonteCarloOptions.hh | |
| ► rna | |
| RNA_AddDeleteMonteCarlo.cc | SWA Monte Carlo – generalization of Monte Carlo to permit addition/deletion of RNA residues |
| RNA_AddDeleteMonteCarlo.fwd.hh | Various suite/nucleoside moves |
| RNA_AddDeleteMonteCarlo.hh | |
| RNA_O2PrimeMover.cc | O2Primes an RNA residue from a chain terminus |
| RNA_O2PrimeMover.fwd.hh | Various suite/nucleoside moves |
| RNA_O2PrimeMover.hh | |
| RNA_TorsionMover.cc | Torsions an RNA residue from a chain terminus |
| RNA_TorsionMover.fwd.hh | Various suite/nucleoside moves |
| RNA_TorsionMover.hh | |
| StepWiseMonteCarlo.cc | |
| StepWiseMonteCarlo.fwd.hh | |
| StepWiseMonteCarlo.hh | |
| SWA_Move.cc | |
| SWA_Move.fwd.hh | |
| SWA_Move.hh | |
| SWA_MoveSelector.cc | |
| SWA_MoveSelector.fwd.hh | |
| SWA_MoveSelector.hh | |
| util.cc | |
| util.hh | |
| ► options | |
| StepWiseBasicOptions.cc | |
| StepWiseBasicOptions.fwd.hh | |
| StepWiseBasicOptions.hh | |
| ► sampler | |
| ► copy_dofs | |
| CopyDofStepWiseSampler.cc | |
| CopyDofStepWiseSampler.fwd.hh | |
| CopyDofStepWiseSampler.hh | |
| ResidueAlternativeSet.cc | |
| ResidueAlternativeSet.fwd.hh | |
| ResidueAlternativeSet.hh | |
| ResidueAlternativeStepWiseSampler.cc | |
| ResidueAlternativeStepWiseSampler.fwd.hh | |
| ResidueAlternativeStepWiseSampler.hh | |
| ResidueAlternativeStepWiseSamplerComb.cc | |
| ResidueAlternativeStepWiseSamplerComb.fwd.hh | |
| ResidueAlternativeStepWiseSamplerComb.hh | |
| ResidueListStepWiseSampler.cc | |
| ResidueListStepWiseSampler.fwd.hh | |
| ResidueListStepWiseSampler.hh | |
| ► input_streams | |
| InputStreamStepWiseSampler.cc | |
| InputStreamStepWiseSampler.fwd.hh | |
| InputStreamStepWiseSampler.hh | |
| ► protein | |
| ProteinBetaAntiParallelStepWiseSampler.cc | |
| ProteinBetaAntiParallelStepWiseSampler.fwd.hh | |
| ProteinBetaAntiParallelStepWiseSampler.hh | |
| ProteinFragmentStepWiseSampler.cc | |
| ProteinFragmentStepWiseSampler.fwd.hh | |
| ProteinFragmentStepWiseSampler.hh | |
| ProteinMainChainStepWiseSampler.cc | |
| ProteinMainChainStepWiseSampler.fwd.hh | |
| ProteinMainChainStepWiseSampler.hh | |
| util.cc | Subclass of StepWisePoseSampleGenerator |
| util.hh | |
| ► rigid_body | |
| EulerAngles.cc | |
| EulerAngles.fwd.hh | |
| EulerAngles.hh | |
| RigidBodyStepWiseSampler.cc | |
| RigidBodyStepWiseSampler.fwd.hh | |
| RigidBodyStepWiseSampler.hh | |
| RigidBodyStepWiseSamplerValueRange.cc | |
| RigidBodyStepWiseSamplerValueRange.fwd.hh | |
| RigidBodyStepWiseSamplerValueRange.hh | |
| RigidBodyStepWiseSamplerWithResidueAlternatives.cc | |
| RigidBodyStepWiseSamplerWithResidueAlternatives.fwd.hh | |
| RigidBodyStepWiseSamplerWithResidueAlternatives.hh | |
| RigidBodyStepWiseSamplerWithResidueList.cc | |
| RigidBodyStepWiseSamplerWithResidueList.fwd.hh | |
| RigidBodyStepWiseSamplerWithResidueList.hh | |
| ► rna | |
| RNA_ChiStepWiseSampler.cc | Generate glycosidic chi rotamers for RNA |
| RNA_ChiStepWiseSampler.fwd.hh | Generate glycosidic chi rotamers for RNA |
| RNA_ChiStepWiseSampler.hh | Generate glycosidic chi rotamers for RNA |
| RNA_KIC_Sampler.cc | Sample and torsions and close an RNA loop |
| RNA_KIC_Sampler.fwd.hh | Sample and torsions and close an RNA loop |
| RNA_KIC_Sampler.hh | Sample and torsions and close an RNA loop |
| RNA_KinematicCloser.cc | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_KinematicCloser.fwd.hh | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_KinematicCloser.hh | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_MC_MultiSuite.cc | Markov chain sampler for mulitple RNA suite |
| RNA_MC_MultiSuite.fwd.hh | Markov chain sampler for mulitple RNA suite |
| RNA_MC_MultiSuite.hh | Markov chain sampler for mulitple RNA suite |
| RNA_MC_Sugar.cc | Markov chain sampler for sugar pucker |
| RNA_MC_Sugar.fwd.hh | Markov chain sampler for sugar pucker |
| RNA_MC_Sugar.hh | Markov chain sampler for sugar pucker |
| RNA_MC_Suite.cc | Markov chain sampler for RNA suite |
| RNA_MC_Suite.fwd.hh | Markov chain sampler for RNA suite |
| RNA_MC_Suite.hh | Markov chain sampler for RNA suite |
| RNA_NucleosideStepWiseSampler.cc | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_NucleosideStepWiseSampler.fwd.hh | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_NucleosideStepWiseSampler.hh | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_SugarStepWiseSampler.cc | Generate sugar pucker rotamers for RNA |
| RNA_SugarStepWiseSampler.fwd.hh | Generate sugar pucker rotamers for RNA |
| RNA_SugarStepWiseSampler.hh | Generate sugar pucker rotamers for RNA |
| RNA_SuiteStepWiseSampler.cc | Generate rotamers for one RNA suite (from residue i to i+1) |
| RNA_SuiteStepWiseSampler.fwd.hh | Generate rotamers for one RNA suite (from residue i to i+1) |
| RNA_SuiteStepWiseSampler.hh | Generate rotamers for one RNA suite (from residue i to i+1) |
| util.cc | |
| util.hh | |
| ► screener | |
| RNA_TorsionScreener.cc | Screener checking whether the rna torsions are resonable |
| RNA_TorsionScreener.fwd.hh | Screener checking whether the rna torsions are resonable |
| RNA_TorsionScreener.hh | Screener checking whether the rna torsions are resonable |
| JumpStepWiseSampler.cc | |
| JumpStepWiseSampler.fwd.hh | |
| JumpStepWiseSampler.hh | |
| MC_Comb.cc | Ensemble of Markov chain samplers for modeler combinatorially |
| MC_Comb.fwd.hh | Ensemble of Markov chain samplers for modeler combinatorially |
| MC_Comb.hh | Ensemble of Markov chain samplers for modeler combinatorially |
| MC_OneTorsion.cc | Markov chain sampler for one torsion |
| MC_OneTorsion.fwd.hh | Markov chain sampler for one torsion |
| MC_OneTorsion.hh | Markov chain sampler for one torsion |
| MC_StepWiseSampler.fwd.hh | Abstract Base Class for Markov chain rotamer sampler |
| MC_StepWiseSampler.hh | Abstract Base Class for Markov chain rotamer sampler |
| NoOpStepWiseSampler.cc | |
| NoOpStepWiseSampler.fwd.hh | |
| NoOpStepWiseSampler.hh | |
| StepWiseSamplerAny.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerAny.fwd.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerAny.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerBase.fwd.hh | Abstract Base Class for StepWiseSampler generator |
| StepWiseSamplerBase.hh | Abstract Base Class for StepWiseSampler generator |
| StepWiseSamplerComb.cc | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerComb.fwd.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerComb.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerOneTorsion.cc | Generate rotamer for one torsion angle |
| StepWiseSamplerOneTorsion.fwd.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerOneTorsion.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerOneValue.cc | Base class for StepWiseSamplerOneValue |
| StepWiseSamplerOneValue.fwd.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerOneValue.hh | Generate rotamer for one value. Abstract base class |
| StepWiseSamplerOneValueComb.cc | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerOneValueComb.fwd.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerOneValueComb.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerSized.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSized.fwd.hh | Abstract Base Class for StepWiseSampler generator with finite size |
| StepWiseSamplerSized.hh | Abstract Base Class for StepWiseSampler sampler with finite size |
| StepWiseSamplerSizedAny.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSizedAny.fwd.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSizedAny.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSizedComb.cc | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerSizedComb.fwd.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerSizedComb.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerType.hh | |
| ► screener | |
| AnchorSugarScreener.cc | |
| AnchorSugarScreener.fwd.hh | |
| AnchorSugarScreener.hh | |
| BaseBinMapUpdater.cc | |
| BaseBinMapUpdater.fwd.hh | |
| BaseBinMapUpdater.hh | |
| BaseCentroidScreener.cc | |
| BaseCentroidScreener.fwd.hh | |
| BaseCentroidScreener.hh | |
| BulgeApplier.cc | |
| BulgeApplier.fwd.hh | |
| BulgeApplier.hh | |
| CentroidDistanceScreener.cc | |
| CentroidDistanceScreener.fwd.hh | |
| CentroidDistanceScreener.hh | |
| FastForwardToNextResidueAlternative.cc | |
| FastForwardToNextResidueAlternative.fwd.hh | |
| FastForwardToNextResidueAlternative.hh | |
| FastForwardToNextRigidBody.cc | |
| FastForwardToNextRigidBody.fwd.hh | |
| FastForwardToNextRigidBody.hh | |
| IntegrationTestBreaker.cc | |
| IntegrationTestBreaker.fwd.hh | |
| IntegrationTestBreaker.hh | |
| NativeRMSD_Screener.cc | |
| NativeRMSD_Screener.fwd.hh | |
| NativeRMSD_Screener.hh | |
| O2PrimeScreener.cc | |
| O2PrimeScreener.fwd.hh | |
| O2PrimeScreener.hh | |
| PackScreener.cc | |
| PackScreener.fwd.hh | |
| PackScreener.hh | |
| PartitionContactScreener.cc | |
| PartitionContactScreener.fwd.hh | |
| PartitionContactScreener.hh | |
| PhosphateScreener.cc | |
| PhosphateScreener.fwd.hh | |
| PhosphateScreener.hh | |
| PoseSelectionScreener.cc | |
| PoseSelectionScreener.fwd.hh | |
| PoseSelectionScreener.hh | |
| ProteinCCD_ClosureScreener.cc | |
| ProteinCCD_ClosureScreener.fwd.hh | |
| ProteinCCD_ClosureScreener.hh | |
| ResidueContactScreener.cc | |
| ResidueContactScreener.fwd.hh | |
| ResidueContactScreener.hh | |
| RNA_ChainClosableGeometryResidueBasedScreener.cc | |
| RNA_ChainClosableGeometryResidueBasedScreener.fwd.hh | |
| RNA_ChainClosableGeometryResidueBasedScreener.hh | |
| RNA_ChainClosableGeometryScreener.cc | |
| RNA_ChainClosableGeometryScreener.fwd.hh | |
| RNA_ChainClosableGeometryScreener.hh | |
| RNA_ChainClosableGeometryStubBasedScreener.cc | |
| RNA_ChainClosableGeometryStubBasedScreener.fwd.hh | |
| RNA_ChainClosableGeometryStubBasedScreener.hh | |
| RNA_ChainClosureScreener.cc | |
| RNA_ChainClosureScreener.fwd.hh | |
| RNA_ChainClosureScreener.hh | |
| SampleApplier.cc | |
| SampleApplier.fwd.hh | |
| SampleApplier.hh | |
| Scorer.cc | |
| Scorer.fwd.hh | |
| Scorer.hh | |
| StepWiseResiduePairScreener.cc | |
| StepWiseResiduePairScreener.fwd.hh | |
| StepWiseResiduePairScreener.hh | |
| StepWiseScreener.cc | |
| StepWiseScreener.fwd.hh | |
| StepWiseScreener.hh | |
| StepWiseScreenerType.hh | |
| StubApplier.cc | |
| StubApplier.fwd.hh | |
| StubApplier.hh | |
| StubDistanceScreener.cc | |
| StubDistanceScreener.fwd.hh | |
| StubDistanceScreener.hh | |
| SugarInstantiator.cc | |
| SugarInstantiator.fwd.hh | |
| SugarInstantiator.hh | |
| TagDefinition.cc | |
| TagDefinition.fwd.hh | |
| TagDefinition.hh | |
| util.cc | |
| util.hh | |
| VDW_BinScreener.cc | |
| VDW_BinScreener.fwd.hh | |
| VDW_BinScreener.hh | |
| ► setup | |
| FullModelInfoSetupFromCommandLine.cc | |
| FullModelInfoSetupFromCommandLine.fwd.hh | |
| FullModelInfoSetupFromCommandLine.hh | |
| StepWiseCSA_JobDistributor.cc | |
| StepWiseCSA_JobDistributor.fwd.hh | |
| StepWiseCSA_JobDistributor.hh | |
| StepWiseJobDistributor.fwd.hh | |
| StepWiseJobDistributor.hh | |
| StepWiseMonteCarloJobDistributor.cc | |
| StepWiseMonteCarloJobDistributor.fwd.hh | |
| StepWiseMonteCarloJobDistributor.hh | |
| StepWiseSampleAndScreen.cc | |
| StepWiseSampleAndScreen.fwd.hh | |
| StepWiseSampleAndScreen.hh | |
| ► surface_docking | |
| CentroidRelaxMover.cc | |
| CentroidRelaxMover.fwd.hh | |
| CentroidRelaxMover.hh | <add a="" description="" of="" the="" class>=""> |
| FullatomRelaxMover.cc | |
| FullatomRelaxMover.fwd.hh | |
| FullatomRelaxMover.hh | |
| SurfaceDockingProtocol.cc | |
| SurfaceDockingProtocol.fwd.hh | <add a="" description="" of="" the="" class>=""> |
| SurfaceDockingProtocol.hh | <add a="" description="" of="" the="" class>=""> |
| SurfaceOrientMover.cc | |
| SurfaceOrientMover.fwd.hh | <add a="" description="" of="" the="" class>=""> |
| SurfaceOrientMover.hh | <add a="" description="" of="" the="" class>=""> |
| SurfaceParameters.cc | |
| SurfaceParameters.fwd.hh | |
| SurfaceParameters.hh | |
| SurfaceVectorFallbackConfiguration.cc | |
| SurfaceVectorFallbackConfiguration.fwd.hh | Forward header for OptionsSystemFallback class |
| SurfaceVectorFallbackConfiguration.hh | |
| SurfaceVectorFallbackConfigurationCreator.hh | |
| SurfaceVectorLoader.cc | |
| SurfaceVectorLoader.fwd.hh | |
| SurfaceVectorLoader.hh | |
| SurfaceVectorLoaderCreator.hh | |
| SurfaceVectorOptions.cc | |
| SurfaceVectorOptions.fwd.hh | SurfaceVectorOptions forward declarations header |
| SurfaceVectorOptions.hh | |
| SurfaceVectorOptionsCreator.hh | |
| ► symmetric_docking | |
| ► membrane | |
| MPSymDockMover.cc | Membrane symmetric docking protocol |
| MPSymDockMover.fwd.hh | Membrane symmetric docking protocol |
| MPSymDockMover.hh | Membrane symmetric docking protocol |
| MPSymDockMoverCreator.hh | Membrane symmetric docking protocol |
| SymDockBaseProtocol.cc | |
| SymDockBaseProtocol.hh | |
| SymDockingHiRes.cc | Protocols that are specific to high resolution docking |
| SymDockingHiRes.fwd.hh | |
| SymDockingHiRes.hh | Initialization protocols for docking |
| SymDockingLowRes.cc | Protocols that are specific to docking low resolution |
| SymDockingLowRes.fwd.hh | |
| SymDockingLowRes.hh | Low resolution mode for symmetrical docking |
| SymDockProtocol.cc | Symmetric Protein-Protein Docking Protocol |
| SymDockProtocol.fwd.hh | |
| SymDockProtocol.hh | Symmetric Protein-Protein Docking Protocol |
| SymDockProtocolCreator.hh | Declaration of the MoverCreator class for the SymDockProtocol |
| SymFoldandDockCreators.hh | Declaration of the MoverCreator class for the SymDockProtocol |
| SymFoldandDockMoveRbJumpMover.cc | |
| SymFoldandDockMoveRbJumpMover.fwd.hh | |
| SymFoldandDockMoveRbJumpMover.hh | |
| SymFoldandDockRbTrialMover.cc | |
| SymFoldandDockRbTrialMover.fwd.hh | |
| SymFoldandDockRbTrialMover.hh | |
| SymFoldandDockSlideTrialMover.cc | |
| SymFoldandDockSlideTrialMover.fwd.hh | |
| SymFoldandDockSlideTrialMover.hh | |
| SymRestrictTaskForDocking.cc | When passed to a PackerTask, pack/design is limited to the protein interface |
| SymRestrictTaskForDocking.fwd.hh | |
| SymRestrictTaskForDocking.hh | When passed to a PackerTask, pack/design is limited to the interface |
| SymSidechainMinMover.cc | |
| SymSidechainMinMover.fwd.hh | |
| SymSidechainMinMover.hh | |
| ► toolbox | |
| ► match_enzdes_util | |
| AlignPoseToInvrotTreeMover.cc | Forward declaration for inverse rotamer tree node base |
| AlignPoseToInvrotTreeMover.fwd.hh | Forward declaration for inverse rotamer tree node base |
| AlignPoseToInvrotTreeMover.hh | Small class to setup an invrot tree in an existing pose |
| AllowedSeqposForGeomCst.cc | Forward declaration for inverse rotamer tree node base |
| AllowedSeqposForGeomCst.fwd.hh | Forward declaration for AllowedSeqposForGeomCst |
| AllowedSeqposForGeomCst.hh | Forward declaration for inverse rotamer tree node base |
| EnzConstraintIO.cc | |
| EnzConstraintIO.fwd.hh | |
| EnzConstraintIO.hh | |
| EnzConstraintParameters.cc | |
| EnzConstraintParameters.hh | |
| EnzCstTemplateRes.cc | |
| EnzCstTemplateRes.hh | |
| EnzdesCacheableObserver.cc | |
| EnzdesCacheableObserver.fwd.hh | |
| EnzdesCacheableObserver.hh | |
| EnzdesCstCache.cc | |
| EnzdesCstCache.fwd.hh | |
| EnzdesCstCache.hh | |
| EnzdesLoopsFile.cc | |
| EnzdesLoopsFile.fwd.hh | |
| EnzdesLoopsFile.hh | |
| EnzdesSeqRecoveryCache.cc | |
| EnzdesSeqRecoveryCache.fwd.hh | |
| EnzdesSeqRecoveryCache.hh | |
| ExternalGeomSampler.cc | |
| ExternalGeomSampler.fwd.hh | |
| ExternalGeomSampler.hh | |
| InvrotTarget.cc | .hh file for inverse rotamer target |
| InvrotTarget.fwd.hh | Forward declaration for inverse rotamer target |
| InvrotTarget.hh | .hh file for inverse rotamer target |
| InvrotTree.cc | Class to model one state of a reaction |
| InvrotTree.fwd.hh | Forward declaration for inverse rotamer tree node base |
| InvrotTree.hh | Class to hold inverse rotamers associated with theozyme / cstfile |
| InvrotTreeNode.cc | .cc file for inverse rotamer tree node |
| InvrotTreeNode.fwd.hh | Forward declaration for inverse rotamer target |
| InvrotTreeNode.hh | .hh file for inverse rotamer tree node |
| InvrotTreeNodeBase.cc | Forward declaration for inverse rotamer tree node base |
| InvrotTreeNodeBase.fwd.hh | Forward declaration for inverse rotamer tree node base |
| InvrotTreeNodeBase.hh | Forward declaration for inverse rotamer tree node base |
| LigandConformer.cc | Implementation for class to hold a ligand conformation |
| LigandConformer.fwd.hh | Forward declaration for a class to hold the geometry of a ligand conformation |
| LigandConformer.hh | Declaration of a class to hold a ligand conformation |
| MatchConstraintFileInfo.cc | |
| MatchConstraintFileInfo.fwd.hh | |
| MatchConstraintFileInfo.hh | |
| util_functions.cc | Bunch of utility functions |
| util_functions.hh | |
| ► pose_manipulation | |
| pose_manipulation.cc | Some general functions to manipulate poses. feel free to add your own |
| pose_manipulation.hh | Some general functions to manipulate poses. feel free to add your own |
| ► pose_metric_calculators | |
| BuriedUnsatisfiedPolarsCalculator.cc | How many buried unsatisfied polars are there? |
| BuriedUnsatisfiedPolarsCalculator.hh | |
| CatPiCalculator.cc | |
| CatPiCalculator.hh | |
| ChargeCalculator.cc | Calculator to compute nonlocal/tertiary contacts in a given pose |
| ChargeCalculator.hh | |
| ClashCountCalculator.cc | ClashCountCalculator class |
| ClashCountCalculator.hh | |
| DecomposeAndReweightEnergiesCalculator.cc | DecomposeAndReweightEnergiesCalculator class |
| DecomposeAndReweightEnergiesCalculator.hh | |
| FragQualCalculator.cc | Calculate rmsd fragment quality given a pose Roughly, fragment quality is number of fragments which are close to a pose in rmsd |
| FragQualCalculator.hh | Header file for FragQualCalculator class. Roughly, fragment quality is number of fragments which are close to a pose in rmsd |
| HPatchCalculator.cc | A class which will keep track of the SASA-based hpatch score of a Pose object |
| HPatchCalculator.hh | A Pose metric which will keep track of the SASA-based hpatch score of a Pose object |
| InterGroupNeighborsCalculator.cc | This is complicated, so pay attention. This calculator is meant for finding interfaces between protein domains - like protein-protein interfaces but within a protein. It's more flexible than that, though. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. This calculator contains a superset of the functionality of some of the other calculators, but is less efficient in simple cases. The pose does NOT have to have been scored |
| InterGroupNeighborsCalculator.fwd.hh | InterGroupNeighborsCalculator can determine all the neighbors of a residue within a certain distance |
| InterGroupNeighborsCalculator.hh | This is complicated, so pay attention. This calculator is meant for finding interfaces between protein domains - like protein-protein interfaces but within a protein. It's more flexible than that, though. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. This calculator contains a superset of the functionality of some of the other calculators, but is less efficient in simple cases. The pose does NOT have to have been scored |
| MetricValueGetter.cc | |
| MetricValueGetter.fwd.hh | |
| MetricValueGetter.hh | |
| NeighborhoodByDistanceCalculator.cc | NeighborhoodByDistanceCalculator can determine all the neighbors of group of residues within a certain distance |
| NeighborhoodByDistanceCalculator.fwd.hh | NeighborhoodByDistanceCalculator can determine all the neighbors of a residue within a certain distance |
| NeighborhoodByDistanceCalculator.hh | NeighborhoodByDistanceCalculator can determine all the neighbors of group of residues within a certain distance |
| NeighborsByDistanceCalculator.cc | NeighborsByDistanceCalculator can determine all the neighbors of a residue within a certain distance. The pose does not have to have been scored (have a full Energies object). It uses the PointGraph tools to find neighbors. There is probably a much more sophisticated way to do this with existing Graph tools but I don't know what it is |
| NeighborsByDistanceCalculator.fwd.hh | NeighborsByDistanceCalculator can determine all the neighbors of a residue within a certain distance |
| NeighborsByDistanceCalculator.hh | NeighborsByDistanceCalculator can determine all the neighbors of a residue within a certain distance. The pose does not have to have been scored (have a full Energies object). It uses the PointGraph tools to find neighbors. There is probably a much more sophisticated way to do this with existing Graph tools but I don't know what it is |
| NonlocalContactsCalculator.cc | Calculator to compute nonlocal/tertiary contacts in a given pose |
| NonlocalContactsCalculator.hh | |
| NumberHBondsCalculator.cc | Number of hbonds calculator class |
| NumberHBondsCalculator.hh | |
| PackstatCalculator.cc | Packstat calculator class |
| PackstatCalculator.hh | |
| PiPiCalculator.cc | |
| PiPiCalculator.hh | |
| ResidueDecompositionByChainCalculator.cc | ResidueDecompositionByChainCalculator class |
| ResidueDecompositionByChainCalculator.hh | |
| ResidueDecompositionCalculator.cc | ResidueDecompositionCalculator class |
| ResidueDecompositionCalculator.hh | |
| RotamerBoltzCalculator.cc | Calculates Rotamer occupancy of each rotameric state in a given set of residues |
| RotamerBoltzCalculator.fwd.hh | Calculates Rotamer occupancy of each rotameric state in a given set of residues |
| RotamerBoltzCalculator.hh | Calculates Rotamer occupancy of each rotameric state in a given set of residues |
| RotamerRecovery.cc | |
| RotamerRecovery.hh | Compare the rotamer recovery between a native protein and a list of other proteins |
| SaltBridgeCalculator.cc | |
| SaltBridgeCalculator.hh | |
| SemiExplicitWaterUnsatisfiedPolarsCalculator.cc | How many unsatisfied polars are there? |
| SemiExplicitWaterUnsatisfiedPolarsCalculator.hh | |
| SequenceComparison.cc | |
| SequenceComparison.hh | |
| SurfaceCalculator.cc | A class which will keep track of surface energy as a Pose metric |
| SurfaceCalculator.hh | A Pose metric which will keep track of the surface energy of a Pose object |
| ► rigid_body | |
| util.cc | |
| util.hh | |
| ► rotamer_set_operations | |
| AddGood2BPairEnergyRotamers.cc | |
| AddGood2BPairEnergyRotamers.fwd.hh | |
| AddGood2BPairEnergyRotamers.hh | Class to add rotamers that interact especially well with desired target residues |
| RigidBodyMoveRotSetOps.cc | Classes for rigid body movement during rotamer packing |
| RigidBodyMoveRotSetOps.fwd.hh | Classes for rigidb body movement during rotamer packing |
| RigidBodyMoveRotSetOps.hh | Classes for rigid body movement during rotamer packing |
| SpecialRotamerRotSetOps.cc | Combine two rotamer sets |
| SpecialRotamerRotSetOps.fwd.hh | Combine two rotamer sets |
| SpecialRotamerRotSetOps.hh | Classes for rigid body movement during rotamer packing |
| ► sample_around | |
| util.cc | |
| util.hh | |
| ► task_operations | |
| AlignedThreadOperation.cc | |
| AlignedThreadOperation.fwd.hh | |
| AlignedThreadOperation.hh | TaskOperation class that restricts a chain to repacking |
| AlignedThreadOperationCreator.hh | |
| CrystalContactsOperation.cc | Exclude crystal contacts from design |
| CrystalContactsOperation.fwd.hh | Exclude crystal contacts from design |
| CrystalContactsOperation.hh | Exclude crystal contacts from design |
| CrystalContactsOperationCreator.hh | Exclude crystal contacts from design |
| DatabaseThread.cc | Picks a sequence from database by start and end position on the pose |
| DatabaseThread.fwd.hh | |
| DatabaseThread.hh | TaskOperation class that restricts a chain to repacking |
| DatabaseThreadCreator.hh | |
| DesignAroundOperation.cc | |
| DesignAroundOperation.fwd.hh | |
| DesignAroundOperation.hh | |
| DesignAroundOperationCreator.hh | |
| DsspDesignOperation.cc | Design residues with selected amino acids depending on DSSP secondary structure assignment. All functionality here is included in the LayerDesign task operation, but this filter has significantly reduced overhead by avoiding slow SASA calculations |
| DsspDesignOperation.fwd.hh | |
| DsspDesignOperation.hh | Design residues with selected amino acids depending on DSSP secondary structure assignment. All functionality here is included in the LayerDesign task operation, but this filter has significantly reduced overhead by avoiding slow SASA calculations |
| DsspDesignOperationCreator.hh | |
| ImportUnboundRotamersOperation.cc | Import unbound (or native) rotamers into Rosetta! |
| ImportUnboundRotamersOperation.fwd.hh | Rotamer set operation forward declaration |
| ImportUnboundRotamersOperation.hh | Eliminate aromatic rotamers, of which chi2 are around 0, 180 degree |
| ImportUnboundRotamersOperationCreator.hh | |
| InteractingRotamerExplosion.cc | |
| InteractingRotamerExplosion.fwd.hh | |
| InteractingRotamerExplosion.hh | TaskOperation class that oversamples rotamers interacting with a certain target |
| InteractingRotamerExplosionCreator.hh | |
| InterfaceTaskOperation.cc | Base class for TaskOperations that will work with docking to define an interface |
| InterfaceTaskOperation.fwd.hh | |
| InterfaceTaskOperation.hh | Base class for TaskOperations that will work with docking to define an interface |
| JointSequenceOperation.cc | Set designable residues to those observed in a set of structures |
| JointSequenceOperation.fwd.hh | |
| JointSequenceOperation.hh | Set every position to be designable to residues observed in a set of structures |
| JointSequenceOperationCreator.hh | |
| LimitAromaChi2Operation.cc | Eliminate aromatic rotamers, of which chi2 are around 0, 180 degree |
| LimitAromaChi2Operation.fwd.hh | Rotamer set operation forward declaration |
| LimitAromaChi2Operation.hh | Eliminate aromatic rotamers, of which chi2 are around 0, 180 degree |
| LimitAromaChi2OperationCreator.hh | |
| LinkResidues.cc | |
| LinkResidues.fwd.hh | |
| LinkResidues.hh | TaskOperation class that restricts a chain to repacking |
| LinkResiduesCreator.hh | |
| ModifyAnnealer.cc | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealer.fwd.hh | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealer.hh | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealerCreator.hh | |
| PreventChainFromRepackingOperation.cc | |
| PreventChainFromRepackingOperation.fwd.hh | |
| PreventChainFromRepackingOperation.hh | TaskOperation class that restricts a chain to repacking |
| PreventChainFromRepackingOperationCreator.hh | |
| PreventResiduesFromRepackingOperation.cc | |
| PreventResiduesFromRepackingOperation.fwd.hh | |
| PreventResiduesFromRepackingOperation.hh | TaskOperation class that prevents a vector of residues indices from repacking parsed as a string that is comma delimited "," |
| PreventResiduesFromRepackingOperationCreator.hh | |
| ProteinCoreResFilter.cc | TaskOperation class that finds an interface and leaves it mobile in the PackerTask |
| ProteinCoreResFilter.hh | |
| ProteinCoreResFilterCreator.hh | |
| ProteinInterfaceDesignOperation.cc | |
| ProteinInterfaceDesignOperation.fwd.hh | |
| ProteinInterfaceDesignOperation.hh | TaskOperation class that restricts a chain to repacking |
| ProteinInterfaceDesignOperationCreator.hh | |
| ReadResfileFromDB.cc | |
| ReadResfileFromDB.fwd.hh | Forward declaration of the ReadResfileFromDB class |
| ReadResfileFromDB.hh | Read a refile indexed by the input structure tag from a supplied relational database |
| ReadResfileFromDBCreator.hh | |
| RestrictByCalculatorsOperation.cc | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperation.fwd.hh | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperation.hh | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperationCreator.hh | |
| RestrictChainToRepackingOperation.cc | |
| RestrictChainToRepackingOperation.fwd.hh | |
| RestrictChainToRepackingOperation.hh | TaskOperation class that restricts a chain to repacking |
| RestrictChainToRepackingOperationCreator.hh | |
| RestrictIdentitiesAtAlignedPositions.cc | |
| RestrictIdentitiesAtAlignedPositions.fwd.hh | |
| RestrictIdentitiesAtAlignedPositions.hh | TaskOperation class that restricts the identities at positions aligned with those of another pdb with the positions observed in that pdb |
| RestrictIdentitiesAtAlignedPositionsCreator.hh | |
| RestrictIdentitiesOperation.cc | Restricts specified residue types to only repack, no design |
| RestrictIdentitiesOperation.fwd.hh | |
| RestrictIdentitiesOperation.hh | TaskOperation class that restricts a vector of Size defined residues to repacking when parsed, it takes in a string and splits by "," |
| RestrictIdentitiesOperationCreator.hh | |
| RestrictInterGroupVectorOperation.cc | |
| RestrictInterGroupVectorOperation.fwd.hh | |
| RestrictInterGroupVectorOperation.hh | Restricts design to only those residues between two groups of structures |
| RestrictInterGroupVectorOperationCreator.hh | |
| RestrictNativeResiduesOperation.cc | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed |
| RestrictNativeResiduesOperation.fwd.hh | |
| RestrictNativeResiduesOperation.hh | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed |
| RestrictNativeResiduesOperationCreator.hh | |
| RestrictNonSurfaceToRepackingOperation.cc | |
| RestrictNonSurfaceToRepackingOperation.fwd.hh | |
| RestrictNonSurfaceToRepackingOperation.hh | TaskOperation class that restrics buried and boundary positions to repacking leaving surface positions designable |
| RestrictNonSurfaceToRepackingOperationCreator.hh | |
| RestrictOperationsBase.cc | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictOperationsBase.fwd.hh | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictOperationsBase.hh | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictResiduesToRepackingOperation.cc | |
| RestrictResiduesToRepackingOperation.fwd.hh | |
| RestrictResiduesToRepackingOperation.hh | TaskOperation class that restricts a vector of Size defined residues to repacking when parsed, it takes in a string and splits by "," |
| RestrictResiduesToRepackingOperationCreator.hh | |
| RestrictToAlignedSegments.cc | |
| RestrictToAlignedSegments.fwd.hh | |
| RestrictToAlignedSegments.hh | |
| RestrictToAlignedSegmentsCreator.hh | |
| RestrictToCDRH3Loop.cc | |
| RestrictToCDRH3Loop.fwd.hh | Forward declaration of the RestrictToCDRH3Loop class |
| RestrictToCDRH3Loop.hh | This class allows the selection for packing of the Antibody CDR-H3 loop by taking advantage of the PDB numbering schemes that are commonly used for Antibodies |
| RestrictToCDRH3LoopCreator.hh | |
| RestrictToInterface.cc | When passed to a PackerTask, pack/design is limited to the protein interface |
| RestrictToInterface.fwd.hh | |
| RestrictToInterface.hh | When passed to a PackerTask, pack/design is limited to the interface |
| RestrictToInterfaceCreator.hh | |
| RestrictToInterfaceOperation.cc | TaskOperation class that finds an interface and leaves it mobile in the PackerTask |
| RestrictToInterfaceOperation.fwd.hh | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask |
| RestrictToInterfaceOperation.hh | TaskOperation class that finds an interface and makes it mobile in the PackerTask |
| RestrictToInterfaceOperationCreator.hh | |
| RestrictToInterfaceVectorOperation.cc | TaskOperation class that finds an interface based on: core/pack/task/operation/util/interface_vector_calculate.hh and leaves it mobile in the PackerTask |
| RestrictToInterfaceVectorOperation.fwd.hh | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask |
| RestrictToInterfaceVectorOperation.hh | TaskOperation class that finds an interface based on InterfaceVectorDefinition and leaves it mobile in the PackerTask. Serves mostly to wrap InterfaceVectorDefinition into a TaskOperation. see src/core/pack/task/operation/util/interface_vector_calculate.hh |
| RestrictToInterfaceVectorOperationCreator.hh | |
| RestrictToLoops.cc | |
| RestrictToLoops.fwd.hh | |
| RestrictToLoops.hh | |
| RestrictToLoopsAndNeighbors.cc | |
| RestrictToLoopsAndNeighbors.fwd.hh | Forward declaration of the RestrictToLoopsAndNeighbors class |
| RestrictToLoopsAndNeighbors.hh | This class allows the selection for packing (and possibly design) of residues contained in a Loops object as well as the neighbors within a specified cutoff distance, with the default and maximum cutoff at 10.0 A |
| RestrictToLoopsAndNeighborsCreator.hh | Creator class for the RestrictToLoopsAndNeighbors TaskOperation |
| RestrictToLoopsCreator.hh | |
| RestrictToMoveMapChiOperation.cc | |
| RestrictToMoveMapChiOperation.fwd.hh | |
| RestrictToMoveMapChiOperation.hh | Makes it easier to use TF and MM in the same class |
| RestrictToMoveMapChiOperationCreator.hh | |
| RestrictToNeighborhoodOperation.cc | TaskOperation class that finds a neighborhood and leaves it mobile in the PackerTask |
| RestrictToNeighborhoodOperation.fwd.hh | Forward declaration of a TaskOperation class that finds a neighborhood; leaves it mobile in the PackerTask |
| RestrictToNeighborhoodOperation.hh | TaskOperation class that finds a neighborhood and makes it mobile in the PackerTask |
| RestrictToNeighborhoodOperationCreator.hh | |
| RestrictToTerminiOperation.cc | Restrict to packing only the residues at either or both termini |
| RestrictToTerminiOperation.fwd.hh | RestrictToTerminiOperation forward header |
| RestrictToTerminiOperation.hh | Restrict to packing only the residues at either or both termini |
| RestrictToTerminiOperationCreator.hh | RestrictToTerminiOperation class creator |
| RetrieveStoredTaskOperation.cc | Retrieves a stored task from the pose's CacheableData. Must be used in conjunction with the StoredTaskMover. Allows storage/retrieval of a task so that particular sets of residues can be stably addressed throughout the entirety of a RosettaScripts protocol |
| RetrieveStoredTaskOperation.fwd.hh | |
| RetrieveStoredTaskOperation.hh | Retrieves a stored task from the pose's CacheableData. Must be used in conjunction with the StoredTaskMover. Allows storage/retrieval of a task so that particular sets of residues can be stably addressed throughout the entirety of a RosettaScripts protocol |
| RetrieveStoredTaskOperationCreator.hh | |
| SelectByDeltaScoreOperation.cc | |
| SelectByDeltaScoreOperation.fwd.hh | |
| SelectByDeltaScoreOperation.hh | |
| SelectByDeltaScoreOperationCreator.hh | |
| SelectByDensityFitOperation.cc | |
| SelectByDensityFitOperation.fwd.hh | |
| SelectByDensityFitOperation.hh | |
| SelectByDensityFitOperationCreator.hh | |
| SelectBySASAOperation.cc | |
| SelectBySASAOperation.fwd.hh | |
| SelectBySASAOperation.hh | |
| SelectBySASAOperationCreator.hh | |
| SelectResiduesWithinChain.cc | |
| SelectResiduesWithinChain.fwd.hh | |
| SelectResiduesWithinChain.hh | TaskOperation class that restricts a chain to repacking |
| SelectResiduesWithinChainCreator.hh | |
| SeqprofConsensusOperation.cc | Set designable residues to those observed in sequence profile |
| SeqprofConsensusOperation.fwd.hh | |
| SeqprofConsensusOperation.hh | Set every position to be designable to residues observed in sequence profile |
| SeqprofConsensusOperationCreator.hh | |
| SetIGTypeOperation.cc | Task operation to set interaction graph type (linmem, lazy or double lazy) |
| SetIGTypeOperation.fwd.hh | Task operation to set Interaction graph Type |
| SetIGTypeOperation.hh | Task operation to set interaction graph type (linear memory, lazy or double lazy) |
| SetIGTypeOperationCreator.hh | |
| STMStoredTask.cc | CacheableData wrapper for PackerTask storage |
| STMStoredTask.fwd.hh | |
| STMStoredTask.hh | |
| StoreCombinedStoredTasksMover.cc | The StoreCombinedStoredTasksMover HAS BEEN DEPRECATED. It was used to combine several STMStoredTasks (protocols/toolbox/task_operations/STMStoredTask.cc), but has been replaced by the StoreCompoundTaskMover (protocols/toolbox/task_operations/StoreCompoundTaskMover.cc), which is much more flexible. It is being moved out of devel/matdes/ into protocols/toolbox/task_operations/ to support the publication King et al., Nature 2014 |
| StoreCombinedStoredTasksMover.fwd.hh | |
| StoreCombinedStoredTasksMover.hh | Headers for StoreCombinedStoredTasksMover class – DEPRECATED (see .cc file) |
| StoreCombinedStoredTasksMoverCreator.hh | |
| StoreCompoundTaskMover.cc | Combine tasks using boolean logic for residues that are packable or designable, assign new packing behavior to residues that match or do not match the specified criteria, and store the resulting task in the pose's cacheable data. TODO (Jacob): Add option to combine allowed amino acid sets |
| StoreCompoundTaskMover.fwd.hh | Combine tasks using boolean logic for residues that are packable or designable, as well as for residue specific AA sets, and store the resulting task in the pose's cacheable data |
| StoreCompoundTaskMover.hh | Combine tasks using boolean logic for residues that are packable or designable, as well as for residue specific AA sets, and store the resulting task in the pose's cacheable data |
| StoreCompoundTaskMoverCreator.hh | Combine tasks using boolean logic for residues that are packable or designable, as well as for residue specific AA sets, and store the resulting task in the pose's cacheable data |
| StoreTaskMover.cc | The StoreTaskMover allows you to create a PackerTask at some point during a RosettaScripts run and save it for access later during the same run. Can be useful for mutating/analyzing a particular set of residues using many different movers/filters |
| StoreTaskMover.fwd.hh | |
| StoreTaskMover.hh | Headers for StoreTaskMover class |
| StoreTaskMoverCreator.hh | This class will create instances of Mover StoreTaskMover for the MoverFactory |
| ThreadSequenceOperation.cc | |
| ThreadSequenceOperation.fwd.hh | |
| ThreadSequenceOperation.hh | TaskOperation class that restricts a chain to repacking |
| ThreadSequenceOperationCreator.hh | |
| AllowInsert.cc | |
| AllowInsert.fwd.hh | AllowInsert forward declarations header |
| AllowInsert.hh | |
| Cluster.cc | Header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| Cluster.hh | |
| Cluster.impl.hh | Template implementation for clustering of silentstructs that are provided by iterators |
| DecoySetEvaluation.cc | |
| DecoySetEvaluation.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| DecoySetEvaluation.hh | |
| DecoySetEvaluation.impl.hh | Template implementation for clustering of silentstructs that are provided by iterators |
| IGEdgeReweighters.cc | Collection of routines to assign different weights to IG edges |
| IGEdgeReweighters.hh | |
| InteratomicVarianceMatrix.cc | Header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| InteratomicVarianceMatrix.hh | Header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| KCluster.cc | Fast clustering algorithm for large silent file |
| KCluster.fwd.hh | |
| KCluster.hh | Fast clustering algorithm for large silent file |
| NetworkAlgorithms.cc | Calculate various network properties from poses |
| NetworkAlgorithms.fwd.hh | FOrward header for class that analyzes properties of residue networks |
| NetworkAlgorithms.hh | Computes network properties of a pose |
| PyReturnValuePolicyTest.hh | A few functions test how PyRosetta handle boost ReturnValuePolicy |
| SelectResiduesByLayer.cc | Select residues depending on layer: core, boundary, and surface The layer of residues are defined by accessible sufrace area of CB + mainchain |
| SelectResiduesByLayer.fwd.hh | |
| SelectResiduesByLayer.hh | Select residues depending on layer: core, boundary, and surface and the layer are defined by accessible sufrace area of each residue |
| superimpose.cc | Header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| superimpose.hh | Header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| ► topology_broker | |
| ► claims | |
| BBClaim.fwd.hh | |
| BBClaim.hh | |
| CutClaim.fwd.hh | |
| CutClaim.hh | |
| DofClaim.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| DofClaim.fwd.hh | |
| DofClaim.hh | |
| JumpClaim.fwd.hh | |
| JumpClaim.hh | |
| LegacyRootClaim.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| LegacyRootClaim.hh | |
| SequenceClaim.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| SequenceClaim.hh | |
| SymmetryClaim.fwd.hh | |
| SymmetryClaim.hh | Claim for Symmetry (includes SymmData) |
| ► weights | |
| AbinitioMoverWeight.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| ConstAbinitioMoverWeight.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| LargeFragWeight.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| SmallFragWeight.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| SmoothFragWeight.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| AsymFoldandDockClaimer.cc | Fold-and-dock |
| AsymFoldandDockClaimer.fwd.hh | AsymFoldandDockClaimer forward declarations header |
| AsymFoldandDockClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| BasicJumpClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| BasicJumpClaimer.fwd.hh | The forward head for the BasicJumpClaimre |
| BasicJumpClaimer.hh | |
| ClaimerMessage.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| ClaimerMessage.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ClaimerMessage.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| ConstraintClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| ConstraintClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ConstraintClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| ConstraintEvaluatorWrapper.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| ConstraintEvaluatorWrapper.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ConstraintEvaluatorWrapper.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| ConstraintEvaluatorWrapperCreator.cc | Header for ConstraintsEvaluatorCreator |
| ConstraintEvaluatorWrapperCreator.hh | Header for ConstraintsEvaluatorCreator |
| CoordConstraintClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| CoordConstraintClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| CoordConstraintClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| CutBiasClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| CutBiasClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| CutBiasClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| DensityScoringClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| DensityScoringClaimer.fwd.hh | |
| DensityScoringClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| DisulfJumpClaimer.cc | Claimer for disulfide jump sampling |
| DisulfJumpClaimer.fwd.hh | Protocols::topology_broker::DisulfJumpClaimer forward declarations header |
| DisulfJumpClaimer.hh | Claimer for disulfide jump sampling |
| Exceptions.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| FibrilModelingClaimer.cc | Fibril Modeling |
| FibrilModelingClaimer.fwd.hh | FibrilModelingClaimer forward declarations header |
| FibrilModelingClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| FoldandDockClaimer.cc | Fold-and-dock |
| FoldandDockClaimer.fwd.hh | FoldandDockClaimer forward declarations header |
| FoldandDockClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| FragmentClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| FragmentClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FragmentClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| FragmentJumpClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| FragmentJumpClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| FragmentJumpClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| LoopFragmentClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| LoopFragmentClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| LoopFragmentClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| MembraneTopologyClaimer.cc | Membrane topology |
| MembraneTopologyClaimer.fwd.hh | Protocols::topology_broker::MembraneTopologyClaimer forward declarations header |
| MembraneTopologyClaimer.hh | Membrane topology |
| MetalloClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| MetalloClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| MetalloClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| PcsEnergyController.cc | |
| PcsEnergyController.fwd.hh | |
| PcsEnergyController.hh | |
| PseudocontactShiftEnergyController.cc | |
| PseudocontactShiftEnergyController.fwd.hh | |
| PseudocontactShiftEnergyController.hh | |
| PseudocontactShiftEnergyController_Ts1.cc | |
| PseudocontactShiftEnergyController_Ts1.fwd.hh | |
| PseudocontactShiftEnergyController_Ts1.hh | |
| PseudocontactShiftEnergyController_Ts2.cc | |
| PseudocontactShiftEnergyController_Ts2.fwd.hh | |
| PseudocontactShiftEnergyController_Ts2.hh | |
| PseudocontactShiftEnergyController_Ts3.cc | |
| PseudocontactShiftEnergyController_Ts3.fwd.hh | |
| PseudocontactShiftEnergyController_Ts3.hh | |
| PseudocontactShiftEnergyController_Ts4.cc | |
| PseudocontactShiftEnergyController_Ts4.fwd.hh | |
| PseudocontactShiftEnergyController_Ts4.hh | |
| RigidBodyRandomTMHMover.cc | |
| RigidBodyRandomTMHMover.fwd.hh | RigidBodyMover forward declarations header |
| RigidBodyRandomTMHMover.hh | |
| RigidChunkClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| RigidChunkClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| RigidChunkClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| SequenceClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| SequenceClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| SequenceClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| SequenceNumberResolver.cc | |
| SequenceNumberResolver.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| SequenceNumberResolver.hh | |
| StartStructClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| StartStructClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| StartStructClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| SymmetryClaimer.cc | Basic Claimer for making Symmetry Claims |
| SymmetryClaimer.fwd.hh | SymmetryClaimer forward declaration header |
| SymmetryClaimer.hh | Basic Claimer for making Symmetry Claims |
| TemplateFragmentClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| TemplateFragmentClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| TemplateFragmentClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| TemplateJumpClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| TemplateJumpClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| TemplateJumpClaimer.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| TMHTopologySamplerClaimer.cc | Source file for TMHTopologySamplerClaimer protocol |
| TMHTopologySamplerClaimer.fwd.hh | Protocols::topology_broker::TMHTopologySamplerClaimer forward declarations header |
| TMHTopologySamplerClaimer.hh | Header file for TMHTopologySamplerClaimer, to be used by the TopologyBroker for de novo folding of TM proteins |
| TopologyBroker.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| TopologyBroker.fwd.hh | |
| TopologyBroker.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| TopologyClaimer.cc | Top-class (Organizer) of the TopologyBroker mechanism |
| TopologyClaimer.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| TopologyClaimer.hh | |
| TopologyClaimerFactory.cc | |
| TopologyClaimerFactory.hh | |
| util.cc | |
| util.hh | |
| ► trajectory | |
| DbTrajectoryReader.cc | |
| DbTrajectoryReader.fwd.hh | |
| DbTrajectoryReader.hh | |
| DbTrajectoryWriter.cc | |
| DbTrajectoryWriter.fwd.hh | |
| DbTrajectoryWriter.hh | |
| ► unfolded_state_energy_calculator | |
| UnfoldedStateEnergyCalculatorJobDistributor.cc | Job distributor for UnfoldedStateEnergyCalculator |
| UnfoldedStateEnergyCalculatorJobDistributor.fwd.hh | Job distributor for UnfoldedStateEnergyCalculator |
| UnfoldedStateEnergyCalculatorJobDistributor.hh | Job distributor for UnfoldedStateEnergyCalculator |
| UnfoldedStateEnergyCalculatorMover.cc | UnfoldedStateEnergyCalculatorMover class definitions |
| UnfoldedStateEnergyCalculatorMover.fwd.hh | Forward declaration of UnfoldedStateEnergyCalculatorMover |
| UnfoldedStateEnergyCalculatorMover.hh | UnfoldedStateEnergyCalculatorMover class decalartion |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc | Job distributor for UnfoldedStateEnergyCalculator |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.fwd.hh | MPI Work Pool Job distributor for UnfoldedStateEnergyCalculator |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.hh | Job distributor for UnfoldedStateEnergyCalculator |
| UnfoldedStateEnergyCalculatorUtil.cc | Utility functions common to both UnfoldedStateEnergyCalculatorjob distributors |
| UnfoldedStateEnergyCalculatorUtil.hh | Utility functions common to both UnfoldedStateEnergyCalculatorjob distributors |
| ► viewer | |
| ConformationViewer.cc | |
| ConformationViewer.fwd.hh | |
| ConformationViewer.hh | |
| GraphicsState.hh | |
| marchingCubes.cc | |
| marchingCubes.hh | |
| SilentObserver.cc | |
| SilentObserver.fwd.hh | |
| SilentObserver.hh | |
| triangle.hh | |
| triangleIterator.cc | |
| triangleIterator.hh | |
| viewers.cc | |
| viewers.hh | |
| visualize.cc | 3-D visualizations of FoldTree and AtomTree in kinemage format |
| visualize.hh | 3-D visualizations of FoldTree and AtomTree in kinemage format |
| ► vip | |
| VIP_Mover.cc | Void Identification and Packing Mover. Identifies buried voids in an input structure and attempts to fill these using fixed backbone packing and the GOE energy |
| VIP_Mover.hh | |
| VIP_Report.cc | Prints information about changes implemented in vip mover |
| VIP_Report.hh | Class for reports from vip mover implementation |
| VIP_Utils.cc | Utility functions for VIP mover |
| VIP_Utils.hh | |
| ► wum | |
| DatabaseEntryWorkUnit.cc | A work unit that runs a database query, processes the results, and returns a string (presumably a database insert statement) |
| DatabaseEntryWorkUnit.fwd.hh | A work unit that runs a database query, processes the results, and returns a string (presumably a database insert statement) |
| DatabaseEntryWorkUnit.hh | A work unit base class that can serialize and deserialize a map representing a database row (keys are column names, values are column values) and a string representing a query to be executed by the master node upon completion of the workunit. This work unit should be treated as a pure virtual since no run() function is implemented |
| MoverList.cc | |
| MoverList.hh | |
| MPI_WorkUnitManager.cc | |
| MPI_WorkUnitManager.fwd.hh | MPI_WorkUnitManager base classes |
| MPI_WorkUnitManager.hh | |
| MPI_WorkUnitManager_Slave.cc | |
| MPI_WorkUnitManager_Slave.hh | |
| SilentStructStore.cc | |
| SilentStructStore.fwd.hh | SilentStructStore class forward declarations header |
| SilentStructStore.hh | |
| WorkUnitBase.cc | |
| WorkUnitBase.fwd.hh | WorkUnitBase base classes |
| WorkUnitBase.hh | |
| WorkUnitList.cc | |
| WorkUnitList.hh | |
| WorkUnitManager.cc | |
| WorkUnitManager.fwd.hh | WorkUnitManager base classes |
| WorkUnitManager.hh | |
| ► wum2 | |
| EndPoint.cc | Non MPI version of EndPoint |
| EndPoint.fwd.hh | Non MPI version of EndPoint This class is required because SingleNode role needs to use an EndPoint that is not MPI dependent (ie just a wrapper for 2 queues) |
| EndPoint.hh | Non-MPI version of EndPoint |
| MPI_EndPoint.cc | Handles communication between different roles in mpi |
| MPI_EndPoint.fwd.hh | Handles communication between different roles in mpi |
| MPI_EndPoint.hh | Handles communication between different roles in mpi |
| WorkUnit.cc | |
| WorkUnit.fwd.hh | Foward decls for base work unit (abstract) for wum2 and some commonly used derived work units |
| WorkUnit.hh | Base work unit (abstract) for wum2 and some commonly used derived work units |
| WUQueue.cc | Deque of WU with memory tracking |
| WUQueue.fwd.hh | Foward decls for WUQueue, deque of WU with memory tracking |
| WUQueue.hh | Deque of WU with memory tracking |
| WUQueueBuffer.cc | Foward decls for WUQueueBuffer, memory aware structure that links irecv and isend with their mpi::request status, so buffers are maintained until messages are sent/recvd |
| WUQueueBuffer.fwd.hh | Foward decls for WUQueueBuffer, memory aware structure that links irecv and isend with their mpi::request status, so buffers are maintained until messages are sent/recvd |
| WUQueueBuffer.hh | Memory aware structure that links irecv and isend with their mpi::request status, so buffers are maintained until messages are sent/recvd |
1.8.7