| ►Ncore | |
| ►Nscoring | |
| ►Nconstraints | |
| CChainbreakDistFunc | |
| ►Ndevel | |
| ►NObjexxFCL | Application level code for relax-type protocols |
| ►Nprotocols | The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP |
| ►Nabinitio | |
| ►Nabscript | |
| CAbscriptLoopCloserCM | |
| CAbscriptLoopCloserCMCreator | |
| ►CAbscriptMover | |
| CStageTracker | |
| CAbscriptMoverCreator | |
| CAbscriptStageMover | |
| CAtomPack | |
| CConstraintPreparer | |
| CConstraintPreparerCreator | |
| CFragmentCM | |
| CFragmentCMCreator | |
| CFragmentJumpCM | |
| CFragmentJumpCMCreator | |
| CJumpSampleData | |
| CJumpSampleDataCreator | |
| CResidueChunkSelection | |
| CRigidChunkCM | |
| CRigidChunkCMCreator | |
| CStagePreparer | |
| CStructPerturberCM | |
| CStructPerturberCMCreator | |
| C_HashEntry | |
| C_MergableEntries | |
| CAbrelaxApplication | Application level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT |
| CAbrelaxMover | |
| CAllResiduesChanged | (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values |
| CAlternativePairings | |
| CClassicAbinitio | |
| CComputeTotalDistCst | |
| CConstraintFragmentSampler | |
| CCoordinateConstraintKC | |
| CDomainAssembly | Insert fragments in a linker region. Very similar to what's in looprelax_main |
| CDomainAssemblyCreator | |
| CDoubleLayerKinematicAbinitio | |
| CFixTemplateJumpSetup | |
| CFoldConstraints | Extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints |
| CFragmentSampler | |
| ChConvergenceCheck | |
| CHedgeArchive | |
| CIterativeAbrelax | |
| CIterativeBase | |
| CIterativeCentroid | |
| CIterativeFullatom | |
| CJumpingFoldConstraintsWrapper | |
| CKinematicAbinitio | |
| CKinematicControl | |
| CKinematicTaskControl | |
| CLoopJumpFoldCst | |
| CMembraneAbinitio | |
| COrderSortPredicate | |
| CPairingStatEntry | |
| CPairingStatistics | |
| CPcaEvaluator | |
| CProtocol | |
| CResolutionSwitcher | |
| CShowViolation | |
| CStage1Sampler | |
| CStrandConstraints | |
| CStructureStore | |
| CTemplate | |
| CTemplateJumpSetup | |
| CTemplates | |
| ►Nanalysis | |
| CInterfaceAnalyzerMover | Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method |
| CInterfaceAnalyzerMoverCreator | |
| CInterfaceData | All interface data. Unless otherwise specified, they refer specifically to the interface |
| CLoopAnalyzerMover | |
| CPackStatMover | |
| CPeptideDeriverBasicStreamOutputter | Outputs a Peptiderive report to a stream in a basic, easily parsable format |
| CPeptideDeriverFilter | Implementation of the Peptiderive protocol - given a pose, it evaluates the binding energy of linear stretches, of given lengths, and indicates which of these contributes more than others to the interaction energy. It also reports on and optionally models cyclizable peptides |
| CPeptideDeriverFilterCreator | |
| CPeptideDeriverMarkdownStreamOutputter | Outputs a Markdown formatted Peptiderive report to a stream |
| CPeptideDeriverOutputter | Abstract base class for handling calculation outputs from PeptideDeriverFilter Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class |
| CPeptideDeriverOutputterContainer | Container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those |
| CPeptideDeriverPoseOutputter | Outputs poses at different points of the Peptiderive protocol, according to the given set of options |
| CPerResidueInterfaceData | All per residue interface data and residue averages. Interface Residues only |
| ►Nanchored_design | |
| CAnchor | Anchor class provides for the "anchor" part of a scaffold in anchored interface design |
| CAnchoredDesignMover | |
| CAnchoredPerturbMover | |
| CAnchoredRefineMover | |
| CAnchorMoversData | This data class wraps all the data needed for the AnchoredDesign movers |
| ►Nantibody | |
| ►Nclusters | |
| CBasicCDRClusterSet | Basic container class for CDRClusterSet |
| CCDRCluster | Simple class to hold and access CDRCluster info for a region of the pose |
| CCDRClusterEnumManager | Interface to this class is in AntibodyInfo. Should be a singleton |
| CCDRClusterFeatures | |
| CCDRClusterFeaturesCreator | |
| CCDRClusterMatcher | Simple class for identifying CDR clusters of an antibody or protein structure |
| CCDRClusterSet | Class that can determine a CDR Cluster, hold that information, and give it out when asked |
| CClusterData | Holds data for each cluster type |
| ►Nconstraints | |
| CParatopeEpitopeSiteConstraintMover | Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope. Will only add the constraint if not already present |
| CParatopeSiteConstraintMover | Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead |
| ►Ndesign | |
| CAntibodyDesignModeler | Basic Class that can run modeling for various protocols. Does not do any design. Mainly deprecated by AntibodyDesignMoverGenerator for the new class |
| CAntibodyDesignMover | Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application |
| CAntibodyDesignMoverGenerator | Generates pre-configured general MoverOPs for use in AntibodyDesign and modeling Helper functions for setting up FoldTrees. Can set the generated mover to apply, which will include the needed FoldTree and any changing of typeset. FoldTree stuff will eventually be refactored in favor of the TopologyBroker/Environment system |
| CAntibodyGraftDesignMover | This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. A 2011 Antibody Database is included in the rosetta datase. Up-to-date versions can be downloaded from |
| CAntibodySeqDesignMover | Designs antibody CDR structures using a variety of different methods. Main methods involve using cluster-based sequence probability statistics and conservative design strategies to limit unknown structural effects caused by aggressive design. Uses North_AHO numbering and cluster-based design. Part of Rosetta Antibody Designer. -> Will be replaced by SnugDesign Mover in the application, but still useful in it's own right |
| CAntibodySeqDesignTFCreator | Create a TaskFactory or individual TaskOperations based on a set of options These options are mainly for per-CDR and per-framework control of sequence design |
| CCDRGraftDesignOptions | |
| CCDRGraftDesignOptionsParser | |
| CCDRSeqDesignOptions | |
| CCDRSeqDesignOptionsParser | |
| CConservativeDesignOperation | A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations |
| CPDBNumbering | Super-basic numbering struct |
| CResidueProbDesignOperation | A TaskOperation that allows amino acids at designable positions through a set of aa probabilities |
| CAb_TemplateInfo | Specifically for AntibodyModeling protocol templates. Not for general use |
| CAntibodyDatabaseManager | Class responsible for loading information from the AntibodyDatabase |
| CAntibodyEnumManager | Interface to this class is in AntibodyInfo |
| CAntibodyFeatures | Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics |
| CAntibodyFeaturesCreator | Creator for the HBondParameterFeatures class |
| CAntibodyInfo | This class is used to get all relevant information you would need when dealing with an antibody |
| CAntibodyModelerProtocol | |
| CAntibodyNumbering | |
| CAntibodyNumberingParser | Class responsible for reading database Numbering Scheme definitions and their transforms from the database |
| CCDRPose | |
| CCDRSetOptions | Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database |
| CCDRSetOptionsParser | Parses CDRSetOptions for a single CDR at a time from a simple instruction file |
| CCDRsMinPackMin | |
| CCloseOneCDRLoop | Closes only one CDR onto a framework |
| CFrameWork | |
| CGraftCDRLoopsProtocol | |
| CGraftedStemOptimizer | Grafts only one CDR onto a framework |
| CGraftOneCDRLoop | Grafts only one CDR onto a framework |
| CH3CterInsert | H3 CDR, Fragment Insertion and CCD |
| CH3PerturbCCD | |
| CH3RefineCCD | |
| CLHRepulsiveRamp | |
| CLHRepulsiveRampLegacy | |
| CLHSnugFitLegacy | |
| CModelCDRH3 | Ab initio modeling of CDR H3 loop |
| CParatopeMetric | Convenience struct for passing around paratope data, including individual data for cdrs. CDRs not present default to 0. Templates are used mainly to have Size/ Real or string values |
| CPDBLandmark | Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions |
| CRefineBetaBarrel | |
| CRefineOneCDRLoop | |
| CRefineOneCDRLoopCentroid | |
| CSnugDock | MoveSet step of Snugdock as described in: |
| CSnugDockProtocol | |
| ►Nantibody_legacy | |
| CAntibody | Antibody definition |
| CAntibodyModeler | |
| CCDRH3Modeler | Ab initio modeling of CDR H3 loop |
| CCloseOneMover | Closes only one CDR onto a framework |
| CGraftMover | Grafts a series of CDR onto a framework |
| CGraftOneMover | Grafts only one CDR onto a framework |
| CLoopRlxMover | Closes only one CDR onto a framework |
| ►Nbackrub | |
| CBackrubMover | Class for applying backrub moves to arbitrary protein segments |
| CBackrubMoverCreator | |
| CBackrubSegment | Class for holind information about individual backrub segments |
| CBackrubSidechainMover | |
| CBackrubSidechainMoverCreator | |
| ►Nboinc | |
| CBoinc | |
| CBoincCurrentPoseObserver | |
| CBoincSharedMemory | |
| ►Nbranch_angle | |
| CBranchAngleOptimizer | |
| CBranchCoef1 | Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors |
| CBranchCoef2 | Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors |
| CBranchParam1 | Class to store bond angle energy parameters around a single atom atom with three bonded neighbors |
| CBranchParam2 | Class to store bond angle energy parameters around a single atom atom with four bonded neighbors |
| ►Ncanonical_sampling | Algorithms for rigorously sampling native state ensembles. See disclaimer in detailed description |
| ►Nmc_convergence_checks | |
| CDataBuffer | |
| CEXCN_Heat_Converged | |
| CEXCN_Pool_Converged | |
| CHeat_ConvergenceCheck | |
| CHierarchicalLevel | |
| CHPool_RMSD | |
| CMPIBPool_RMSD | |
| CMPIHPool_RMSD | |
| CMPIPool_RMSD | |
| CPool_ConvergenceCheck | |
| CPool_Evaluator | |
| CPool_RMSD | |
| CPoolData | |
| CTransferBuffer | |
| ►CAsyncMPITemperingBase | |
| CExchangeRequest | |
| CBiasedMonteCarlo | |
| ►CBiasEnergy | |
| CHistogram | |
| CCanonicalSamplingMover | |
| CDbTrajectoryReader | |
| ►CDbTrajectoryRecorder | Record a trajectory to an SQL database |
| CFrame | Helper struct used store cached poses |
| CDbTrajectoryRecorderCreator | RosettaScripts factory for DbTrajectoryRecorder |
| CFixedTemperatureController | Maintain a constant temperature |
| CHamiltonianExchange | |
| CHamiltonianExchangeCreator | RosettaScripts factory for HamiltonianExchange |
| CMetricRecorder | Periodically output miscellaneous information |
| CMetricRecorderCreator | RosettaScripts factory for MetricRecorder |
| CMetropolisHastingsMover | Manage the main loop of a canonical Monte Carlo simulation |
| CMetropolisHastingsMoverCreator | RosettaScripts factory for MetropolisHastingsMover |
| CMultiTemperatureTrialCounter | Keep track of trial statistics for any number of replicas |
| CParallelTempering | |
| CParallelTemperingCreator | RosettaScripts factory for ParallelTempering |
| CPatchOperation | |
| CPDBTrajectoryRecorder | Record a trajectory to the PDB file format |
| CPDBTrajectoryRecorderCreator | RosettaScripts factory for PDBTrajectoryRecorder |
| CProgressBarObserver | Print an progress bar that updated on each iteration |
| CProgressBarObserverCreator | RosettaScripts factory for ProgressBarObserver |
| CSidechainMetropolisHastingsMover | Run a sidechain-only canonical Monte Carlo simulation |
| CSidechainMetropolisHastingsMoverCreator | RosettaScripts factory for SidechainMetropolisHastingsMover |
| CSilentTrajectoryRecorder | Record a trajectory to the rosetta-specific silent file format |
| CSilentTrajectoryRecorderCreator | RosettaScripts factory for SilentTrajectoryRecorder |
| CSimulatedTempering | |
| CSimulatedTemperingCreator | RosettaScripts factory for SimulatedTempering |
| CTemperatureController | Base class for controlling the temperature of a simulation |
| CTemperingBase | Base class for tempering Monte Carlo optimizations |
| CThermodynamicMover | Base class for moves that can obey detailed balance |
| CThermodynamicObserver | Base class for reporting and recording data from a simulation |
| CTrajectoryRecorder | Base class for recording a simulation trajectory |
| CTrialCounterObserver | Record the acceptance rate for every type of move attempted |
| CTrialCounterObserverCreator | RosettaScripts factory for TrialCounterObserver |
| CWTEBiasEnergy | |
| ►Ncartesian | |
| CCartesianAtom | |
| CMD_Angle | |
| CMD_Bond | |
| CMD_HarmonicDihedral | |
| CMolecularDynamics | |
| ►Ncheckpoint | |
| CCheckPointer | |
| CFileBuffer | |
| CTimer | : singleton checkpoint timer class |
| ►Ncluster | |
| CAPCluster | Public interface for doing affinity propagation clustering |
| CAssignToClustersMover | |
| CCluster | |
| CClusterBase | |
| CClusterPhilStyle | |
| CClusterPhilStyle_Loop | |
| CClusterPhilStyle_PoseReporter | |
| CDataPoint | Data structure for one input data point for affinity propagation clustering |
| CEnsembleConstraints | |
| CEnsembleConstraints_Simple | |
| CExemplar | Data structure for one similarity measurement (s_ik) for affinity propagation clustering |
| CGatherPosesMover | |
| ►Ncoarse_rna | |
| CCoarseRNA_DeNovoProtocol | The RNA de novo structure modeling protocol |
| CCoarseRNA_Fragments | |
| CCoarseRNA_LoopCloser | The RNA de novo structure modeling protocol |
| CSourcePositions | |
| ►Ncomparative_modeling | |
| ►Nfeatures | |
| CResidueFeature | |
| CResidueFeatureFactory | |
| CSSFeature | |
| CTorsionFeature | |
| CAlign_RmsdEvaluator | |
| CAlign_RotamerEvaluator | |
| CAlignmentCluster | |
| CAlignmentClustering | |
| CAlignmentSet | |
| CAlignRmsdTargetEvaluatorCreator | Creator for the AlignRmsdTargetEvaluatorCreator class |
| CExtraThreadingMover | |
| CGenericJobInputter | |
| CGenericJobInputterCreator | |
| CIgnoreSubsetConstraintSet | |
| CLoopRelaxMover | |
| CLoopRelaxMoverCreator | |
| CLoopRelaxThreadingMover | |
| CMultiThreadingMover | |
| CPartialThreadingMover | |
| CRecoverSideChainsMover | |
| CStealLigandMover | |
| CStealSideChainsMover | |
| CThreadingJob | |
| CThreadingJobInputter | |
| CThreadingJobInputterCreator | |
| CThreadingMover | |
| ►Nconstraints_additional | |
| CAmbiguousMultiConstraint | |
| CBindingSiteConstraint | |
| CBindingSiteConstraintCreator | Mover creator for the BindingSiteConstraint constraint |
| CCombinedConstraintEvaluator | |
| CCombinedConstraintEvaluatorCreator | Creator for the CombinedConstraintsEvaluatorCreator class |
| CCOMCoordinateConstraint | |
| CConstraintEvaluator | |
| CConstraintEvaluatorCreator | Creator for the ConstraintsEvaluatorCreator class |
| CMaxSeqSepConstraintSet | |
| CNamedAtomPairConstraintCreator | This class can be used to replace the standard AtomPairConstraintsCreator; see BrokerMain.cc for an example |
| CSequenceCoupling1BDConstraint | |
| CSequenceCoupling1BDConstraintCreator | Mover creator for the SequenceCoupling1BDconstraint |
| CSequenceCouplingConstraint | |
| CSequenceCouplingConstraintCreator | Mover creator for the SequenceCouplingconstraint |
| ►Ncontact_map | |
| CContact | Simple class representing a contact between two atoms |
| CContactMap | |
| CContactMapCreator | |
| CContactPartner | Simple class that holds the information on an atom involved in a contact |
| ►Ncryst | |
| CFitBfactorsMover | |
| CFitBfactorsMoverCreator | |
| CLoadDensityMapMover | |
| CLoadDensityMapMoverCreator | |
| CRecomputeDensityMapMover | |
| CRecomputeDensityMapMoverCreator | |
| CSetCrystWeightMover | |
| CSetCrystWeightMoverCreator | |
| CSetRefinementOptionsMover | |
| CSetRefinementOptionsMoverCreator | |
| CTagPoseWithRefinementStatsMover | |
| CTagPoseWithRefinementStatsMoverCreator | |
| CUpdateSolventMover | |
| CUpdateSolventMoverCreator | |
| ►Ncyclic_peptide | |
| CCreateAngleConstraint | |
| CCreateAngleConstraintCreator | |
| CCreateDistanceConstraint | |
| CCreateDistanceConstraintCreator | |
| CCreateTorsionConstraint | |
| CCreateTorsionConstraintCreator | |
| CDeclareBond | |
| CDeclareBondCreator | |
| CPeptideStubMover | |
| CPeptideStubMoverCreator | |
| ►Nddg | |
| CddGMover | |
| ►NddG | |
| CddGData | |
| ►Ndenovo_design | |
| ►Nfilters | |
| CExposedHydrophobicsFilter | |
| CExposedHydrophobicsFilterCreator | |
| ►Ndesign_opt | |
| CGreedyOptMutationMover | |
| CGreedyOptMutationMoverCreator | |
| CParetoOptMutationMover | |
| CParetoOptMutationMoverCreator | |
| CPointMutationCalculator | |
| ►Ndna | |
| CDesignProteinBackboneAroundDNA | |
| CDesignProteinBackboneAroundDNACreator | |
| CDNABase | |
| CDNABasepair | |
| CDNABasestep | |
| CDnaChains | |
| CDnaDesignDef | Command-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience |
| CDnaInterfaceFinder | |
| CDnaInterfaceMinMover | |
| CDnaInterfaceMinMoverCreator | |
| CDnaInterfaceMultiStateDesign | Wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework |
| CDnaInterfaceMultiStateDesignCreator | |
| CDnaInterfacePacker | |
| CDnaInterfacePackerCreator | |
| CDnaNeighbor | |
| CDNAParameters | |
| CDnaPosition | |
| CPDBOutput | |
| CPositionType | Basic struct for remembering position/type information before/during/after design |
| CRestrictDesignToProteinDNAInterface | |
| CRestrictDesignToProteinDNAInterfaceCreator | |
| CResTypeSequence_lt | |
| CReversion | |
| CRotamerDNAHBondFilter | |
| CSeparateDnaFromNonDna | |
| CSeparateDnaFromNonDnaCreator | |
| CWatsonCrickRotamerCouplings | |
| CWatsonCrickRotamerCouplingsCreator | |
| ►Ndocking | |
| ►Nmembrane | |
| CMPDockingMover | Docks two proteins together in the membrane bilayer |
| CMPDockingMoverCreator | Mover Creator |
| CMPDockingSetupMover | Setup for MPDocking |
| CMPDockingSetupMoverCreator | Mover Creator |
| ►Nstateless | |
| CSaneDockingProtocol | |
| CConformerSwitchMover | This mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction |
| CConformerSwitchMoverCreator | |
| CDockingEnsemble | This mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction |
| CDockingEnsemblePrepackProtocol | |
| CDockingHighRes | |
| CDockingHighResFilter | High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given (2) interface_score must be negative |
| CDockingHighResLegacy | This mover does the high resolution refinement stage of the RosettaDock algorithm |
| CDockingInitialPerturbation | This mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options |
| CDockingInitialPerturbationCreator | |
| CDockingLowRes | |
| CDockingLowResEnsemble | |
| CDockingLowResFilter | Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners, (2) clashes are limited so partners are not overlapping and (3) constraints, if present, are met |
| CDockingPrepackProtocol | |
| CDockingProtocol | This is the standard RosettaDock protocol |
| CDockingProtocolCreator | |
| CDockingSlideIntoContact | Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently) |
| CDockMCMCycle | |
| CDockMCMProtocol | |
| CDockMinMover | |
| CDockSetupMover | Allows docking using simulated or parallel tempering |
| CDockSetupMoverCreator | |
| CDockTaskFactory | |
| CEllipsoidalRandomizationMover | |
| CFaDockingSlideIntoContact | Slides docking partners together by monitoring fa_rep |
| CInterfaceSidechainMinMover | |
| CRigidBodyInfo | |
| CSidechainMinMover | |
| CTemperedDocking | Allows docking using simulated or parallel tempering |
| CTemperedDockingCreator | |
| ►Ndomain_assembly | |
| CAddAssemblyConstraints | |
| CAssembleLinkerMover | |
| CCombineChainsMover | |
| CPostDockAssemblyScorer | |
| ►Nelectron_density | |
| CBfactorFittingMover | Mover to fit B factors |
| CBfactorFittingMoverCreator | |
| CBfactorMultifunc | Bfactor multifunc |
| CDensityMorphingMover | |
| CDensityMorphingMoverCreator | |
| CReportFSC | Scale density map intensities to match a pose's |
| CReportFSCCreator | |
| CScaleMapIntensities | Scale density map intensities to match a pose's |
| CScaleMapIntensitiesCreator | |
| CSetupForDensityScoringMover | |
| CSetupForDensityScoringMoverCreator | |
| ►Nenvironment | |
| ►Nclaims | |
| CClaimStrength | |
| CCutBiasClaim | |
| CCutBiasElement | |
| CCutElement | |
| CDOFElement | |
| CEnvClaim | |
| CEnvLabelSelector | |
| CJumpClaim | |
| CJumpElement | |
| CResidueElement | |
| CTorsionClaim | |
| CVirtResClaim | |
| CXYZClaim | |
| CAutoCutData | |
| CAutoCutDataCreator | |
| CClientMover | |
| CComparator | A brief comparator object initialized with the correct strength accessor for reuse of setup_passports |
| CCoMTrackerCM | |
| CCoMTrackerCMCreator | |
| CDofUnlock | |
| ►CEnvClaimBroker | |
| CBrokeredJumpData | Inner class for tracking the properties of jumps that've been brokered |
| CBrokerResult | |
| CEnvironment | |
| CEnvMover | |
| CEnvMoverCreator | |
| CEXCN_Env_Passport | |
| CEXCN_Env_Security_Exception | |
| CProtectedConformation | |
| CScriptCM | |
| CScriptCMCreator | |
| ►Nenzdes | |
| CAddLigandMotifRotamers | |
| CAddLigandMotifRotamersOperationCreator | |
| CAddOrRemoveMatchCsts | A simple wrapper to get the functionality in EnzConstraintIO into mover format |
| CAddOrRemoveMatchCstsCreator | |
| CAddRigidBodyLigandConfs | |
| CAddRigidBodyLigandConfsCreator | |
| CApplyRandomStoredRBConf | For every ligand that has additional stored rb conformations in the enzdes cacheable observer, the one currently in the pose gets exchanged with a random stored one |
| CBackboneSampler | |
| CBackboneSamplerCreator | |
| CDesignVsNativeComparison | Class that holds a bunch of native poses and compares them |
| CDetectProteinLigandInterface | Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile |
| CDetectProteinLigandInterfaceOperationCreator | |
| CDiffAtomSasaFilter | |
| CDiffAtomSasaFilterCreator | |
| CDiversifyStoredRBConfs | Uses a docking mover to diversiy the stored confs until they're all min_rms_ away from each other note: no scorefunction used here |
| CEnzdesBaseProtocol | |
| CEnzdesConstraintReporter | |
| CEnzdesFixBBProtocol | |
| CEnzdesFlexBBProtocol | |
| CEnzdesFlexibleRegion | |
| CEnzdesJobInputter | |
| CEnzdesJobInputterCreator | |
| CEnzdesJobOutputter | For now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb |
| CEnzdesJobOutputterCreator | |
| CEnzdesScorefileFilter | |
| CEnzdesScorefileFilterCreator | |
| CEnzRepackMinimize | |
| CEnzRepackMinimizeCreator | |
| CEnzScoreFilter | |
| CEnzScoreFilterCreator | |
| CGenerateStoredRBConfs | Generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used |
| CLigBurialFilter | |
| CLigBurialFilterCreator | |
| CLigDSasaFilter | |
| CLigDSasaFilterCreator | |
| CLigInterfaceEnergyFilter | |
| CLigInterfaceEnergyFilterCreator | |
| CMinimizeStoredRBConfs | Rotamer trials/minimizes each of the ligand conformations stored in the enzdes cacheable observer and overwrites them with the minimized position. if the new, minimized position is too close to one that already exists, a random small perturbation is applied to ensure diversity note: only jump minimization |
| CModifyStoredRBConfs | Virtual base class that has some common functionality |
| CPackRotamersMoverPartGreedy | Mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer |
| CPackRotamersMoverPartGreedyCreator | |
| CPoseFoundResiduesCombination | Helper class to process and output the different found poses |
| CPredesignPerturbMover | |
| CPredesignPerturbMoverCreator | |
| CProteinLigandInterfaceUpweighter | Class to alter a packer task to speficially upweight the protein-ligand interaction energies |
| CProteinLigandInterfaceUpweighterOperationCreator | |
| CRemoveLigandFilter | |
| CRemoveLigandFilterCreator | |
| CRepackLigandSiteWithoutLigandMover | Class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues |
| CRepackWithoutLigandFilter | |
| CRepackWithoutLigandFilterCreator | |
| CResidueConformerFilter | Filter that figures out which rotamer of a given rotamer lib is in the pose at apply time, and can be used to filter on it. supposed to be used for ligands, and for now only tested for them, but should also work with any other residue. can be used for example in specificity redesign, if one wants to divide up a bunch of designs according to the orientation in which they bind the ligand |
| CResidueConformerFilterCreator | |
| CSecondaryMatchProtocol | |
| CSetCatalyticResPackBehavior | Queries the pose cst cache for the catalytic residues, and sets the behavior for them as specified in the cstfile |
| CSetCatalyticResPackBehaviorCreator | |
| CUpdateEnzdesHeaderMover | Mover that updates the enzdes pdb header, for use in cases where catalytic residues may be designed |
| CUpdateEnzdesHeaderMoverCreator | |
| CValueEvaluator | Tiny helper struct for EnzdesScoreFileFilter |
| ►Nevaluation | |
| CAlignEvaluator | |
| CEvaluatorCreator | The Creator class is responsible for creating a particular mover class |
| CEvaluatorFactory | Create Evaluator Reporters |
| CEvaluatorRegistrator | This templated class will register an instance of an EvaluatorCreator (class T) with the EvaluatorFactory. It will ensure that no EvaluatorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CMetaPoseEvaluator | |
| CPCA | |
| CPoseEvaluator | |
| CSingleValuePoseEvaluator | |
| CSingleValuePoseEvaluator_Size | |
| CSingleValuePoseEvaluator_SSize | |
| CTimeEvaluator | |
| ►Nfarna | |
| CBasePairStep | |
| CBasePairStepLibrary | |
| CBasePairStepSequence | |
| CBasePairType | |
| CChunkSet | |
| CFragmentLibrary | |
| CFullAtomRNA_Fragments | |
| CMultipleDomainMover | The RNA de novo structure modeling protocol |
| CRNA_ChunkLibrary | |
| CRNA_DeNovoProtocol | The RNA de novo structure modeling protocol |
| CRNA_FragmentMover | The RNA de novo structure modeling protocol |
| CRNA_Fragments | |
| CRNA_JumpLibrary | |
| CRNA_LoopCloser | The RNA de novo structure modeling protocol |
| CRNA_Minimizer | The RNA de novo structure modeling protocol |
| CRNA_Pairing | |
| CRNA_PairingTemplate | |
| CRNA_Relaxer | The RNA de novo structure modeling protocol |
| CRNA_SecStructInfo | Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! |
| CRNA_StructureParameters | |
| CTorsionSet | |
| ►Nfeatures | |
| ►NhelixAssembly | |
| CConcurrencyTest | |
| CConcurrencyTestCreator | Creator for the HelixBundleFeatures class |
| CFragmentPair | |
| CHelicalFragment | |
| CHelixBundleFeatures | |
| CHelixBundleFeaturesCreator | Creator for the HelixBundleFeatures class |
| ►Nstrand_assembly | |
| CSandwichFeatures | |
| CSandwichFeaturesCreator | Creator for the SandwichFeatures class |
| CSandwichFragment | |
| CStrandBundleFeatures | |
| CStrandBundleFeaturesCreator | Creator for the StrandBundleFeatures class |
| CStrandFragment | |
| CAtomAtomPairFeatures | |
| CAtomAtomPairFeaturesCreator | Creator for the AtomAtomPairFeatures class |
| CAtomInResidueAtomInResiduePairFeatures | |
| CAtomInResidueAtomInResiduePairFeaturesCreator | Creator for the AtomInResidueAtomInResiduePairFeatures class |
| CAtomTypesFeatures | |
| CAtomTypesFeaturesCreator | Creator for the AtomTypesFeatures class |
| CBatchFeatures | |
| CBetaTurnDetection | |
| CBetaTurnDetectionFeatures | |
| CBetaTurnDetectionFeaturesCreator | Creator for the BetaTurnDetectionFeatures class |
| CChargeChargeFeatures | |
| CChargeChargeFeaturesCreator | Creator for the ChargeChargeFeatures class |
| CDatabaseFilter | |
| CDatabaseJobInputter | |
| CDatabaseJobInputterCreator | |
| CDatabaseJobOutputter | |
| CDatabaseJobOutputterCreator | |
| CDdGFeatures | |
| CDdGFeaturesCreator | Creator for the DdGFeatures class |
| CFeaturesReporter | |
| CFeaturesReporterCreator | The Creator class is responsible for creating a particular mover class |
| CFeaturesReporterFactory | Create Features Reporters |
| CFeaturesReporterRegistrator | This templated class will register an instance of an FeaturesReporterCreator (class T) with the FeaturesReporterFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CGeometricSolvationFeatures | |
| CGeometricSolvationFeaturesCreator | Creator for the GeometricSolvationFeatures class |
| CHBondFeatures | |
| CHBondFeaturesCreator | Creator for the HBondFeatures class |
| CHBondParameterFeatures | |
| CHBondParameterFeaturesCreator | Creator for the HBondParameterFeatures class |
| CHelixCapFeatures | |
| CHelixCapFeaturesCreator | Creator for the HelixCapFeaturesCreator class |
| CInterfaceFeatures | Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS |
| CInterfaceFeaturesCreator | Creator for the HBondParameterFeatures class |
| CJobDataFeatures | |
| CJobDataFeaturesCreator | Creator for the JobDataFeatures class |
| CLoopAnchorFeatures | |
| CLoopAnchorFeaturesCreator | Creator for the LoopAnchorFeatures class |
| COrbitalsFeatures | |
| COrbitalsFeaturesCreator | Creator for the OrbitalsFeatures class |
| CPairFeatures | |
| CPairFeaturesCreator | Creator for the PairFeatures class |
| CPdbDataFeatures | |
| CPdbDataFeaturesCreator | Creator for the PdbDataFeatures class |
| CPoseCommentsFeatures | |
| CPoseCommentsFeaturesCreator | Creator for the PoseCommentsFeatures class |
| CPoseConformationFeatures | |
| CPoseConformationFeaturesCreator | Creator for the PoseConformationFeatures class |
| CProteinBackboneAtomAtomPairFeatures | |
| CProteinBackboneAtomAtomPairFeaturesCreator | Creator for the ProteinBackboneAtomAtomPairFeatures class |
| CProteinBackboneTorsionAngleFeatures | |
| CProteinBackboneTorsionAngleFeaturesCreator | Creator for the ProteinBackboneTorsionAngleFeatures class |
| CProteinBondGeometryFeatures | |
| CProteinBondGeometryFeaturesCreator | Creator for the ProteinBondGeometryFeatures class |
| CProteinResidueConformationFeatures | |
| CProteinResidueConformationFeaturesCreator | Creator for the ProteinResidueConformationFeatures class |
| CProteinRMSDFeatures | |
| CProteinRMSDFeaturesCreator | Creator for the ProteinRMSDFeatures class |
| CProteinRMSDNoSuperpositionFeatures | |
| CProteinRMSDNoSuperpositionFeaturesCreator | Creator for the ProteinRMSDNoSuperpositionFeatures class |
| CProteinSilentReport | |
| CProtocolFeatures | |
| CRadiusOfGyrationFeatures | |
| CRadiusOfGyrationFeaturesCreator | Creator for the RadiusOfGyrationFeatures class |
| CReport | |
| CReportToDB | |
| CReportToDBCreator | |
| CResidueBurialFeatures | |
| CResidueBurialFeaturesCreator | Creator for the ResidueBurialFeatures class |
| CResidueConformationFeatures | |
| CResidueConformationFeaturesCreator | Creator for the ResidueConformationFeatures class |
| CResidueFeatures | |
| CResidueFeaturesCreator | Creator for the ResidueFeatures class |
| CResidueGridScoresFeatures | |
| CResidueGridScoresFeaturesCreator | Creator for the ResidueGridScoresFeatures class |
| CResidueScoresFeatures | |
| CResidueScoresFeaturesCreator | Creator for the ResidueScoresFeatures class |
| CResidueSecondaryStructureFeatures | |
| CResidueSecondaryStructureFeaturesCreator | Creator for the ResidueSecondaryStructureFeatures class |
| CResidueTotalScoresFeatures | |
| CResidueTotalScoresFeaturesCreator | Creator for the ResidueTotalScoresFeatures class |
| CResidueTypesFeatures | |
| CResidueTypesFeaturesCreator | Creator for the ResidueTypesFeatures class |
| CRotamerBoltzmannWeightFeatures | |
| CRotamerBoltzmannWeightFeaturesCreator | Creator for the RotamerBoltzmannWeightFeatures class |
| CRotamerFeatures | |
| CRotamerFeaturesCreator | Creator for the RotamerFeatures class |
| CRotamerInitializer | |
| CRotamerRecoveryFeatures | |
| CRotamerRecoveryFeaturesCreator | Creator for the RotamerRecoveryFeatures class |
| CRuntimeFeatures | |
| CRuntimeFeaturesCreator | |
| CSaltBridgeFeatures | |
| CSaltBridgeFeaturesCreator | Creator for the SaltBridgeFeatures class |
| CScoreFunctionFeatures | |
| CScoreFunctionFeaturesCreator | Creator for the ScoreFunctionFeatures class |
| CScoreTypeFeatures | |
| CScoreTypeFeaturesCreator | Creator for the ScoreTypeFeatures class |
| CScreeningFeatures | |
| CScreeningFeaturesCreator | Creator for the ScreeningFeaturesCreator class |
| CSecondaryStructureSegment | |
| CSecondaryStructureSegmentFeatures | |
| CSecondaryStructureSegmentFeaturesCreator | Creator for the SecondaryStructureSegmentFeaturesCreator class |
| CSmotifFeatures | |
| CSmotifFeaturesCreator | Creator for the SmotifFeaturesCreator class |
| CStructureFeatures | |
| CStructureFeaturesCreator | Creator for the StructureFeatures class |
| CStructureScoresFeatures | |
| CStructureScoresFeaturesCreator | Creator for the StructureScoresFeatures class |
| ►CTaskOperationFeatures | |
| CTaskop_id_name_factory_ | |
| CTaskOperationFeaturesCreator | Creator for the TaskOperationFeatures class |
| CTopCountOfAllInputs | |
| CTopCountOfEachInput | |
| CTopPercentOfAllInputs | |
| CTopPercentOfEachInput | |
| CTotalScoreFeatures | |
| CTotalScoreFeaturesCreator | |
| CTrajectoryMapFeatures | |
| CTrajectoryMapFeaturesCreator | Creator for the TrajectoryMapFeatures class |
| CTrajectoryReportToDB | |
| CTrajectoryReportToDBCreator | |
| CUnrecognizedAtomFeatures | |
| CUnrecognizedAtomFeaturesCreator | Creator for the UnrecognizedAtomFeatures class |
| CWaterFeatures | |
| CWaterFeaturesCreator | Creator for the WaterFeatures class |
| ►Nfibril | |
| CSetupForFibrilMover | |
| ►Nfilters | |
| CCalculatorFilter | |
| CCalculatorFilterCreator | |
| CCombinedFilter | Used to combine multiple seperate filters into a single filter value |
| CCombinedFilterCreator | |
| CCompoundFilter | Used to define a compound logical statement involving other filters with AND, OR and XOR |
| CCompoundFilterCreator | |
| CContingentFilter | |
| CContingentFilterCreator | |
| CFalseFilter | |
| CFalseFilterCreator | |
| CFilter | |
| CFilterCollection | Wrapper-class that contains a vector1 of Filters |
| CFilterCreator | Abstract base class for a Filter factory; the Creator class is responsible for creating a particular filter class |
| CFilterFactory | |
| CFilterRegistrator | This templated class will register an instance of an FilterCreator (class T) with the FilterFactory. It will ensure that no FilterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CIfThenFilter | Evaluate to a value contingent on the evaluation of another filter |
| CIfThenFilterCreator | |
| CMoveBeforeFilter | Apply a sub-mover prior to calculating a filter value |
| CMoveBeforeFilterCreator | |
| CReplicateFilter | |
| CReplicateFilterCreator | |
| CStochasticFilter | |
| CStochasticFilterCreator | |
| CTimeFilter | |
| CTimeFilterCreator | |
| CTrueFilter | |
| CTrueFilterCreator | |
| ►Nfldsgn | |
| ►Nfilters | |
| CCoreDunbrackFilter | |
| CCoreDunbrackFilterCreator | |
| CFragQualFilter | |
| CFragQualFilterCreator | |
| CHelixKinkFilter | |
| CHelixKinkFilterCreator | |
| CHelixPairingFilter | |
| CHelixPairingFilterCreator | |
| CHSSTripletFilter | |
| CHSSTripletFilterCreator | |
| CInterlockingAromaFilter | |
| CInterlockingAromaFilterCreator | |
| CNcontactsFilter | |
| CNcontactsFilterCreator | |
| CParallelBetaPairingPreferenceFilter | |
| CParallelBetaPairingPreferenceFilterCreator | |
| CSecondaryStructureCountFilter | |
| CSecondaryStructureCountFilterCreator | |
| CSecondaryStructureFilter | |
| CSecondaryStructureFilterCreator | |
| CSecondaryStructureHasResidueFilter | |
| CSecondaryStructureHasResidueFilterCreator | |
| CSheetTopologyFilter | |
| CSheetTopologyFilterCreator | |
| ►Npotentials | |
| ►Nsspot | |
| CHSPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CNatbiasHelicesSheetPotential | |
| CNatbiasHelixPairPotential | |
| CNatbiasSecondaryStructureEnergy | NatbiasSecondaryStructureEnergy |
| CNatbiasSecondaryStructureEnergyCreator | |
| CNatbiasStrandPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CSSPairPotential | Secondary structure scoring cut from classic rosetta structure.h/structure.cc |
| CAACompositionEnergy | AACompositionEnergy |
| CAACompositionEnergyCreator | |
| CSetAACompositionPotential | |
| CSetAACompositionPotentialCreator | |
| CSetSecStructEnergies | |
| CSetSecStructEnergiesCreator | |
| ►Ntopology | |
| CBB_Pos | |
| CBetaAlphaBetaMotif | |
| CBetaAlphaBetaMotifSet | |
| CDimerPairing | |
| CDimerPairings | |
| CHelix | |
| CHelixPairing | |
| CHelixPairingSet | |
| CHSSTriplet | |
| CHSSTripletSet | |
| CLoop | |
| CSheet | |
| CSheetFoldTypeManager | |
| CSheetSet | |
| CSS_Base | |
| CSS_Info2 | |
| CStrand | |
| CStrandPairing | |
| CStrandPairingSet | |
| CBluePrintBDR | |
| CBluePrintBDRCreator | |
| CCircularPermutation | |
| CCircularPermutationCreator | |
| CMatchResidues | |
| CMatchResiduesMover | |
| CMatchResiduesMoverCreator | |
| CMyAtom | |
| CNcontactsCalculator | |
| CSheetConstraintsRCG | |
| CSheetCstGeneratorCreator | |
| ►Nflexpack | |
| ►Nannealer | |
| CFlexbbSimAnnealer | |
| ►Ninteraction_graph | |
| CFlexbbEdge | |
| CFlexbbIGFactory | |
| CFlexbbInteractionGraph | |
| CFlexbbNode | |
| CFlexbbSparseMatrixIndex | |
| CMinimalistFlexbbEdge | |
| CMinimalistFlexbbInteractionGraph | |
| CMinimalistFlexbbNode | |
| COTFFlexbbEdge | |
| COTFFlexbbInteractionGraph | |
| COTFFlexbbNode | |
| CPrecomputedFlexbbInteractionGraph | |
| ►Nrotamer_set | |
| CFlexbbRotamerSet | |
| CFlexbbRotamerSets | |
| CFlexPacker | |
| COtherContextScoreFunction | |
| ►Nflexpep_docking | |
| CFlexPepDockingAbInitio | |
| CFlexPepDockingFlags | |
| CFlexPepDockingLowRes | |
| CFlexPepDockingPoseMetrics | |
| CFlexPepDockingProtocol | |
| CFlexPepDockingProtocolCreator | |
| ►Nfloppy_tail | |
| CFloppyTailMover | FloppyTail mover |
| ►Nflxbb | |
| CCombinedTaskOperation | |
| CDesignTask | |
| CDesignTask_Layer | |
| CDesignTask_Normal | |
| CFilterStructs | |
| CFilterStructs_Packstat | |
| CFilterStructs_TotalCharge | |
| CFlxbbDesign | |
| CFlxbbDesignCreator | |
| CFlxbbDesignPack | |
| CInterlockAroma | |
| CInterlockAromaCreator | |
| CLayerDesignOperation | |
| CLayerDesignOperationCreator | |
| ►Nforge | |
| ►Nbuild | |
| CBridge | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| CBuildInstruction | Tracks modifications to be made and is capable of making residue length changes on a Pose |
| CBuildManager | Container for managing BuildInstructions |
| CConnectRight | Instruction to connect one Pose onto the right side of another |
| CCountFromLeft | Count starting from interval().left in a BuildInstruction |
| CGrowLeft | Instruction to create an n-side extension |
| CGrowRight | Instruction to create a c-side extension |
| CInterval | Simple struct defining a closed interval of residues [left, right] where left <= right |
| CRelativeConnectRight | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| CRelativeSequencePosition | Computes a position wrt values in given BuildInstruction |
| CSegmentInsert | Insert an external segment flanked by new regions |
| CSegmentRebuild | Instruction to rebuild a segment |
| CSegmentSwap | Instruction to swap a segment with an external segment |
| ►Ncomponents | |
| CBDR | |
| CVarLengthBuild | Component that performs a protocol for user-specified variable length remodeling of protein backbone segments |
| ►Nconstraints | |
| CConstraintFileCstGeneratorCreator | |
| CConstraintFileRCG | |
| CInverseRotamersCstGeneratorCreator | |
| CInverseRotamersRCG | RemodelConstraintGenerator that creates AmbiguousConstraints for all positions in a remodeled region towards a list of inverse rotamers. For every remodel position/inverse rotamer pair, there will be one MultiConstraint consisting of three CoordinateConstraints. the three coordinate constraints will be between: 1) remodel res N - invrot N coords 2) remodel res Ca - invrot Ca coords 3) remodel res Cb - invrot Cb coords All of these MultiConstraints are combined to form one AmbiguousConstraint. In effect, this RCG should bias the remodel trajectory such that one remodel residue backbone overlays with one inverse rotamer backbone |
| CInvrotTreeCstGeneratorCreator | |
| CInvrotTreeRCG | RemodelConstraintGenerator wrapper that makes the constraints generated by an InvrotTree available in VLB or XML |
| CNtoC_RCG | |
| CNtoCCstGeneratorCreator | |
| CRemoveCsts | |
| CRemoveCstsCreator | |
| ►Nremodel | |
| CLineObject | |
| CRemodelAccumulator | |
| CRemodelConstraintGenerator | Pure virtual base class |
| CRemodelData | |
| CRemodelDesignMover | |
| CRemodelEnzdesCstModule | |
| CRemodelGlobalFrame | |
| CRemodelLoopMover | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| ►CRemodelMover | |
| Cinstruction_flags | |
| CRemodelMoverCreator | |
| CRemodelRotamerLinks | |
| CRemodelRotamerLinksCreator | |
| CRemodelWorkingSet | |
| CResidueVicinityCstGeneratorCreator | |
| CResidueVicinityInfo | Small helper class for the ResidueVicinityRCG |
| CResidueVicinityRCG | RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions |
| CSegment | |
| ►Nfrag_picker | |
| ►Nnonlocal | |
| CNonlocalFrags | |
| CNonlocalPair | Nonlocal fragment pair |
| ►Nquota | |
| CABEGO_SS_Config | Read a config file for quota selector |
| CABEGO_SS_Map | Single pool used by quota selector |
| CABEGO_SS_Pool | Single pool used by quota selector |
| Cmissing_fraction_sorter_biggest_first | |
| Cquota_limits_sorter_biggest_first | |
| Cquota_limits_sorter_smallest_first | |
| CQuotaCollector | A base class for collecting fragments |
| CQuotaConfig | Read a config file for quota selector |
| CQuotaPool | Single pool used by quota selector |
| CQuotaSelector | Selects a given number of fragments using a quota scheme |
| CSecondaryStructurePool | Single pool used by quota selector |
| ►Nscores | |
| CABEGO_SS_Score | |
| CAdaptiveScoreHistogram | |
| CAmbigCSScore | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CAtomBasedConstraintsScore | A base class for all scoring methods that need atom coordinates |
| CAtomPairConstraintsData | Holds data about a single distance constraint in the form AtomPairConstraintsScore needs |
| CAtomPairConstraintsScore | Scores a fragment with a set of AtomPair constraints |
| CBFactor | BFactor score counts identical residues |
| CCachingScoringMethod | |
| CConstScore | ConstScore adds a constant to the total score for each position |
| CCSScore | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CDihedralConstraintsScore | Scores a fragment with a set of Dihedral constraints |
| CDisulfideDistance | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CDisulfideIdentity | DisulfideIdentity score counts identical residues |
| CFourAtomsConstraintData | Holds data about a single four-body constraint in the form usefull for InterbondAngleScore and DihedralConstraintsScore classes |
| CFragmentAllAtomCrmsd | Scores a fragment by its crmsd to the given reference structure |
| CFragmentChunkCrms | Scores a fragment by its tmscore to the given reference structure |
| CFragmentCrmsd | Scores a fragment by its crmsd to the given reference structure |
| CFragmentCrmsdResDepth | Scores a fragment by its crmsd to the given reference structure |
| CFragmentDME | Scores a fragment by its DME to the given reference structure |
| CFragmentScoreManager | Holds particular score components, weights and calculates the total score for a fragment candidate |
| CFragmentScoreMap | Holds all small scores (score components) for a given fragment |
| CFragmentScoringMethod | Fragment candidate score |
| CGunnCost | |
| CGunnCostScore | Scores a fragment by its crmsd to the given reference structure |
| CGunnTuple | |
| CHydrophobicityProfileSimilarity | Scores a fragment by its hydrophobicity similarity |
| CHydrophobicitySimilarity | Scores a fragment by its hydrophobicity similarity |
| CInterbondAngleScore | Scores a fragment with a set of Dihedral constraints |
| CJCoupling | Scores a fragment by the JCouplings |
| CLAMBEGO_Similarity | Scores a fragment by torsion bin similarity |
| CMakeABEGO_SS_Score | Maker class that produces a new ABEGO_SS_Score object |
| CMakeAmbigCSScore | Maker class that produces a new AmbigCSScore object |
| CMakeAtomPairConstraintsScore | Maker class that produces a new AtomPairConstraintsScore object |
| CMakeBFactor | Maker class that produces a new BFactor object |
| CMakeConstScore | Maker class that produces a new ConstScore object |
| CMakeCSScore | Maker class that produces a new CSScore object |
| CMakeDihedralConstraintsScore | Maker class that produces a new DihedralConstraintsScore object |
| CMakeDisulfideDistance | Matker class that produces a new DisulfideDistance object |
| CMakeDisulfideIdentity | Maker class that produces a new DisulfideIdentity object |
| CMakeFragmentAllAtomCrmsd | Maker class that produces a new FragmentAllAtomCrmsd object |
| CMakeFragmentChunkCrms | Maker class that produces a new FragmentChunkCrms object |
| CMakeFragmentCrmsd | Maker class that produces a new FragmentCrmsd object |
| CMakeFragmentCrmsdResDepth | Maker class that produces a new FragmentCrmsdResDepth object |
| CMakeFragmentDME | Maker class that produces a new FragmentDME object |
| CMakeFragmentScoringMethod | Fragment candidate |
| CMakeGunnCostScore | Maker class that produces a new GunnCostScore object |
| CMakeHydrophobicityProfileSimilarity | Maker class that produces a new HydrophobicityProfileSimilarity object |
| CMakeHydrophobicitySimilarity | Maker class that produces a new HydrophobicitySimilarity object |
| CMakeInterbondAngleScore | Maker class that produces a new InterbondAngleScore object |
| CMakeJCoupling | Matker class that produces a new JCoupling object |
| CMakeLAMBEGO_Similarity | Maker class that produces a new TorsionBin object |
| CMakeMidPhiOut | Matker class that produces a new MidPhiOut object |
| CMakeMidPsiOut | Matker class that produces a new MidPsiOut object |
| CMakePartialSecondarySimilarity | Maker class that produces a new PartialSecondarySimilarity object |
| CMakePCS_FragDistance | Matker class that produces a new PCS_FragDistance object |
| CMakePhi | Maker class that produces a new Phi object |
| CMakePhiPsiRmsd | Matker class that produces a new PhiPsiRmsd object |
| CMakePhiPsiSquareWell | Matker class that produces a new PhiPsiSquareWell object |
| CMakeProfileScore | |
| CMakeProfileScoreBlosum62 | |
| CMakeProfileScoreDistWeight | |
| CMakeProfileScoreL1 | |
| CMakeProfileScoreStructL1 | |
| CMakeProfileScoreSubMatrix | |
| CMakeProlinePhiScore | Maker class that produces a new ProlinePhiScore object |
| CMakePsi | Maker class that produces a new Psi object |
| CMakeRamaScore | Maker class that produces a new RamaScore object |
| CMakeRDCScore | Maker class that produces a new RDCScore object |
| CMakeScoreEValuator | |
| CMakeSecondaryIdentity | Maker class that produces a new SecondaryIdentity object |
| CMakeSecondarySimilarity | Maker class that produces a new SecondarySimilarity object |
| CMakeSequenceIdentity | Maker class that produces a new SequenceIdentity object |
| CMakeSolventAccessibility | Maker class that produces a new SolventAccessibility object |
| CMakeTalosSSSimilarity | Maker class that produces a new TalosSSSimilarity object |
| CMakeTorsionBinSimilarity | Maker class that produces a new TorsionBin object |
| CMidPhiOut | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CMidPsiOut | Scores a fragment by the root mean square deviation of Psi and Psi angles |
| CPartialSecondarySimilarity | Scores a fragment by secondary structure similarity |
| CPCS_FragDistance | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CPhi | Scores a fragment by its predicted phi similarity |
| CPhiPsiRmsd | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CPhiPsiSquareWell | Scores a fragment by the root mean square deviation of Phi and Psi angles |
| CProfileScore | Fragment candidate |
| CProfileScoreBlosum62 | Fragment candidate |
| CProfileScoreDistWeight | Fragment candidate |
| CProfileScoreL1 | Fragment candidate |
| CProfileScoreStructL1 | Fragment candidate |
| CProfileScoreSubMatrix | Fragment candidate |
| CProlinePhiScore | ProlinePhiScore score counts identical residues |
| CPsi | Scores a fragment by its predicted psi similarity |
| CPValuedFragmentScoreManager | Holds particular score components, weights and calculates the total score for a fragment candidate |
| CRamaScore | RamaScore score counts identical residues |
| CRDCScore | Scores a fragment by its crmsd to the given reference structure |
| CScoreEValuator | Computes E-Value for a Profile object |
| CSecondaryIdentity | SequenceIdentity score counts how many residues share the same secondary structure |
| CSecondarySimilarity | Scores a fragment by secondary structure similarity |
| CSequenceIdentity | SequenceIdentity score counts identical residues |
| CSolventAccessibility | Scores a fragment by its predicted solvent accessibility |
| CTalosSSSimilarity | Scores a fragment by secondary structure similarity |
| CTorsionBinSimilarity | Scores a fragment by torsion bin similarity |
| CAllowPdbIdFilter | Accepts a chunk based on the pdb id of the source protein |
| CBestTotalScoreSelector | Selects a given number of fragments using a quota scheme |
| CBoundedCollector | Keeps the N best fragments candidates for the final selection |
| CBoundedCollector_CompareTotalScore | |
| CBoundedPriorityQueue | |
| CCandidatesCollector | A base class for collecting fragments |
| CCompareByScoreCombination | Comparator based on the linear combination of some score components |
| CCompareQueryPosition | Comparator based on a sequence position in a query |
| CCompareScoreComponent | Comparator based on one of the score components calculated for fragments |
| CCompareTotalScore | Comparator based on the total score of fragments |
| CCompositeFragmentSelector | Selects fragments by running several selectors |
| CContact | |
| CContactCounts | |
| CCS2ndShift | |
| CCSTalosIO | |
| CCustomScoreSelector | Selects a given number of fragments using a quota scheme |
| CDenyPdbIdFilter | Denies a chunk based on the pdb id of the source protein |
| CDiversifyCrmsdByClustering | Selects fragments by running several selectors |
| CDiversifyCrmsdSelector | Selects fragments by running several selectors |
| CDiversifyDihedralsSelector | Selects fragments by running several selectors |
| CFragmentCandidate | Vector candidate says which X-mer from vall fits to a query sequence |
| CFragmentComparatorBase | |
| CFragmentPicker | The core of the fragment picking machinery |
| CFragmentSelectingRule | Selects a given number of fragments just by selecting the best ones |
| CGrabAllCollector | Keeps all fragments candidates for the final selection |
| CJCouplingIO | |
| CLAMBEGO_IO | |
| CLazySortedVector1 | |
| CPdbIdChunkFilter | |
| CPhiPsiTalosIO | |
| CQuotaDebug | |
| CSidechainContactDistCutoff | Defines sidechain contact distance cutoffs |
| CTorsionBinIO | |
| CVallChunk | Chunk of residues extracted from a vall |
| CVallChunkFilter | Base class for a chunk filtering mechanism |
| CVallProvider | Vector of vall chunks |
| CVallResidue | Class for managing a line of the Vall fragment library |
| ►Nfrags | |
| CFragLib | |
| CRMSVallData | |
| CSingleResidueTorsionFragmentLibrary | Class for collection of fragments for a single residue position |
| CTorsionFragment | Class for single piece of torsion fragment |
| CTorsionFragmentLibrary | Class for classic Rosetta fragment library |
| CTorsionFragmentMover | |
| CVallData | |
| ►Ngeneralized_kinematic_closure | |
| ►Nfilter | |
| CGeneralizedKICfilter | |
| ►Nperturber | |
| CGeneralizedKICperturber | |
| ►Nselector | |
| CGeneralizedKICselector | |
| CGeneralizedKIC | |
| CGeneralizedKICCreator | |
| ►Ngenetic_algorithm | |
| CDiscreteRandomizer | |
| CEntity | |
| CEntityElement | Entity element |
| CEntityElementCreator | Entity element creator |
| CEntityElementFactory | The EntityElementFactory is responsible for instantiating entity elements from strings |
| CEntityElementRegistrator | |
| CEntityElementsEqual | |
| CEntityRandomizer | |
| CFitnessFunction | |
| CGeneticAlgorithm | |
| CGeneticAlgorithmBase | |
| CMutate1Randomizer | |
| CPositionSpecificRandomizer | Different set of choices at each position in Entity's traits |
| CVec1Hash | |
| ►Ngrafting | |
| ►Nsimple_movers | |
| CDeleteRegionMover | Delete a region of a pose. Mover Wrapper to grafting utility function |
| CDeleteRegionMoverCreator | |
| CInsertPoseIntoPoseMover | Insert a whole pose into another. Loops, linkers, whaterver. No modeling here. Wrapper to utility function insert_pose_into_pose |
| CInsertPoseIntoPoseMoverCreator | |
| CKeepRegionMover | Keep a contiguous region of a pose, delete the rest. Re-detect disulfides |
| CKeepRegionMoverCreator | |
| CReplaceRegionMover | Replace a region of residues with another from a pose piece. Wrapper to grafting utility function |
| CReplaceRegionMoverCreator | |
| CAnchoredGraftMover | Grafting class adapted from Steven Lewis' pose_into_pose algorithm |
| CAnchoredGraftMoverCreator | |
| CCCDEndsGraftMover | General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of: a) SmallMover for sampling (Can be disabled)) b) CCDs both terminal ends of the scaffold using flexibility settings or movemap To close the graft. c) MinMover to help close the graft through chainbreak terms d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion |
| CCCDEndsGraftMoverCreator | |
| CGraftMoverBase | Fairly abstract base class for GraftMover classes |
| ►Nhelical_bundle | |
| ►Nparameters | |
| CBundleParameters | Parameters class, used to store sets of parameters for parametric backbone generation |
| CBundleParametersSet | BundleParametersSet class, used to store sets of parameters for parametric helical bundle generation |
| CBundleGridSampler | |
| CBundleGridSamplerCreator | |
| CBundleGridSamplerHelper | BundleGridSamplerHelper class, which stores options for the PerturbBundle mover |
| CFitSimpleHelix | |
| CFitSimpleHelixCreator | |
| CFitSimpleHelixMultiFunc | Multifunction class for fitting a simple (straight) helix to the Crick parameters |
| CMakeBundle | |
| CMakeBundleCreator | |
| CMakeBundleHelix | |
| CMakeBundleHelixCreator | |
| CPerturbBundle | |
| CPerturbBundleCreator | |
| CPerturbBundleHelix | |
| CPerturbBundleHelixCreator | |
| CPerturbBundleOptions | PerturbBundleOptions class, which stores options for the PerturbBundle mover |
| ►Nhelix_capper | |
| CHelixNCapperMover | |
| ►Nhotspot_hashing | |
| ►Nmovers | |
| CPlaceProbeMover | |
| CPlaceSurfaceProbe | |
| CPlaceSurfaceProbeCreator | |
| CAddSearchPatternRotSetOp | |
| CCartesianSearchPattern | |
| CComposeSearchPatterns | |
| CConstPattern | |
| CHotspotStub | |
| CHotspotStubSet | |
| CLSMSearchPattern | |
| CPartitionedSearchPattern | |
| CRotationSearchPattern | |
| CSearchPattern | |
| CSearchPatternExpansion | |
| CSearchPatternRotSetOp | |
| CSearchPatternTransform | |
| CSICPatternAtTransform | |
| CSphericalRotationSearchPattern | |
| CStubGenerator | |
| CSurfaceSearchPattern | |
| CTestPattern | |
| CVectorPair | |
| ►Nhybridization | |
| CAllResiduesChanged | (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values |
| CBackboneTorsionPerturbation | |
| CBackboneTorsionPerturbationCreator | |
| CBackboneTorsionSampler | |
| CBackboneTorsionSamplerCreator | |
| CCartesianHybridize | |
| CCartesianHybridizeCreator | |
| CCartesianSampler | |
| CCartesianSamplerCreator | |
| CChunkTrialMover | |
| CDDomainParse | |
| CDomainAssembly | |
| CFoldTreeHybridize | |
| CFoldTreeHybridizeCreator | |
| ChConvergenceCheck | |
| CHybridizeFoldtreeDynamic | |
| CHybridizeProtocol | |
| CHybridizeProtocolCreator | |
| CHybridizeSetup | |
| CHybridizeSetupMover | |
| CHybridizeSetupMoverCreator | |
| CInsertChunkMover | |
| CMRMover | |
| CTemplateHistory | |
| CTMalign | |
| CWeightedFragmentSmoothTrialMover | |
| CWeightedFragmentTrialMover | |
| ►Nidealize | |
| CIdealizeMover | Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points |
| CIdealizeMoverCreator | |
| ►Nindexed_structure_store | |
| ►Nfilters | |
| CFragmentLookupFilter | |
| CFragmentLookupFilterCreator | |
| ►Ninputter | |
| CFastaInputter | |
| CInputter | |
| CInputterStream | |
| CPDBInputter | |
| CSilentFileInputter | |
| ►Njd2 | |
| ►Narchive | |
| CAbstractArchiveBase | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| CArchiveBase | |
| CArchiveManager | ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys |
| CBaseArchiveManager | ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys |
| CBatch | Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files |
| CEvaluatedArchive | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| CEXCN_Archive | |
| ►CMPIArchiveJobDistributor | JobDistributor for the iterative ArchiveManager/Archive Framework |
| CCompletionMessage | CompletionMessage(s) are send to the ArchiveManager whenever more than nr_notify decoys have been finished / or when the full batch is finished |
| CNormalizedEvaluatedArchive | Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input |
| CSortPredicate | |
| CVarianceStatisticsArchive | |
| ►Nparser | |
| CBluePrint | |
| CDataLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CDataLoaderCreator | A class for creating new instances of DataLoaders for use in the XML Parser |
| CDataLoaderFactory | A factory for creating DataLoaders, which are able to load arbitrary data into the basic::datacache::DataMap used in the XML-based parser. This factory supports the load-time registration scheme allowing DataLoaders to be defined in libraries outside of protocols.lib |
| CDataLoaderRegistrator | This templated class will register an instance of an DataLoaderCreator (class T) with the DataLoaderFactory. It will ensure that no DataLoaderCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CFragmentReader | |
| CFragSetLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CFragSetLoaderCreator | |
| CMonteCarloLoader | The MonteCarloLoader will create named MonteCarlo objects and load them into the basic::datacache::DataMap |
| CMonteCarloLoaderCreator | |
| CResidueSelectorLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CResidueSelectorLoaderCreator | |
| CScoreFunctionLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CScoreFunctionLoaderCreator | |
| CTaskOperationLoader | A class for loading arbitrary data into the XML parser's basic::datacache::DataMap |
| CTaskOperationLoaderCreator | |
| CAtomTreeDiffJobInputter | |
| CAtomTreeDiffJobInputterCreator | |
| CAtomTreeDiffJobOutputter | |
| CAtomTreeDiffJobOutputterCreator | |
| CBatchJobInputter | |
| CBOINCJobDistributor | |
| CCompareTags | |
| CDebugOut_MpiFileBuffer | |
| CFileJobOutputter | |
| CFileSystemJobDistributor | |
| CInnerJob | |
| CInnerMultiThreadingJob | |
| CJD2ResourceManager | The JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor |
| CJD2ResourceManagerCreator | The JD2ResourceManagerCreator is responsible for instantiating the JD2ResourceManager for the ResourceManagerFactory |
| CJD2ResourceManagerJobInputter | The JD2ResourceManagerJobInputter works with the JobDistributor to define the set of jobs that are to be executed. It reads the list of jobs and the set of resouces they require from one or more XML files |
| CJD2ResourceManagerJobInputterCreator | JD2ResourceManagerJobInputterCreator is responsible for instantiating the JD2ResourceManagerJobInputter for the JobDistributorFactory |
| CJob | |
| CJobDistributor | |
| CJobDistributorFactory | |
| CJobInputter | |
| CJobInputterCreator | Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class |
| CJobInputterFactory | |
| CJobInputterRegistrator | This templated class will register an instance of an JobInputterCreator (class T) with the JobInputterFactory. It will ensure that no JobInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CJobOutputter | |
| CJobOutputterCreator | Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class |
| CJobOutputterFactory | |
| CJobOutputterObserver | |
| CJobOutputterRegistrator | This templated class will register an instance of an JobOutputterCreator (class T) with the JobOutputterFactory. It will ensure that no JobOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CLazySilentFileJobInputter | |
| CLazySilentFileJobInputterCreator | |
| CMpiFileBuffer | |
| CMPIFileBufJobDistributor | |
| CMPIMultiCommJobDistributor | |
| CMPIWorkPartitionJobDistributor | |
| CMPIWorkPoolJobDistributor | |
| CMSDJobDistributor | |
| CMultiThreadingJob | |
| CNoOutputJobOutputter | |
| CNoOutputJobOutputterCreator | |
| CParser | |
| CPDBJobInputter | |
| CPDBJobInputterCreator | |
| CPDBJobOutputter | |
| CPDBJobOutputterCreator | |
| CPoseInputStreamJobInputter | |
| CPoseInputStreamJobInputterCreator | |
| CScoreMap | |
| CScoreOnlyJobOutputter | |
| CScoreOnlyJobOutputterCreator | |
| CScreeningJobInputter | |
| CScreeningJobInputterCreator | |
| CShuffleFileSystemJobDistributor | |
| CSilentFileJobInputter | |
| CSilentFileJobInputterCreator | |
| CSilentFileJobOutputter | |
| CSilentFileJobOutputterCreator | |
| CSingleFileBuffer | |
| CWriteFileSFB | |
| CWriteOut_MpiFileBuffer | |
| ►Njobdist | |
| CAtomTreeDiffJobDistributor | Distributor for use with atomtree_diff silent files |
| CBaseJobDistributor | Coordinates processing of jobs across multiple Rosetta processes |
| CBasicJob | Each Job object describes a particular input to Rosetta |
| CPlainPdbJobDistributor | Distributor for use with plain old PDB files. Use is strongly discouraged in production environments! |
| CPlainRawJobDistributor | Distributor for use with raw files |
| CPlainSilentFileJobDistributor | Distributor for use with silent files |
| ►Njumping | |
| CBaseDisulfPairingLibrary | |
| CBaseJumpSetup | Virtual base class: can create a set of jumps and cuts |
| CBasePairingLibrary | Returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors |
| CDisulfPairing | |
| CDisulfPairingLibrary | |
| CDisulfTemplate | |
| CInterval | Two numbers, i.e., jump start end residue, or cut-regions.. |
| CJumpSample | |
| ►CJumpSelector | |
| CJumpWeightDef | |
| ►CJumpSetup | |
| CJumpDef | |
| CJumpsFromAllPairings | |
| CMembraneJump | |
| CPairingLibrary | |
| CPairingTemplate | |
| CRandomSheetBuilder | Select jumps to build a given topology |
| CResiduePairJump | |
| ►CResiduePairJumpSetup | |
| CJumpDef | |
| CResiduePairJumpSingle | Single residue component of a ResiduePairJump class |
| CSameStrand | Tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, |
| CSheetBuilder | Select jumps to build a given topology |
| CSpecificGeometryLibrary | |
| CStandardDisulfPairingLibrary | The StandardDisulfPairingsLibrary initializes itself in its constructor from the sampling/disulfide_jump_database_wip.dat file in the database. Users should not in any circumstance invoke any of its non-const methods that are defined in the subclass. This class ought to be reworked to ensure that it is threadsafe |
| CStandardPairingLibrary | This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn't be |
| ►Nkinematic_closure | Implementation of the kinematic closure algorithm for sampling protein backbone conformations |
| ►Nperturbers | Algorithms for sampling new backbone torsions |
| CBondAnglePerturber | Resample each backbone bond angle from a gaussian distribution |
| CFragmentPerturber | Pick phi/psi torsions from the given fragment library |
| CIdealizeNonPhiPsi | Set all the non-phi/psi DOFs to ideal values |
| CLogFilePerturber | Read torsion angles, bond angles, and bond lengths from a log file |
| COmegaPerturber | |
| CPerturber | Base class for all of the perturber algorithms |
| CPerturberSet | Maintain a set of perturbers to be executed together |
| CRama2bPerturber | Pick phi/psi pairs from the neighbor-dependent rama distribution |
| CRamaPerturber | Pick phi/psi pairs from the rama distribution |
| CUniformPerturber | Sample backbone torsions from a uniform distribution |
| CVicinityPerturber | Limit sampling to phi/psi pairs within some distance of a target loop |
| CWalkingBondAnglePerturber | Resample each backbone bond angle from a gaussian distribution |
| CWalkingPerturber | Make small perturbations to the previous backbone torsions |
| ►Npivot_pickers | Algorithms for choosing pivot residues |
| CEndToEndPivots | Pick pivots that span the entire loop to sample |
| CFixedOffsetPivots | Randomly pick pivots which are always offset by the same amount, but which can appear anywhere in the loop |
| CFixedPivots | Use a fixed set of pivots specified in advance |
| CLoopPivots | Use the start, stop, and cut points of the given loop as pivots |
| CPivotPicker | Base class for all the pivot picking algorithms |
| CStandardPivots | Randomly pick pivots in a way that may or may not span the whole loop |
| ►Nsolution_pickers | Algorithms for picking one of the 0 to 16 solutions generated by kinematic closure |
| CFilteredSolutions | Apply rama and bump checks to quickly filter out bad solutions |
| CRandomSolutions | Pick a completely random solution to return |
| CSolutionPicker | Base class for all the solution picking algorithms |
| CBalancedKicMover | Make a kinematic closure move that obeys detailed balance |
| ►CClosureProblem | Represent and solve a kinematic closure problem |
| CMemento | Save the current state of the closure problem. This is meant to facilitate undoing rejected perturbations when necessary |
| CClosureSolution | Represent a single solution to a kinematic closure problem |
| CKicMover | Find a new backbone conformation for some region of a protein |
| CKicMoverCreator | |
| ►Nkinmatch | |
| CBruteFunGroupTK | |
| CFunGroupTK | |
| CKinFunGroupTK | |
| CKRSQuery | |
| ►Nligand_docking | |
| ►Nligand_options | |
| CInterface | For each residue is it in the interface, a mobile region or a non-mobile region? |
| CInterfaceInfo | Info for each residue- is it part of the interface and if so, what ligands is it near |
| ►Nrdf | |
| CAtomPairData | Simple struct for storing information needed to compute an RDF interaction |
| CRDFBase | |
| CRDFBinaryHbondCreator | Creator to geneate a new RDFBinaryHbondFunction |
| CRDFBinaryHbondFunction | RDFBinaryHbondFunction returns 1.0 if a pair of atoms are donor and acceptor, 0.0 otherwise |
| CRDFBinaryOrbitalFunction | RDFBinaryOrbitalFunction returns 1 for various orbital pairs and 0 otherwise |
| CRDFBinaryOrbitalFunctionCreator | Creator to geneate a new RDFBinaryOrbitalFunction |
| CRDFChargeCreator | Creator to geneate a new RDFChargeFunction |
| CRDFChargeFunction | RDFChargeFunction computes fa_elec for a pair of atoms |
| CRDFElecCreator | Creator to geneate a new RDFElecFunction |
| CRDFElecFunction | RDFElecFunction computes fa_elec for a pair of atoms |
| CRDFEtableCreator | Creator to geneate a new RDFEtableFunction |
| CRDFEtableFunction | RDFEtableFunction computes fa_sol,fa_rep,fa_atr for a pair of atoms |
| CRDFFunctionCreator | The Creator class is responsible for creating a particular RDF Function class |
| CRDFFunctionFactory | Create RDFFunctions |
| CRDFFunctionRegistrator | This templated class will register an instance of an RDFFunctionCreator (class T) with the RDFFunctionFactory. It will ensure that no FeaturesReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRDFHbondCreator | Creator to geneate a new RDFHbondFunction |
| CRDFHbondFunction | RDFHbondFunction computes h-bonding energy for a pair of atoms |
| CRDFOrbitalFunction | RDFOrbitalFunction computes the orbital score energies of a pair of atoms |
| CRDFOrbitalFunctionCreator | Creator to geneate a new RDFOrbitalFunction |
| CAddHydrogen | |
| CAddHydrogens | |
| CAddHydrogensCreator | |
| CAtomCountFilter | |
| CAtomCountFilterCreator | |
| CChainExistsFilter | |
| CChainExistsFilterCreator | |
| CCompleteConnectionsFilter | |
| CCompleteConnectionsFilterCreator | |
| CCompoundTranslate | |
| CCompoundTranslateCreator | |
| CComputeLigandRDF | |
| CComputeLigandRDFCreator | |
| CDistributionMap | A singleton class that returns a map of strings to enum types |
| CFinalMinimizer | |
| CFinalMinimizerCreator | |
| CGrowLigand | |
| CGrowLigandCreator | |
| CHBondAcceptorFilter | |
| CHBondAcceptorFilterCreator | |
| CHBondDonorFilter | |
| CHBondDonorFilterCreator | |
| CHeavyAtomFilter | |
| CHeavyAtomFilterCreator | |
| CHighResDocker | |
| CHighResDockerCreator | |
| CInterfaceBuilder | |
| CInterfaceBuilderLoader | A class for loading InterfaceBuilders into the XML parser's basic::datacache::DataMap |
| CInterfaceBuilderLoaderCreator | |
| CInterfaceScoreCalculator | |
| CInterfaceScoreCalculatorCreator | |
| CLigand_info | |
| CLigandArea | |
| CLigandAreaLoader | |
| CLigandAreaLoaderCreator | |
| CLigandBaseProtocol | Shared functionality for protocols that dock ligands |
| CLigandDesign | |
| CLigandDesignCreator | |
| CLigandDockMain | |
| CLigandDockProtocol | |
| CMinimizeBackbone | |
| CMinimizeBackboneCreator | |
| CMinimizeLigand | |
| CMolarMassFilter | |
| CMolarMassFilterCreator | |
| CMolecularMassFilter | |
| CMolecularMassFilterCreator | |
| CMoveMapBuilder | |
| CMoveMapBuilderLoader | A class for loading MoveMapBuilders into the XML parser's basic::datacache::DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder |
| CMoveMapBuilderLoaderCreator | |
| CRandomConformerMover | Replace the residue at the given position with a randomly selected conformer from its rotamer library |
| CRandomConformers | |
| CRandomConformersCreator | |
| CResidueTorsionRestraints | Manages harmonic restraints on torsions, so they can be turned off for packing |
| CRigidSearchMover | An optimized mover for Monte Carlo trial of rigid body perturbations |
| CRotate | |
| CRotate_info | |
| CRotateCreator | |
| CRotates | |
| CRotatesCreator | |
| CSlideTogether | |
| CSlideTogetherCreator | |
| CStartFrom | |
| CStartFromCreator | |
| CTetherLigand | |
| CTransform | |
| CTransform_info | |
| CTransformCreator | |
| CTranslate | |
| CTranslate_info | |
| CTranslateCreator | |
| CUnconstrainedTorsionsMover | Juggles torsional constraints with packing or rotamer trials |
| CWriteLigandMolFile | |
| CWriteLigandMolFileCreator | |
| ►Nloop_build | |
| CLoopBuildMover | |
| CLoopmodelWrapper | |
| CLoopmodelWrapperCreator | |
| CLoopMover_SlidingWindow | LoopMover utilizing fragment insertion, ccd loop closure, and minimization |
| CLoopMover_SlidingWindowCreator | Creator for the LoopMover_SlidingWindowCreator class |
| ►Nloop_modeling | Framework for loop structure prediction |
| ►Nrefiners | Algorithms for lowering loop region scores during sampling |
| CMinimizationRefiner | Refine sampled loops using gradient minimization |
| CMinimizationRefinerCreator | |
| CRepackingRefiner | Refine sampled loops using sidechain repacking |
| CRepackingRefinerCreator | |
| CRotamerTrialsRefiner | Refine sampled loops using rotamer trials |
| CRotamerTrialsRefinerCreator | |
| ►Nsamplers | Algorithms for generating new loop conformations |
| CLegacyKicSampler | Apply the legacy KinematicMover |
| CLegacyKicSamplerCreator | |
| ►Nutilities | Generally useful loop-sampling meta-algorithms |
| CAcceptanceCheck | Apply an additional Monte Carlo acceptance check |
| CLoopFilter | Apply any filter in the context of a loop modeling simulation |
| CLoopMoverGroup | Manage a collection of loop-sampling algorithms |
| CPrepareForCentroid | Convert a pose to centroid mode for low-resolution loop modeling |
| CPrepareForCentroidCreator | |
| CPrepareForFullatom | Convert a pose to fullatom mode for high-resolution loop modeling |
| CPrepareForFullatomCreator | |
| CLoopBuilder | Build loops from scratch |
| CLoopBuilderCreator | |
| CLoopModeler | Attempt to find the native structure for one or more loops |
| CLoopModelerCreator | |
| CLoopMover | Base class for loop-sampling algorithms |
| CLoopProtocol | Monte Carlo search for low energy loop conformations |
| CLoopProtocolCreator | |
| CToolboxKeys | Key names for data shared between loop movers |
| ►Nloophash | |
| CBackboneDB | |
| CBackboneSegment | |
| CBBData | |
| CBBExtraData | |
| CEXCN_bbdb_Merge_Failed | |
| CEXCN_DB_IO_Failed | |
| CEXCN_Invalid_Hashmap | |
| CEXCN_No_Extra_Data_To_Write | |
| CEXCN_Wrong_DB_Format | |
| CFastGapMover | Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much |
| CFilterBucket | |
| CLeapIndex | The LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful |
| CLegacyLeapIndex | |
| CLocalInserter | |
| CLocalInserter_SimpleMin | |
| CLoopHashDiversifier | |
| CLoopHashDiversifierCreator | |
| CLoopHashLibrary | |
| CLoopHashLibraryLoader | LoopHashLibraryLoader constructs a LoopHashLibrary instance from data provided by the ResourceManager |
| CLoopHashLibraryLoaderCreator | LoopHashLibraryLoaderCreator allows the ResourceLoaderFactory to create a LoopHashLibraryLoader instance |
| CLoopHashLibraryOptions | LoopHashLibraryOptions encapsulates the options associated with LoopHashLibrary resources |
| CLoopHashLibraryOptionsCreator | LoopHashLibraryOptionsCreator allows the ResourceLoaderFactory to create a LoopHashLibraryOptions instance |
| ►CLoopHashMap | Loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates |
| Cby_index | A functor for sort() |
| CLoopHashMoverWrapper | |
| CLoopHashMoverWrapperCreator | |
| CLoopHashRelaxProtocol | |
| CLoopHashSampler | |
| CMover_LoopHashRefine | |
| CMPI_LoopHashRefine | |
| CMPI_LoopHashRefine_Emperor | |
| CMPI_LoopHashRefine_Master | |
| CWorkUnit_LoopHash | |
| ►Nloops | |
| ►Nloop_closure | |
| ►Nccd | |
| CCCDLoopClosureMover | Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent |
| CCCDLoopClosureMoverCreator | CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance |
| CFASelectSlidingWindowLoopClosure | |
| CLoopClosure | |
| CRamaCheck1B | |
| CRamaCheck2B | |
| CRamaCheckBase | |
| CShortLoopClosure | |
| CSlidingWindowLoopClosure | |
| CWidthFirstSlidingWindowLoopClosure | |
| ►Nkinematic_closure | |
| CBaseTabooPerturber | Taboo-sampling perturber base class, the two variants of which, share much code in common, but interface with separate Ramachandran potentials |
| CKinematicMover | A mover class for performing kinematic loop closure on a peptide segment |
| CKinematicPerturber | Pure virtual base class for KinematicPerturber. KinematicPerturbers determine HOW loops should be perturbed. The base class contains a provision for determining WHERE they should be perturbed: MoveMap sensitivity |
| CKinematicWrapper | |
| CNeighborDependentTabooSamplingKinematicPerturber | Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) |
| CNeighborDependentTorsionSamplingKinematicPerturber | Neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup |
| CTabooSamplingKinematicPerturber | Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration) |
| CTorsionRestrictedKinematicPerturber | Torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) |
| CTorsionSamplingKinematicPerturber | Torsion sampling kinematic perturber |
| CTorsionSweepingKinematicPerturber | WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber |
| CVicinitySamplingKinematicPerturber | Vicinity sampling kinematic perturber |
| ►Nloop_mover | |
| ►Nperturb | |
| CLoopMover_Perturb_CCD | |
| CLoopMover_Perturb_CCDCreator | Creator for the LoopMover_Perturb_CCDCreator class |
| CLoopMover_Perturb_KIC | |
| CLoopMover_Perturb_KICCreator | Creator for the LoopMover_Perturb_KICCreator class |
| CLoopMover_Perturb_QuickCCD | LoopMover utilizing fragment insertion, ccd loop closure, and minimization |
| CLoopMover_Perturb_QuickCCD_Moves | |
| CLoopMover_Perturb_QuickCCD_MovesCreator | Creator for the LoopMover_Perturb_QuickCCD_MovesCreator class |
| CLoopMover_Perturb_QuickCCDCreator | Creator for the LoopMover_Perturb_QuickCCDCreator class |
| ►Nrefine | |
| CLoopMover_Refine_Backrub | |
| CLoopMover_Refine_BackrubCreator | Creator for the LoopMover_Refine_BackrubCreator class |
| CLoopMover_Refine_CCD | |
| CLoopMover_Refine_CCDCreator | Creator for the LoopMover_Refine_CCDCreator class |
| CLoopMover_Refine_KIC | |
| CLoopMover_Refine_KICCreator | Creator for the LoopMover_Perturb_KICCreator class |
| CLoopRefineInnerCycle | |
| CLoopRefineInnerCycleContainer | |
| CLoopRefineInnerCycleContainerCreator | Creator for the LoopRefineInnerCycleContainer class |
| CLoopRefineInnerCycleFactory | Create LoopMover Reporters |
| CRepackTrial | |
| CRepackTrialCreator | Creator for the RepackTrial class |
| CShearMinCCDTrial | |
| CShearMinCCDTrialCreator | Creator for the ShearMinCCDTrial class |
| CSmallMinCCDTrial | |
| CSmallMinCCDTrialCreator | Creator for the SmallMinCCDTrial class |
| CIndependentLoopMover | |
| CLoopCM | |
| CLoopCMCreator | |
| CLoopMover | The loop-rebuild protocol |
| ►Nloops_definers | |
| CLoopsDatabaseDefiner | |
| CLoopsDatabaseDefinerCreator | Creator for the LoopsDatabaseDefiner class |
| CLoopsDefiner | |
| CLoopsDefinerCreator | Creator for the LoopsDefiner class |
| CLoopsDefinerFactory | Create LoopsDefiner Reporters |
| CLoopsDefinerLoader | A class for loading Loops data into the XML parser's basic::datacache::DataMap |
| CLoopsDefinerLoaderCreator | |
| CLoopsDefinerRegistrator | This templated class will register an instance of an LoopsDefinerCreator (class T) with the LoopsDefinerFactory. It will ensure that no LoopsDefinerCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CLoopsExplicitDefiner | |
| CLoopsExplicitDefinerCreator | Creator for the LoopsExplicitDefiner class |
| CLoopsFileDefiner | |
| CLoopsFileDefinerCreator | Creator for the LoopsFileDefiner class |
| CEXCN_Loop_not_closed | |
| CFoldTreeFromLoops | |
| CFoldTreeFromLoopsCreator | |
| CGuardedLoopsFromFile | This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure |
| CJSONFormattedLoopsFileReader | |
| CLoop | Single loop definition |
| CLoop_lt | Used to sort Loops by start-res |
| CLoopFromFileData | |
| CLoopMoverFactory | Create LoopMover Reporters |
| CLoops | |
| CLoopsFileData | |
| CLoopsFileFallbackConfiguration | LoopsFileFallbackConfiguration provides instructions to the ResourceManager for loading loops_files in the absence of a resource definition file |
| CLoopsFileFallbackConfigurationCreator | LoopsFileFallbackConfigurationCreator allows the ResourceManager to create a LoopsFileIO instance |
| CLoopsFileIO | |
| CLoopsFileLoader | LoopsFileLoader constructs a LoopsFileData instance from data provided by the ResourceManager |
| CLoopsFileLoaderCreator | LoopsFileLoaderCreator allows the ResourceLoaderFactory to create a LoopsFileLoader instance |
| CLoopsFileOptions | LoopsFileOptions ecapsulates the options associated with LoopsFile resources |
| CLoopsFileOptionsCreator | LoopsFileOptionsCreator allows the ResourceLoaderFactory to create a LoopsFileOptions instance |
| CPoseNumberedLoopFileReader | |
| CRationalLoopComparator | Orders loops by start position |
| CResidueIndexDescription | Class which can represent one of many ways in which to describe a particular residue in a pose, and can, when given a pose, find its index. The object should be constructed with all its needed parameters, but, one instance may be copied from another |
| CResidueIndexDescriptionFromFile | |
| CSerializedLoop | Bare-bones representation of a loop |
| ►Nmake_rot_lib | |
| CCentroidRotNum | |
| CMakeRotLibJob | |
| CMakeRotLibJobInputter | |
| CMakeRotLibJobInputterCreator | |
| CMakeRotLibMover | |
| CMakeRotLibOptionsData | |
| CRotData | |
| Crunning_average_pair | Struct that is used in calc_centroids, values init to zero |
| CTorsionRange | |
| ►Nmatch | |
| ►Ndownstream | |
| CActiveSiteGrid | |
| CAtomAngleSecMatchRPE | RPE to figure out if three atoms are within a given angle atoms need to be set through the parent class add_at_ind function |
| CAtomDihedralSecMatchRPE | RPE to figure out if four atoms are within a given dihedral angle atoms need to be set through the parent class add_at_ind function also checks whether a dihedral is periodic, i.e. multiple minima |
| CAtomDistanceSecMatchRPE | RPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function |
| CAtomGeometrySecMatchRPE | Helper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes |
| CClassicMatchAlgorithm | Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner |
| CDownstreamAlgorithm | A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits |
| CDownstreamBuilder | |
| CGeometrySecMatchRPE | Holds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence when an instance of this class is asked to evaluate two residues |
| Chash_upstream_hit | |
| CLigandConformerBuilder | |
| CRigidLigandBuilder | |
| CScoringSecMatchRPE | |
| CSecMatchEvaluatorFactory | Collection of functions making a single score_function |
| CSecMatchResiduePairEvaluator | Base for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue |
| CSecondaryMatcherToDownstreamResidue | A class for an algorithm. Given a conformation of the downstream partner, the algorithm is responsible for producing a set of hits |
| CSecondaryMatcherToUpstreamResidue | A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits |
| CSecondaryMatchUpstreamResProcessor | A simple class to respond to the UpstreamBuilder's process_hit method and pass on the coordinates to its "owning" SecondaryMatcherToUpstreamResidue object |
| CTargetRotamerCoords | |
| Cus_secmatch_hit_compare | A simple struct to use in list.sort() to ensure that the hits returned by a secondary matcher which has possibly generated upstream hits out-of-order, will return an ordered-hit-list in its build_hits_at_all_positions() method |
| ►Noutput | |
| CBestMatchesCollection | |
| CCloudPDBWriter | Output writer that uses a grouper to group matches and then writes out one pdb file per group, with the different hits from the group in different MODEL sections |
| CDownstreamCoordinateKinemageWriter | |
| CDownstreamRMSEvaluator | In the best of all possible worlds, this class would be sufficiently generic such that I could compare RMS for arbitrary subsets of atoms on the downstream partner, but in my first pass implementation, I'm writing while aiming at the RigidLigandBuilder – 1 residue – and I'll compare all heavy atoms |
| CLimitHitsPerRotamerFilter | |
| CMatchCollisionFilter | |
| CMatchConsolidator | |
| CMatchEvaluator | |
| CMatchFilter | |
| CMatchGrouper | |
| CMatchOutputter | |
| CMatchProcessor | |
| CMatchScoreWriter | |
| COutputWriter | |
| CPDBWriter | |
| CPoseInserter | |
| CPoseMatchOutputWriter | Helper class for the MatcherMover that will put a match into a supplied pose |
| CProcessorFactory | |
| CResidueKinemageWriter | |
| CSameChiBinComboGrouper | |
| CSameRotamerComboGrouper | |
| CSameSequenceAndDSPositionGrouper | Class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account |
| CSameSequenceGrouper | Class to group matches that represent the same amino acids at the same launch points. E.g. Two matches that both put a cys at launch point #33, a ser a launch point #42 and another ser at launch point #80 would be grouped together – even if they are different rotamers |
| CSingleDownstreamResidueWriter | Class for writing conformations of the downstream partner in a kinemage description |
| CStateAccumulatingMatchFilter | |
| CUpstreamCollisionFilter | This class is used to detect collisions between the upstream residues and filter out matches that have too much collision. It can perform either hard-sphere collision detection, or score-function (Etable) driven collision detection. Four command-line flags are read by the MatcherTask to initialize this class: match::filter_colliding_upstream_residues match::upstream_residue_collision_tolerance match::upstream_residue_collision_score_cutoff match::upstream_residue_collision_Wfa_atr match::upstream_residue_collision_Wfa_rep match::upstream_residue_collision_Wfa_sol |
| CUpstreamDownstreamCollisionFilter | This class is used to detect collisions between upstream residues and downstream poses |
| CUpstreamHitCacher | |
| CWriteKinemageOutputter | |
| CWriteUpstreamCoordinateKinemage | |
| CWriteUpstreamHitKinemage | |
| ►Nupstream | |
| CBuildSet | A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom |
| CDunbrackSCSampler | Basic class for sidechain sampling that pulls data from the Dunbrack rotamer library. The samples that are returned are the basic rotamers and do not include any expansions by the "ex" flags |
| CFullChiSampleSet | |
| COriginalBackboneBuildPoint | |
| CProteinBackboneBuildPoint | |
| CProteinSCSampler | |
| CProteinUpstreamBuilder | |
| CSampleStrategyData | This class holds all of the data associated with the logic for generating extra samples for a particular chi angle. There are tons of ways concievable to build extra rotamers; the data in this class is intended to group all of that data into one place. This class is not responsible for building extra rotamer samples; that responsibility is given to class FullChiSampleSet |
| CScaffoldBuildPoint | |
| CUpstreamBuilder | |
| CUpstreamResidueProcessor | |
| CUpstreamResTypeGeometry | A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom |
| CAddAllPositionsMPM | MPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere |
| CBfactorMPM | Removes positions at which the bfactors for c-alpha atoms are above a desired cutoff. bfactors stored in the pose pdbinfo are taken. if relative bfactors are used, all bfactors are divided by the largest observed bfactor |
| CBool3DGrid | |
| CBool3DGridKinemageWriter | |
| CBumpGrid | |
| Cdownstream_hit | |
| CHit | |
| CHitHasher | This object hashes hits into 6D voxels. This hash can then be traversed to retrieve the hits that hash to the same voxel (matches!). There are 64 hashes representing the 2^6 ways to perturb the bins in 6D by 1/2 of their bin width |
| CHitNeighborFinder | |
| Cmatch_dspos1 | Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position) |
| Cmatch_lite_equals | |
| Cmatch_lite_hasher | |
| CMatchCounter | Class for counting the number of matches given a particular discretization level |
| CMatcher | |
| CMatcherMover | |
| CMatcherMoverCreator | |
| CMatcherOutputStats | |
| CMatcherTask | |
| CMatchOutputTracker | |
| CMatchPositionModifier | Base class for objects that modify the match positions based on some criterion |
| CNumNeighborsMPM | Removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward |
| COccupiedSpaceHash | This class keeps track of the active voxels "up until now" with 64 hashes |
| CRemoveNorCTermMPM | Added by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching |
| CSecondaryStructureMPM | Removes positions at which the pose does not have the desired secondary structure |
| CTaskOperationMPM | Mpm that will get a task operation as specified in the tag from the TaskOperationFactory, apply the task operation to the pose and every residue that is then set to designing in the task will be a match position |
| Cupstream_hit | |
| CVoxelSetIterator | Helper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers |
| ►Nmatdes | |
| CBuildingBlockInterfaceOperation | |
| CBuildingBlockInterfaceOperationCreator | |
| CClashCheckFilter | |
| CClashCheckFilterCreator | |
| CExtractSubposeMover | |
| CExtractSubposeMoverCreator | |
| CGetRBDOFValues | WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE |
| CGetRBDOFValuesCreator | |
| CInterfacePackingFilter | |
| CInterfacePackingFilterCreator | |
| CMatDesGreedyOptMutationMover | |
| CMatDesGreedyOptMutationMoverCreator | |
| CMatDesPointMutationCalculator | |
| COligomericAverageDegreeFilter | |
| COligomericAverageDegreeFilterCreator | |
| CSchemePlaceMotifsMover | |
| CSchemePlaceMotifsMoverCreator | |
| CSymDofMover | |
| CSymDofMoverCreator | |
| CSymDofMoverSampler | WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED |
| CSymUnsatHbondFilter | Filters based on an upper bound # of buried unsatisfied polar residues |
| CSymUnsatHbondFilterCreator | |
| ►Nmd | |
| CCartesianMD | |
| CCartesianMDCreator | |
| CConstraint | |
| CMDBase | |
| CMDscheduleData | |
| CRattle | |
| CThermostat | |
| ►Nmedal | |
| CMedalExchangeMover | |
| CMedalMover | |
| ►Nmembrane | |
| ►Ngeometry | |
| CEmbedding | |
| CEmbeddingDef | Embedding Setup Helper Class |
| ►Nio | |
| CLipoFileLoader | Load Lipid Acc data object |
| CLipoFileLoaderCreator | Lipo File Loader Creator |
| CLipoFileOptions | Lipo File Options |
| CLipoFileOptionsCreator | Options Creator for Lipo Files |
| CSpanFileLoader | Span File Loader |
| CSpanFileLoaderCreator | Span File Loader Creator Class |
| CSpanFileOptions | Options for generating per-chain membrane spanning data |
| CSpanFileOptionsCreator | Options for generating per-chain membrane spanning data |
| ►Nsymmetry | |
| CSymmetricAddMembraneMover | |
| CSymmetricAddMembraneMoverCreator | Mover Creator |
| ►Nvisualize | |
| CVisualizeEmbeddingMover | Adds virtual residues to visualize span embeddings of the membrane protein |
| CVisualizeEmbeddingMoverCreator | Mover Creator |
| CVisualizeMembraneMover | Add membrane planes to the pose represented by 2 layers of MEM virtual residues |
| CVisualizeMembraneMoverCreator | Mover Creator |
| CAddMembraneMover | Add Membrane components to the pose, sets up MembraneInfo object includes: spanning topology, lips info, embeddings, and a membrane virtual residue describing the membrane position |
| CAddMembraneMoverCreator | Mover Creator |
| CFlipMover | Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane. CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!! |
| CFlipMoverCreator | Mover Creator |
| CMembranePositionFromTopologyMover | Compute the initial position of the membrane based upon sequence or structure |
| CMembranePositionFromTopologyMoverCreator | Mover Creator |
| CRandomPositionRotationMover | Random Position Rotation Move |
| CRandomPositionTranslationMover | Random Position Translation Move |
| CRotationMover | Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors |
| CRotationMoverCreator | Mover Creator |
| CSetMembraneCenterMover | Membrane Position Translation Move |
| CSetMembraneCenterMoverCreator | Mover Creator for membrane translation mover |
| CSetMembraneNormalMover | Membrane Position Rotation Move |
| CSetMembraneNormalMoverCreator | Mover creator for membrane rotation mover |
| CSetMembranePositionMover | Membrane Position Translation-Rotation Mover |
| CSetMembranePositionMoverCreator | Mover Creator for composed RT mover |
| CTransformIntoMembraneMover | Takes a pose, calculates the best possible center and normal from the topology object (through spanfile from OCTOPUS) and the coordinates of the pose CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!! |
| CTransformIntoMembraneMoverCreator | Mover Creator |
| CTranslationMover | Translation vector can be defined in -mp:setup center flag to translate the new pose to. The mover is a general mover but used mainly on membrane proteins, that's why we use this flag here The default jump is going to be the membrane jump, but you can also specify your own |
| CTranslationMoverCreator | Mover Creator |
| CTranslationRotationMover | Translation and Rotation of a pose. The new position can be defined by the -mp:setup center and normal flags. The mover is a general mover, but used mainly on membrane proteins, that's why we use this flag here. The default jump is going to be the membrane jump, but you can also specify your own. See above for the TranslationMover and the RotationMover |
| CTranslationRotationMoverCreator | Mover Creator |
| ►Nmetal_interface | |
| CAddZincSiteConstraints | Add metalsite geometry constraints to pose |
| CMatchGrafter | |
| CMetalSiteResidue | |
| CZincHeterodimerMover | |
| CZincSiteFinder | |
| ►Nmotif_grafting | ...that lives inside of motif_grafting.. |
| ►Nmovers | ...and belongs to the movers class.. |
| Cmotif2scaffold_data | Structure that contains the motif2scaffold_indexes data in a vector and adds fields for fragment matching information |
| Cmotif2scaffold_indexes | Structure that contains the data of corresponding fragments in the motif and scaffold |
| CMotifGraftCreator | |
| CMotifGraftMover | |
| CMotifMatch | |
| ►Nmotifs | |
| CBuildPosition | |
| CIRCollection | |
| CLigandMotifSearch | |
| CMotif | |
| CMotifDnaPacker | |
| CMotifDnaPackerCreator | |
| CMotifHit | |
| CMotifLibrary | |
| CMotifSearch | |
| CSingleMotif | |
| ►Nmoves | |
| CChangeFoldTreeMover | |
| CCompositionMover | |
| CCycleMover | CycleMover iterates through its vector of Movers one at a time over many calls to apply() |
| CCyclicMover | |
| CDsspMover | |
| CDsspMoverCreator | |
| CDualMonteCarlo | |
| CEXCN_Converged | |
| CFastLinearFunc | |
| CFilterMover | |
| CFilterReporterMover | A FilterMover that also calls report() on apply() |
| CGeometricFunc | Ramps rapidly from the starting value to the final value. Not 1 at x=1. Doesn't really finish at (1,1). func(x) = 1 - exp( -1 * x * inv_xval_at_0p5 * 0.6931 ); |
| CIfMover | |
| CIfMoverCreator | |
| CInvGeometricFunc | Ramps slowly from the starting value to the final value Non-zero for x = 0. Doesn't really start at (0,0). func(x) = exp( -1 * ( 1 - x ) / ( 1 - xval_at_0p5 ) * 0.6931 ); |
| CIteratedConvergenceMover | A mover that repeatedly applies a sub-mover (up to a given maximum) until the given filter returns values within a certain delta for a given number of cycles |
| CIteratedConvergenceMoverCreator | |
| CJumpOutMover | |
| CLinearFunc | |
| CMCShowMover | |
| CMonteCarlo | This object is responsible for all of the major functions needed in a Monte Carlo simulation. Its main purpose is to apply the Metropolis Criterion on a pose, based on a ScoreFunction, temperature, and the previously accepted pose. It stores the lowest-energy pose ecountered, the last-accepted pose in the simulation, and various other statistics |
| CMonteCarloExceptionConverge | |
| CMonteCarloUtil | MCResetMover applies a monte carlo reset |
| CMoveMapMover | |
| CMover | |
| CMoverApplyingMover | |
| CMoverContainer | |
| CMoverCreator | Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class |
| CMoverFactory | |
| CMoverForPoseList | |
| CMoverRegistrator | This templated class will register an instance of an MoverCreator (class T) with the MoverFactory. It will ensure that no MoverCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CMoverStatistics | |
| CNullMover | |
| CPDBDumpMover | |
| CPoseCondition | |
| CProfilerMover | |
| CPyMolMover | |
| CPyMolMoverCreator | |
| CPyMolObserver | |
| CRampingFunc | |
| CRampingMover | |
| CRampingMoverCreator | |
| CRandomMover | RandomMover picks a random move and applies it |
| CRandomMoverCreator | |
| CRepeatMover | A Mover that repeats an input Mover a user-specified number of times |
| CReplicaExchangeMC | |
| CResId | |
| CSequenceMover | A Mover that iterates through a vector of Movers, applying each one sequentially |
| CSimulatedTempering | |
| CStructureRestrictor | |
| CTrialCounter | |
| CTrialMover | A TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object |
| ►CUDPSocketClient | PyMolMover helper class. Handle low level UDP transactions stuff. This is a port of original Python version of UDP socket client written writen for PyRosetta |
| CUUID | Unique id of this socket client |
| CVectorPoseMover | |
| CWhileMover | |
| ►Nmpi_refinement | |
| CClusterer | |
| CMethodParams | |
| CMPI_Refine_Emperor | |
| CMPI_Refine_Master | |
| CMPI_Refinement | |
| CMultiObjective | |
| CScheduler | |
| CSerial_Refine | |
| CStructAvrgMover | |
| CWorkUnit_bbGauss | |
| CWorkUnit_CombinePose | |
| CWorkUnit_FragInsert | |
| CWorkUnit_KicCloser | |
| CWorkUnit_LoopHash | |
| CWorkUnit_MD | |
| CWorkUnit_NormalMode | |
| CWorkUnit_PartialAbinitio | |
| CWorkUnit_RamaPerturber | |
| CWorkUnit_Relax | |
| CWorkUnit_Sampler | |
| ►Nmultistate_design | |
| CMetricCalculatorFitnessFunction | |
| CMultiStateAggregateFunction | |
| CMultiStateEntity | |
| CMultiStateFitnessFunction | |
| CMultiStatePacker | |
| CPackingState | |
| CPartitionAggregateFunction | |
| CPosType | |
| CPosTypeCreator | |
| CSingleState | |
| CSingleStateEntityData | |
| CSingleStateFitnessFunction | |
| ►Nncbb | |
| ►Noop | |
| COopCreatorMover | |
| COopCreatorMoverCreator | |
| COopDockDesignProtocol | |
| COopDockDesignProtocolCreator | |
| CNcbbDockDesignProtocol | |
| CNcbbDockDesignProtocolCreator | |
| ►Nneighbor | |
| CNeighborhood | A class to determine the neighborhood of a set of residues within a pose |
| ►Nnoesy_assign | |
| CCovalentCompliance | WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST JOB-SPECIFIC DATA AND MAKES EVERYTHING THAT RELIES ON IT THREAD-UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED |
| ►CCrossPeak | |
| CSpin | Single dimension of a multidimensional peak, stores putative assignments as indices into Resonance table |
| CCrossPeak3D | |
| CCrossPeak4D | |
| CCrossPeakInfo | Shared information about CrossPeak (one for each proton dimension) |
| CCrossPeakList | |
| CDistanceScoreMover | Maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility) |
| CEXCN_AssignmentNotFound | |
| CEXCN_FileFormat | |
| CEXCN_NoesyAssign | |
| CEXCN_UnknownAtomname | |
| CEXCN_UnknownResonance | |
| CFloatingResonance | |
| CFoldResonance | |
| ►CFragsToAtomDist | |
| CDistanceRecord | |
| CLabelResonance | |
| CMethylNameLibrary | |
| CMethylNames | |
| CNoesyModule | WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY |
| CPeakAssignment | Fast access to assignments that are stored in CrossPeak – similar to FragID WARNING WARNING WARNING THREAD UNSAFE. THIS CLASS USES THE FUNCTION covalent_compliance WHICH RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance |
| CPeakAssignmentParameters | |
| CPeakAssignmentResidueMap | Fast access to assignments by residue number |
| CPeakCalibrator | |
| CPeakCalibratorMap | |
| CPeakFileFormat | |
| CPeakFileFormat_Base | |
| CPeakFileFormat_Sparky | |
| CPeakFileFormat_xeasy | |
| CPeakFileFormat_xpk | |
| CProtonResonance | |
| CResonance | |
| CResonanceList | |
| CStructureDependentPeakCalibrator | |
| CStructureIndependentPeakCalibrator | |
| ►Nnonlocal | |
| CBiasedFragmentMover | |
| CChunk | |
| CHelixRotate | |
| CPolicy | |
| CPolicyFactory | |
| CRegion | |
| CSheetTranslate | |
| CSimpleTreeBuilder | |
| CSingleFragmentMover | |
| CSingleFragmentMoverCreator | |
| ►CSmoothPolicy | |
| CCandidate | |
| CStarTreeBuilder | |
| CTreeBuilder | |
| CTreeBuilderFactory | |
| CUniformPolicy | |
| ►Nnormalmode | |
| CCartesianNormalModeMover | |
| CContactStruct | |
| CNormalMode | |
| CNormalModeMinimizer | High-level atom tree minimizer class |
| CNormalModeMinimizerCreator | |
| CNormalModeMultifunc | Atom tree multifunction class |
| CNormalModeRelaxMover | |
| CTorsionNormalModeMover | |
| ►Noptimize_weights | |
| CConstraintedOptimizationWeightFunc | |
| CDDGBindOptEData | |
| CDDGMutationOptEData | |
| CDGBindOptEData | Score a "bound" and an "unbound" structure, and minimize the squared error between the difference in their scores and the experimental delta_G of binding |
| CIterativeOptEDriver | |
| CNestedEnergyTermDDGMutationOptEData | |
| CNestedEnergyTermPNatAAOptEPositionData | |
| COptEData | |
| COptEMultifunc | OptE mode multifunction class |
| COptEPositionData | |
| COptEPositionDataFactory | |
| COptEVariableExpression | |
| CPNatAAOptEPositionData | |
| CPNatAAOptERotamerData | |
| CPNatLigPoseOptEData | |
| CPNatRotOptEPositionData | |
| CPNatRotOptERotamerData | |
| CPNatStructureOptEData | |
| CPSSMOptEPositionData | |
| CScaleAnnealerTemperatureOperation | |
| CSingleStructureData | |
| CWeightRangeConstraint | |
| CWrappedOptEExpressionCreator | |
| CWrapperOptEMultifunc | OptE mode multifunction class |
| ►Noutputter | |
| CFormatStringOutputter | |
| COutputter | |
| CPDBOutputter | |
| CResFileOutputter | |
| CSilentFileOutputter | |
| ►Npack_daemon | |
| CBasicSimAnnealerRepacker | |
| CDaemonSet | |
| CDenseIGRepacker | |
| CDoubleDenseIGRepacker | |
| CDynamicAggregateFunction | |
| CDynamicAggregateFunctionDriver | |
| CEntityCorrespondence | |
| CEntityFunc | |
| CEntityFuncExpressionCreator | |
| CEntityHistoryLT | |
| CExpExpression | |
| CFASTER_IG_Repacker | |
| CInSetExpression | Returns "true" if the expression ex evaluates to one of a set of indicated values |
| CIterativeVectorExpression | |
| CLnExpression | |
| CMPIMultistateFitnessFunction | |
| CMultistateAggregateFunction | |
| CMultistateFitnessFunction | |
| CNPDPropCalculator | |
| CNPDPropCalculatorCreator | |
| CPackDaemon | |
| CPowExpression | |
| CQuickRepacker | |
| CRotamerSubsetRepacker | |
| CStructureFileNames | |
| CSurrogateVariableExpression | Stores the result of the surragate expression as if this expression were a variable, but defers to the root expression for questions of deriviatives and which variables are active (this is not a real variable) |
| CTopEntitySet | |
| CVariableVectorExpression | |
| CVectorExpression | |
| CVectorExpressionCreator | |
| CVectorFunction | |
| CVectorFunction2 | |
| CVMax | |
| CVMaxBy | Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the largest value in expression 1 |
| CVMin | |
| CVMinBy | Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the smallest value in expression 1 |
| ►Npb_potential | |
| CSetupPoissonBoltzmannPotential | |
| CSetupPoissonBoltzmannPotentialCreator | |
| ►Npmut_scan | |
| CAlterSpecDisruptionDriver | |
| CMutant | |
| CMutationData | |
| CPointMutScanDriver | |
| ►Npockets | |
| ►CCCluster | @ Cluster of exemplar points |
| CCxyz | |
| CCClusterSet | @ Set of clusters of exemplar points |
| CComparisonGrid | @ |
| CDarcParticleSwarmMinimizer | |
| CEggshellGrid | @ |
| CElectrostaticpotentialGrid | |
| CFingerprintBase | |
| CFingerprintMultifunc | Atom tree multifunction class |
| CGenPharmacophore | |
| CNonPlaidFingerprint | |
| ►CPCluster | @ Cluster of Pocket points |
| CCxyz | |
| CPClusterSet | @ Set of cluster of pocket points |
| CPlaidFingerprint | |
| CPocketConstraint | This constraint favors creating a pocket suitable for a small-molecule |
| CPocketConstraintCreator | Mover creator for the PocketConstraint constraint |
| CPocketExemplarMultifunc | Pocket multifunction class, does objective function of optimization |
| CPocketGrid | @ |
| Cray_distance_derivs | |
| CSmallMol | |
| Cspherical_coor_triplet | |
| CTargetPocketGrid | @ |
| Ctriplet_and_originnum | |
| CUnionEdge | |
| ►Npose_reporters | |
| CEnergyReporter | Report the pose score or a specific energy term |
| CEnergyReporterCreator | |
| CFilterReporter | Use a RosettaScripts filter as a reporter |
| CFilterReporterCreator | |
| CRMSDReporter | Report the RMSD between two poses |
| CRMSDReporterCreator | |
| ►Npose_selectors | |
| CAndSelector | AND Selector: select poses that were selected by all child selectors |
| CAndSelectorCreator | |
| CClusterPoseSelector | Cluster poses by some real property as reported by the connected reporter (RMSD, ...) |
| CClusterPoseSelectorCreator | |
| CFilter | Use existing RosettaScripts filter as a post selector |
| CFilterCreator | |
| CLogicalSelector | Logical boolean selector base class |
| COrSelector | OR Selector: select poses that were selected by any child selectors |
| COrSelectorCreator | |
| CTopNByProperty | Select top N poses by a specific pose property |
| CTopNByPropertyCreator | |
| ►Nprotein_interface_design | |
| ►Nfilters | |
| CAtomicContactCountFilter | |
| CAtomicContactCountFilterCreator | |
| CAverageDegreeFilter | |
| CAverageDegreeFilterCreator | |
| CBindingStrainFilter | |
| CBindingStrainFilterCreator | |
| CBoltzmannFilter | |
| CBoltzmannFilterCreator | |
| CClashWithTargetFilter | |
| CClashWithTargetFilterCreator | |
| CDesignableResiduesFilter | |
| CDesignableResiduesFilterCreator | |
| CDisulfideFilter | Filters for structures which could form a disulfide bond across the docking interface |
| CDisulfideFilterCreator | |
| CFilterScanFilter | |
| CFilterScanFilterCreator | |
| CFNatFilter | |
| CFNatFilterCreator | |
| CHbondsToAtomFilter | Returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class |
| CHbondsToAtomFilterCreator | |
| CHbondsToResidueFilter | Returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class |
| CHbondsToResidueFilterCreator | |
| CInterfaceHolesFilter | |
| CInterfaceHolesFilterCreator | |
| CIRmsdFilter | |
| CIRmsdFilterCreator | |
| CLRmsdFilter | |
| CLRmsdFilterCreator | |
| CRelativeSegmentFilter | Returns the residues aligned to a segment on the input pdb to the source pdb |
| CRelativeSegmentFilterCreator | |
| CRmsdFilter | |
| CRmsdFilterCreator | |
| CRmsdSimpleFilter | |
| CRmsdSimpleFilterCreator | |
| CSequenceRecoveryFilter | |
| CSequenceRecoveryFilterCreator | |
| CSpecificResiduesNearInterfaceFilter | |
| CSpecificResiduesNearInterfaceFilterCreator | |
| CSSamountFilter | |
| CSSamountFilterCreator | |
| CStubScoreFilter | |
| CStubScoreFilterCreator | |
| CStubScoreLoopsFilter | |
| CStubScoreLoopsFilterCreator | |
| CTorsion | |
| CTorsionCreator | |
| ►Nmovers | |
| CAddChainBreak | Mover that sets a chainbreak in a specified position |
| CAddChainBreakCreator | |
| CAddSidechainConstraintsToHotspots | |
| CAddSidechainConstraintsToHotspotsCreator | |
| CBackrubDDMover | |
| CBackrubDDMoverCreator | |
| CBestHotspotCstMover | Remove all HotspotCst's from the pose except the best X |
| CBestHotspotCstMoverCreator | |
| CBuildAlaPose | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CBuildAlaPoseCreator | |
| CDesignMinimizeHbonds | Used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined |
| CDesignMinimizeHbondsCreator | |
| CDisulfideMover | |
| CDisulfideMoverCreator | |
| CDockAndRetrieveSidechains | |
| CDockAndRetrieveSidechainsCreator | |
| CDockWithHotspotMover | A mover to mutate a single residue |
| CDockWithHotspotMoverCreator | |
| CFavorNativeResiduePreCycle | |
| CFavorNativeResiduePreCycleCreator | |
| CFavorNonNativeResiduePreCycle | |
| CFavorNonNativeResiduePreCycleCreator | |
| CHotspotDisjointedFoldTreeMover | |
| CHotspotDisjointedFoldTreeMoverCreator | |
| CHotspotHasherMover | |
| CHotspotHasherMoverCreator | |
| CInterfaceRecapitulationMover | Pure virtual base class for movers which redesign and repack the interface |
| CInterfaceRecapitulationMoverCreator | |
| CLoopFinder | |
| CLoopFinderCreator | |
| CLoopLengthChange | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CLoopLengthChangeCreator | |
| CLoopMoverFromCommandLine | |
| CLoopMoverFromCommandLineCreator | |
| CLoopOver | Essentially the same as the WhileMover but allows parsing and cloning. Will be removed at a future point. This should now be incorporated into WhileMover |
| CLoopOverCreator | |
| CLoopRemodel | |
| CLoopRemodelCreator | |
| CMapHotspot | |
| CMapHotspotCreator | |
| CPatchdockTransform | Wrapper around protocols::protein_interface_design::PatchdockReader class. That class is derived from JobInputter and handles input situations that involve patchdock output files. Here, we provide an entry point for a patchdock transformation within the RosettaScripts trajectory |
| CPatchdockTransformCreator | |
| CPeptideStapleDesignMover | Introduces a peptide staple (ala G. Verdine) to the pose |
| CPeptideStapleDesignMoverCreator | |
| CPlacementAuctionMover | |
| CPlacementAuctionMoverCreator | |
| CPlacementMinimizationMover | Simple rb-minimization in a bb-stub constraint biased forcefield. Note that this mover is dependent on a placement mover for setting its stubsets |
| CPlacementMinimizationMoverCreator | |
| CPlaceOnLoop | |
| CPlaceOnLoopCreator | |
| CPlaceSimultaneouslyMover | Choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria |
| CPlaceSimultaneouslyMoverCreator | |
| CPlaceStubMover | Choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria |
| CPlaceStubMoverCreator | |
| CPrepackMover | |
| CPrepackMoverCreator | |
| CProteinInterfaceMultiStateDesignMover | Wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework |
| CProteinInterfaceMultiStateDesignMoverCreator | |
| CRandomMutation | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CRandomMutationCreator | |
| CRepackMinimize | One round of design/repacking followed by interface sc/bb and rigid-body minimization |
| CRepackMinimizeCreator | |
| CSaveAndRetrieveSidechains | Saves a pose and reapplies its sequence and rotamers at a later stage. The constructor saves the initial pose, and then any calls to apply replace the residues on the input pose with that saved pose. Notice, that only ALA positions will be replaced, so this is meant to work strictly along with BuildAlaPose moves. This way, if in the design process an interface residue is designed, that will not be reverted to w/t |
| CSaveAndRetrieveSidechainsCreator | |
| CSetAtomTree | Mover that sets a user-defined atom tree |
| CSetAtomTreeCreator | |
| CSetTemperatureFactor | Set the temperature (b-)factor column in the PDB according to som filter's value. The filter needs to be ResId-compatible, i.e. to report values on a per-residue basis |
| CSetTemperatureFactorCreator | |
| CSetupHotspotConstraintsLoopsMover | |
| CSetupHotspotConstraintsLoopsMoverCreator | |
| CSetupHotspotConstraintsMover | |
| CSetupHotspotConstraintsMoverCreator | |
| CShoveResidueMover | |
| CShoveResidueMoverCreator | |
| CSpinMover | |
| CSpinMoverCreator | |
| CSubroutineMover | |
| CSubroutineMoverCreator | |
| CTaskAwareCsts | Applies csts (currently only coordinate csts) to every designable position in pose according to taskoperations |
| CTaskAwareCstsCreator | |
| CTopologyBrokerMover | Designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines |
| CTopologyBrokerMoverCreator | |
| CTryRotamers | |
| CTryRotamersCreator | |
| CVLB | User interface for YAB's Variable Length Build |
| CVLBCreator | |
| CDockDesignFilterFactory | |
| CFavorNativeResidue | |
| CFavorNonNativeResidue | |
| CParserJobInputter | |
| CParserJobInputterCreator | |
| CPatchdockReader | |
| CReportPSSMDifferences | |
| CReportSequenceDifferences | |
| CRevert | |
| CTransformation | |
| ►Nqsar | |
| ►Nscoring_grid | |
| CAllAtomNormalization | |
| CAtrGrid | |
| CAtrGridCreator | |
| CChargeAtom | Very light representation of an atom that is just a charge and a cartesian space position |
| CChargeGrid | |
| CChargeGridCreator | |
| CChiAngleNormalization | |
| CClassicGrid | |
| CClassicGridCreator | |
| CConstantScoreBase | |
| CGridBase | |
| CGridCreator | Abstract class fora mover factory. The creator class is responsible for creating a particular mover class |
| CGridFactory | |
| CGridInitMover | |
| CGridInitMoverCreator | |
| CGridManager | |
| CGridRegistrator | This templated class will register an instance of a GridCreator (class T) with the GridFactory. It will ensure that no GridCreator is registered twice and centralizes the registration logic |
| CHbaGrid | |
| CHbaGridCreator | |
| CHbdGrid | |
| CHbdGridCreator | |
| CHeavyAtomNormalization | |
| CLigandPropertyScore | |
| CLigandPropertyScoreCreator | |
| CMolecularWeightNormalization | |
| CRepGrid | |
| CRepGridCreator | |
| CScoreNormalization | |
| CScoringGridLoader | A class for loading ScoringGrids into the XML parser's basic::datacache::DataMap |
| CScoringGridLoaderCreator | |
| CShapeGrid | |
| CShapeGridCreator | |
| CSingleGrid | |
| CSolvationGrid | |
| CSolvationGridCreator | |
| CSolvationMetaGrid | |
| CSolvationMetaGridCreator | |
| CVdwGrid | |
| CVdwGridCreator | |
| CColorGradient | |
| CqsarCreator | |
| CqsarMap | |
| CqsarMover | |
| CqsarOptData | |
| CqsarOptFunc | |
| CqsarPoint | |
| CRenderGridsToKinemage | |
| CRenderGridsToKinemageCreator | |
| ►Nrbsegment_relax | |
| CAutoRBMover | |
| CCCDMoveWrapper | |
| CFragInsertAndAlignMover | Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply' |
| CGaussianRBSegmentMover | |
| CHelicalGaussianMover | |
| CIdealizeHelicesMover | |
| CIdealizeHelicesMoverCreator | |
| CMakeStarTopologyMover | |
| CMakeStarTopologyMoverCreator | |
| COptimizeThreadingMover | |
| COptimizeThreadingMoverCreator | |
| CRB_lt | |
| CRBResidueRange | RB residue range |
| CRBSegment | Rigid-body segments in a protein |
| CRBSegmentMover | Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply' |
| CRBSegmentRelax | |
| CSequenceShiftMover | |
| CStrandTwistingMover | |
| ►Nrelax | |
| ►Nmembrane | |
| CMPFastRelaxMover | |
| CMPFastRelaxMoverCreator | Mover Creator |
| CAtomCoordinateCstMover | |
| CAtomCoordinateCstMoverCreator | |
| ►CCentroidRelax | Relax a pose using Frank Dimaio's smooth centroid statistics. Currently under optimization |
| Cparameters | Container for ramp settings |
| CClassicRelax | A functor class which implements the classic Rosetta++ pose_relax protocol |
| CClassicRelaxCreator | |
| CFastRelax | |
| CFastRelaxCreator | |
| CMiniRelax | |
| CRelaxProtocolBase | |
| CRelaxScriptCommand | |
| CSRelaxPose | |
| CWorkUnit_BatchRelax | |
| CWorkUnit_BatchRelax_and_PostRescore | |
| ►Nrigid | |
| CMembraneCenterPerturbationMover | Perturb the pose along membrane normal |
| CMembraneNormalPerturbationMover | Rotation pose around membrane center, perturb the membrane normal vector relative to the pose |
| CMovePoseToMembraneCenterMover | Move pose into a membrane |
| CRigidBodyDeterministicSpinMover | |
| CRigidBodyDofPerturbMover | This Mover does a perturbation defined by the rotational and translational magnitudes. Allowed dofs are specified by a map. Can be defined through a move map or with rb_jump. A single jump is selected |
| CRigidBodyDofRandomizeMover | A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only |
| CRigidBodyDofRandomTransMover | A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a randomly selected jump |
| CRigidBodyDofSeqPerturbMover | This Mover does a perturbation defined by the rotational and translational magnitudes. Allowed dofs are specified by a map. Can be defined through a move map or with rb_jump. All jumps are selected in random order |
| CRigidBodyDofSeqRandomizeMover | A Mover that initializes all DOFs in the system randomly. It starts with rotation angles only |
| CRigidBodyDofSeqTransMover | A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. Jumps are visited in random order |
| CRigidBodyDofTransMover | A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump |
| CRigidBodyMotionMover | |
| CRigidBodyMover | Rigid-body random translate/rotate around centroid of downstream side of a jump |
| CRigidBodyPerturbMover | This Mover does a perturbation defined by the rotational and translational magnitudes |
| CRigidBodyPerturbNoCenterMover | Does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump |
| CRigidBodyPerturbNoCenterMoverCreator | |
| CRigidBodyPerturbRandomJumpMover | |
| CRigidBodyRandomizeMover | |
| CRigidBodySpinMover | A Mover that spins about a random axis |
| CRigidBodyTransMover | This Mover translate down an axis |
| CRigidBodyTransMoverCreator | |
| CRollMover | |
| CRollMoverCreator | |
| CRotateJumpAxisMover | |
| CUniformRigidBodyCM | |
| CUniformRigidBodyCMCreator | |
| CUniformRigidBodyMover | |
| CUniformRigidBodyMoverCreator | |
| CUniformSphereTransMover | Rigid-body move that evenly samples the space within a sphere |
| CWholeBodyRotationMover | Rotate the whole pose |
| CWholeBodyTranslationMover | Translate the whole pose |
| ►Nrosetta_scripts | |
| CAdditionalOutputWrapper | |
| CAdditionalOutputWrapperCreator | |
| CMultipleOutputWrapper | |
| CMultipleOutputWrapperCreator | |
| CMultiplePoseMover | |
| CMultiplePoseMoverCreator | |
| ►CParsedProtocol | |
| CMoverFilterPair | |
| CParsedProtocolCreator | |
| CPosePropertyReporter | |
| CPosePropertyReporterCreator | Abstract base class for a PosePropertyReporter factory; the Creator class is responsible for creating a particular PosePropertyReporter class |
| CPosePropertyReporterFactory | |
| CPosePropertyReporterRegistrator | This templated class will register an instance of an PosePropertyReporterCreator (class T) with the PosePropertyReporterFactory. It will ensure that no PosePropertyReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CPoseSelector | |
| CPoseSelectorCreator | Abstract base class for a PoseSelector factory; the Creator class is responsible for creating a particular PoseSelector class |
| CPoseSelectorFactory | |
| CPoseSelectorRegistrator | This templated class will register an instance of an PoseSelectorCreator (class T) with the PoseSelectorFactory. It will ensure that no PoseSelectorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRosettaScriptsParser | Reading the xml file and generating the mover |
| CSavePoseMover | Mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls |
| CSavePoseMoverCreator | |
| ►Nrotamer_recovery | |
| CPerNativeRRReporterHuman | |
| CRotamerRecovery | |
| CRotamerRecoveryFactory | Create Rotamer_Recovery Reporters |
| CRotamerRecoveryMover | |
| CRotamerRecoveryMoverCreator | |
| CRotamerRecoveryRegistrator | This templated class will register an instance of an RotamerRecoveryCreator (class T) with the RotamerRecoveryFactory. It will ensure that no RotamerRecoveryCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place |
| CRRComparer | The comparison functionality for the rotamer recovery test |
| CRRComparerAutomorphicRMSD | |
| CRRComparerAutomorphicRMSDCreator | |
| CRRComparerChiDiff | |
| CRRComparerChiDiffCreator | |
| CRRComparerCreator | The Creator class is responsible for creating a particular mover class |
| CRRComparerElecDensDiff | |
| CRRComparerElecDensDiffCreator | |
| CRRComparerRotBins | |
| CRRComparerRotBinsCreator | |
| CRRProtocol | The protocol to run to compute the rotamer recovery the rotamer recovery test |
| CRRProtocolCreator | The Creator class is responsible for creating a particular mover class |
| CRRProtocolMinPack | |
| CRRProtocolMinPackCreator | |
| CRRProtocolMover | |
| CRRProtocolMoverCreator | |
| CRRProtocolPackRotamers | |
| CRRProtocolPackRotamersCreator | |
| CRRProtocolReferenceStructure | |
| CRRProtocolReferenceStructureCreator | |
| CRRProtocolRelax | |
| CRRProtocolRelaxCreator | |
| CRRProtocolRotamerTrials | |
| CRRProtocolRotamerTrialsCreator | |
| CRRProtocolRTMin | |
| CRRProtocolRTMinCreator | |
| CRRReporter | The reporting functionality for the rotamer recovery test |
| CRRReporterCreator | The Creator class is responsible for creating a particular mover class |
| CRRReporterHuman | The reporting functionality for the rotamer recovery test in a human readable format |
| CRRReporterHumanCreator | |
| CRRReporterSimple | |
| CRRReporterSimpleCreator | |
| CRRReporterSQLite | |
| CRRReporterSQLiteCreator | |
| ►NRotamerDump | |
| CRotamerDumpMover | Mover for dumping interaction graph information. The information is appended to the current job |
| ►Nrpc | |
| CBasicCmdLineInit | |
| CBasicInit | |
| CJSON_RPC | |
| ►Nsasa_scores | |
| CPoly | |
| CPPoly | |
| ►Nscoring | |
| ►Nmethods | |
| ►Npcs | |
| CGridSearchIterator | |
| CPCS_data | |
| CPCS_data_input | PCS_data_input contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_input_manager | |
| CPCS_data_per_lanthanides | |
| CPCS_Energy | |
| CPCS_Energy_parameters_manager | |
| CPCS_file_data | PCS_file_data contain all the information of a .npc file one per lanthanide |
| CPCS_line_data | PCS_line_data class: hold a line of the input file information (.npc format) One PCS_line_data per line in the input file |
| CPCS_tensor | |
| CPseudocontactShiftEnergyCreator | |
| CTensorsOptimizer | |
| ►Npcs2 | |
| CGridSearchIterator | |
| CGridSearchIteratorCA | |
| CPcsDataCenter | |
| CPcsDataCenterManager | |
| CPcsDataCenterManagerSingleton | |
| CPcsDataLanthanide | |
| CPcsEnergy | |
| CPcsEnergyCreator | |
| CPcsEnergyParameter | |
| CPcsEnergyParameterManager | |
| CPcsGridSearchParameter | |
| CPcsGridSearchParameterManager | |
| CPcsInputCenter | PcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set |
| CPcsInputCenterManager | |
| CPcsInputFile | PcsInputFile contain all the information of a .npc file one per lanthanide |
| CPcsInputLine | PcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file |
| CPcsTensor | |
| CTensorsOptimizer | |
| CTensorsOptimizerFix | |
| CTensorsOptimizerSvd | |
| ►NpcsTs1 | |
| CGridSearchIterator_Ts1 | |
| CPCS_data_input_manager_Ts1 | |
| CPCS_data_input_Ts1 | PCS_data_input_Ts1 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts1 | |
| CPCS_data_Ts1 | |
| CPCS_Energy_parameters_manager_Ts1 | |
| CPCS_Energy_Ts1 | |
| CPCS_file_data_Ts1 | PCS_file_data_Ts1 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts1 | PCS_line_data_Ts1 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts1 per line in the input file |
| CPCS_tensor_Ts1 | |
| CPseudocontactShiftEnergyCreator_Ts1 | |
| CTensorsOptimizer_Ts1 | |
| ►NpcsTs2 | |
| CGridSearchIterator_Ts2 | |
| CPCS_data_input_manager_Ts2 | |
| CPCS_data_input_Ts2 | PCS_data_input_Ts2 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts2 | |
| CPCS_data_Ts2 | |
| CPCS_Energy_parameters_manager_Ts2 | |
| CPCS_Energy_Ts2 | |
| CPCS_file_data_Ts2 | PCS_file_data_Ts2 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts2 | PCS_line_data_Ts2 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts2 per line in the input file |
| CPCS_tensor_Ts2 | |
| CPseudocontactShiftEnergyCreator_Ts2 | |
| CTensorsOptimizer_Ts2 | |
| ►NpcsTs3 | |
| CGridSearchIterator_Ts3 | |
| CPCS_data_input_manager_Ts3 | |
| CPCS_data_input_Ts3 | PCS_data_input_Ts3 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts3 | |
| CPCS_data_Ts3 | |
| CPCS_Energy_parameters_manager_Ts3 | |
| CPCS_Energy_Ts3 | |
| CPCS_file_data_Ts3 | PCS_file_data_Ts3 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts3 | PCS_line_data_Ts3 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts3 per line in the input file |
| CPCS_tensor_Ts3 | |
| CPseudocontactShiftEnergyCreator_Ts3 | |
| CTensorsOptimizer_Ts3 | |
| ►NpcsTs4 | |
| CGridSearchIterator_Ts4 | |
| CPCS_data_input_manager_Ts4 | |
| CPCS_data_input_Ts4 | PCS_data_input_Ts4 contain all the input information for the PCS. This includes all the information from the .npc files |
| CPCS_data_per_lanthanides_Ts4 | |
| CPCS_data_Ts4 | |
| CPCS_Energy_parameters_manager_Ts4 | |
| CPCS_Energy_Ts4 | |
| CPCS_file_data_Ts4 | PCS_file_data_Ts4 contain all the information of a .npc file one per lanthanide |
| CPCS_line_data_Ts4 | PCS_line_data_Ts4 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts4 per line in the input file |
| CPCS_tensor_Ts4 | |
| CPseudocontactShiftEnergyCreator_Ts4 | |
| CTensorsOptimizer_Ts4 | |
| ►Nsaxs | |
| CPDDFEnergy | |
| CPDDFEnergyCreator | |
| CEnsembleEnergy | |
| CEnsembleEnergyCreator | |
| CInterchainEnvEnergy | |
| CInterchainEnvEnergyCreator | |
| CInterchainPairEnergy | |
| CInterchainPairEnergyCreator | |
| CResidualDipolarCouplingEnergyRigidSegments | |
| CResidualDipolarCouplingEnergyRigidSegmentsCreator | |
| CSpecialRotamerEnergy | |
| CSpecialRotamerEnergyCreator | |
| CImplicitFastClashCheck | |
| CInterchainPotential | Singleton class to hold the interface-derived statistics for residue-pair scores at protein/protein interfaces |
| CInterface | |
| CInterfaceInfo | Keep track of the interface information |
| CResidualDipolarCouplingRigidSegments | ResidualDipolarCouplingRigidSegmentss are mainly handled by this class |
| ►Nseeded_abinitio | |
| CCAcstGenerator | |
| CCAcstGeneratorCreator | |
| CCloseFold | |
| CCloseFoldCreator | |
| CCoordinateCst | |
| CCoordinateCstCreator | |
| CDefineMovableLoops | |
| CDefineMovableLoopsCreator | |
| CGrowPeptides | |
| CGrowPeptidesCreator | |
| CSeedFoldTree | |
| CSeedFoldTreeCreator | |
| CSeedSetupMover | |
| CSeedSetupMoverCreator | |
| CSegmentHybridizer | |
| CSegmentHybridizerCreator | |
| CSwapSegment | |
| CSwapSegmentCreator | |
| ►Nsic_dock | |
| ►Nscores | |
| CMotifHashRigidScore | |
| CTrisBpyScore | |
| CAtomIDHashFunction | |
| CBuriedPolarScore | |
| CCBScore | |
| CCBScoreVisitor | |
| CConstraintSetScore | |
| CCorrectionVisitor | |
| CEdgeStandScore | |
| CHelixScore | |
| CJointScore | |
| CLinkerScore | |
| CNoPoseXYX_Func | |
| CRigidScore | |
| CRose | |
| CSICFast | |
| CVec3 | |
| CXfoxmScore | |
| CxyzStripeHashPoseWithMeta | |
| ►Nsimple_filters | |
| CAbinitioBaseFilter | |
| CAlaScan | |
| CAlaScanFilterCreator | |
| CAngleToVector | |
| CAngleToVectorFilterCreator | |
| CAtomicContactFilter | Detects atomic (<4Ang) contacts between any two atoms of two residues |
| CAtomicContactFilterCreator | |
| CAtomicDistanceFilter | Detects atomic contacts between two atoms of two residues |
| CAtomicDistanceFilterCreator | |
| CAveragePathLengthFilter | |
| CAveragePathLengthFilterCreator | |
| CBatchEvaluator | |
| CBatchNrEvaluator | |
| CBuriedUnsatHbondFilter | Filters based on an upper bound # of buried unsatisfied polar residues |
| CBuriedUnsatHbondFilterCreator | |
| CCamShiftEvaluator | |
| CCamShiftEvaluatorCreator | Creator for the CamShiftEvaluatorCreator class |
| CChiWellRmsdEvaluator | |
| CChiWellRmsdEvaluatorCreator | Creator for the ChiWellRmsdEvaluatorCreator class |
| CCOFilter | |
| CConservedPosMutationFilter | |
| CConservedPosMutationFilterCreator | |
| CConstraintScoreCutoffFilter | |
| CConstraintScoreCutoffFilterCreator | |
| CContactMapEvaluator | |
| CContactMapEvaluatorCreator | Creator for the ContactMapEvaluatorCreator class |
| CDdgFilter | |
| CDdgFilterCreator | |
| CDdGScan | |
| CDdGScanCreator | |
| CDeltaFilter | |
| CDeltaFilterCreator | |
| CDisulfideEntropyFilter | |
| CDisulfideEntropyFilterCreator | |
| CDomainInterfaceFilter | |
| CEnergyPerResidueFilter | |
| CEnergyPerResidueFilterCreator | |
| CEvaluatedTrialMover | |
| CExpiryFilter | |
| CExpiryFilterCreator | |
| CExternalEvaluator | |
| CExtraScoreEvaluatorCreator | Creator for the ExtraScoreEvaluatorCreator class |
| CFileExistFilter | |
| CFileExistFilterCreator | |
| CFileRemoveFilter | |
| CFileRemoveFilterCreator | |
| CGeometryFilter | |
| CGeometryFilterCreator | |
| CHolesFilter | |
| CHolesFilterCreator | |
| CInterfaceBindingEnergyDensityFilter | |
| CInterfaceBindingEnergyDensityFilterCreator | |
| CInterfaceSasaFilter | |
| CInterfaceSasaFilterCreator | |
| CInterRepeatContactFilter | |
| CInterRepeatContactFilterCreator | |
| CIntraRepeatContactFilter | |
| CIntraRepeatContactFilterCreator | |
| CJScoreEvaluator | |
| CJScoreEvaluatorCreator | Creator for the JScoreEvaluatorCreator class |
| CJumpEvaluator | |
| CJumpNrEvaluator | |
| CJumpNrEvaluatorCreator | Creator for the JumpNrEvaluatorCreator class |
| CLoopRmsdEvaluator | |
| CMotifScoreFilter | |
| CMotifScoreFilterCreator | |
| CMultipleSigmoids | Simply takes a list of pdbs and creates relative pose then extract sigmoids and call operator (product) |
| CMultipleSigmoidsFilterCreator | |
| CMutationsFilter | |
| CMutationsFilterCreator | |
| CNativeEvaluatorCreator | Creator for the NativeEvaluatorCreator class |
| CNeighborTypeFilter | |
| CNeighborTypeFilterCreator | |
| CNetChargeFilter | |
| CNetChargeFilterCreator | |
| Cnmer_svm_res_data | |
| CNMerPSSMEnergyFilter | |
| CNMerPSSMEnergyFilterCreator | |
| CNMerSVMEnergyFilter | |
| CNMerSVMEnergyFilterCreator | |
| CNonSequentialNeighborsFilter | |
| CNonSequentialNeighborsFilterCreator | |
| COperator | Simply take a list of filters and combine them using the operation above |
| COperatorFilterCreator | |
| CPackerNeighborGraphFilter | |
| CPackStatFilter | |
| CPackStatFilterCreator | |
| CPalesEvaluator | |
| CPalesEvaluatorCreator | Creator for the PalesEvaluatorCreator class |
| CPDDFScoreFilter | |
| CPoolEvaluatorCreator | Creator for the PoolEvaluatorCreator class |
| CPoseComment | Test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts |
| CPoseCommentFilterCreator | |
| CPoseInfoFilter | Detects atomic contacts between two atoms of two residues |
| CPoseInfoFilterCreator | |
| CPoseMetricEvaluator | |
| CPredictedBurialEvaluator | |
| CPredictedBurialFnEvaluatorCreator | Creator for the PredictedBurialFnEvaluatorCreator class |
| CQuat | |
| CRangeFilter | |
| CRangeFilterCreator | |
| CRDC_Evaluator | |
| CRdcEvaluatorCreator | Creator for the RdcEvaluatorCreator class |
| CRdcSelectEvaluatorCreator | Creator for the RdcSelectEvaluatorCreator class |
| CRdcTargetEvaluatorCreator | Creator for the RdcTargetEvaluatorCreator class |
| CRegionalConnections | |
| CRelativePoseFilter | |
| CRelativePoseFilterCreator | |
| CRepeatParameterFilter | |
| CRepeatParameterFilterCreator | |
| CReportFilter | |
| CReportFilterCreator | |
| CResidueBurialFilter | |
| CResidueBurialFilterCreator | |
| CResidueCountFilter | |
| CResidueCountFilterCreator | |
| CResidueDistanceFilter | |
| CResidueDistanceFilterCreator | |
| CResidueIEFilter | |
| CResidueIEFilterCreator | |
| CResidueSetChainEnergyFilter | |
| CResidueSetChainEnergyFilterCreator | |
| CResiduesInInterfaceFilter | |
| CResiduesInInterfaceFilterCreator | |
| CRGFilter | |
| CRmsdEvaluator | |
| CRmsdEvaluatorCreator | Creator for the RmsdEvaluatorCreator class |
| CRmsdTargetEvaluatorCreator | Creator for the RmsdTargetEvaluatorCreator class |
| CRotamerBoltzmannWeight | |
| CRotamerBoltzmannWeightFilterCreator | |
| CSavePoseConstraintToFileFilter | Detects atomic contacts between two atoms of two residues |
| CSavePoseConstraintToFileFilterCreator | |
| CSaveResfileToDiskFilter | |
| CSaveResfileToDiskFilterCreator | |
| CSAXSScoreFilter | |
| CScoreCutoffFilter | |
| CScoreCutoffFilterCreator | |
| CScoreEvaluator | That rewrites the whole pss struct all previous entries will be lost... probably not what one wants.. |
| CScoreTypeFilter | |
| CScoreTypeFilterCreator | |
| CSelectGdtEvaluator | |
| CSelectMaxsubEvaluator | |
| CSelectRDC_Evaluator | |
| CSelectRmsdEvaluator | |
| CShapeComplementarityFilter | |
| CShapeComplementarityFilterCreator | |
| CSheetFilter | |
| CSidechainRmsdFilter | |
| CSidechainRmsdFilterCreator | |
| CSigmoid | Transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset |
| CSigmoidFilterCreator | |
| CSSMotifFinder | |
| CSSMotifFinderFilterCreator | |
| CStemFinder | |
| CStemFinderFilterCreator | |
| CStructuralSimilarityEvaluator | |
| CStructureSimilarityEvaluatorCreator | Creator for the StructureSimilarityEvaluatorCreator class |
| CSymmetricMotifFilter | |
| CSymmetricMotifFilterCreator | |
| CSymmetricRmsdEvaluator | |
| CTaskAwareSASAFilter | |
| CTaskAwareSASAFilterCreator | |
| CTaskAwareScoreTypeFilter | |
| CTaskAwareScoreTypeFilterCreator | |
| CTerminusDistanceFilter | |
| CTerminusDistanceFilterCreator | |
| CTotalSasaFilter | |
| CTotalSasaFilterCreator | |
| CTruncatedScoreEvaluator | |
| ►Nsimple_moves | |
| ►Nasym_fold_and_dock | |
| CAsymFoldandDockMoveRbJumpMover | |
| CAsymFoldandDockRbTrialMover | |
| ►Nbin_transitions | |
| CInitializeByBins | A mover to set mainchain torsions by bin transition probabilities |
| CInitializeByBinsCreator | |
| CPerturbByBins | A mover to set mainchain torsions by bin transition probabilities |
| CPerturbByBinsCreator | |
| ►Nchiral | |
| CChiralMover | |
| ►Nhbs | |
| CHbsPatcher | |
| ►Noop | |
| COopDPuckMinusMover | |
| COopDPuckPlusMover | |
| COopMover | |
| COopPatcher | |
| COopPuckMinusMover | |
| COopPuckPlusMover | |
| COopRandomPuckMover | |
| COopRandomSmallMover | |
| ►Nrational_mc | |
| CRationalMonteCarlo | |
| ►Nsidechain_moves | |
| CJumpRotamerSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CJumpRotamerSidechainMoverCreator | |
| CPerturbChiSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CPerturbChiSidechainMoverCreator | |
| CPerturbRotamerSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CPerturbRotamerSidechainMoverCreator | |
| CSetChiMover | A mover to change one chi angle |
| CSetChiMoverCreator | |
| CSidechainMCMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CSidechainMCMoverCreator | |
| CSidechainMover | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CSidechainMoverBase | Class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions |
| CSidechainMoverCreator | |
| ►Nsymmetry | |
| CDetectSymmetry | |
| CDetectSymmetryMoverCreator | |
| CExtractAsymmetricPoseMover | |
| CExtractAsymmetricPoseMoverCreator | |
| CExtractAsymmetricUnitMover | |
| CExtractAsymmetricUnitMoverCreator | |
| CFaSymDockingSlideTogether | Slides docking partners together by monitoring fa_rep |
| CNCSResMapping | |
| COrderedSequentialSymmetrySlider | |
| CRandomSymmetrySlider | |
| CSequentialSymmetrySlider | |
| CSetupForSymmetryMover | |
| CSetupForSymmetryMoverCreator | |
| CSetupNCSMover | |
| CSetupNCSMoverCreator | |
| CSymDockingInitialPerturbation | |
| CSymDockingSlideIntoContact | Contrary to the name, slides things apart first, then together |
| CSymEnergyCutRotamerTrialsMover | |
| CSymmetricRMSMover | |
| CSymmetrySlider | |
| CSymMinMover | |
| CSymMinMoverCreator | |
| CSymPackRotamersMover | |
| CSymPackRotamersMoverCreator | |
| CSymRotamerTrialsMover | |
| CSymRotamerTrialsMoverCreator | |
| CSymShakeStructureMover | |
| CTaskAwareSymMinMover | |
| CTaskAwareSymMinMoverCreator | |
| CAddCavitiesMover | |
| CAddChainMover | |
| CAddChainMoverCreator | |
| CAddConstraintsToCurrentConformationMover | |
| CAddConstraintsToCurrentConformationMoverCreator | |
| CAddJobPairData | Add an arbitrary piece of data to the current Job, which will be output in the silent file, database, etc. This is useful for adding metadata to keep track of data generated using multiple experimental conditions. Currently ONLY RosettaScript interface supported |
| CAddJobPairDataCreator | |
| CAlignChainMover | Align a chain in the working pose to a chain. CA superposition |
| CAlignChainMoverCreator | |
| CBackboneMover | BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.) |
| CBBConRotMover | |
| CBBG8T3AMover | Particular gaussian mover from the original paper |
| CBBGaussianMover | Basic class for implementing Gaussian Perturbation of bb |
| CBBGaussianMoverCreator | |
| CBoltzmannRotamerMover | |
| CBoltzmannRotamerMoverCreator | |
| CChainGroupDiscriminator | |
| CChainSplitMover | ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover |
| CChangeAndResetFoldTreeMover | Basic mover used primarily for setting up atomic protocols, especially in generator functions |
| CChangeAndResetFoldTreeMoverCreator | |
| CClassicFragmentMover | A FragmentMover that applies uniform sampling of fragments |
| CClearConstraintsMover | |
| CClearConstraintsMoverCreator | |
| CCombinePoseMover | |
| CConsensusDesignMover | This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed |
| CConsensusDesignMoverCreator | |
| CConstrainToIdealMover | |
| CConstraintSetMover | |
| CConstraintSetMoverCreator | |
| CContingentAcceptMover | |
| CContingentAcceptMoverCreator | |
| CCopyDofMover | |
| CCoupledMover | |
| CCoupledMoverCreator | |
| CCutChainMover | Simple mover that sperates Fv from Fl into two seperate chains |
| CCutChainMoverCreator | |
| CCyclizationMover | |
| CddG | |
| CddGCreator | |
| CDesignRepackMover | Pure virtual base class for movers which redesign and repack the interface |
| CDisulfideInsertionMover | |
| CDME_FilterMover | |
| CDOFHistogramRecorder | |
| CDumpPdb | What you think this can now be assimilated into DumpPdbMover |
| CDumpPdbCreator | |
| CEnergyCutRotamerTrialsMinMover | Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant |
| CEnergyCutRotamerTrialsMover | |
| CExtendedPoseMover | |
| CExtendedPoseMoverCreator | |
| CFavorSequenceProfile | |
| CFavorSequenceProfileCreator | |
| CFavorSymmetricSequence | |
| CFavorSymmetricSequenceCreator | |
| CFindConsensusSequence | |
| CFindConsensusSequenceCreator | |
| CForceDisulfidesMover | Simple mover that fixes disulfides according to a defined list and then simultaneously repacks within 6A shells around each affected cystein residue |
| CForceDisulfidesMoverCreator | |
| CFragmentCost | |
| CFragmentMover | Abstract base class for FragmentMovers |
| CGenericMonteCarloMover | |
| CGenericMonteCarloMoverCreator | |
| CGreenPacker | |
| CGroupDiscriminator | Interface class used to break a pose down into a set of component "groups" where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings |
| CGunnCost | |
| CGunnTuple | |
| CIonizableResidue | |
| CLoadPDBMover | |
| CLoadPDBMoverCreator | |
| CLoadUnboundRotMover | |
| CLoadUnboundRotMoverCreator | |
| ►CLoggedFragmentMover | |
| CItem | |
| CMakePolyXMover | |
| CMakePolyXMoverCreator | |
| CMembraneTopology | A mover to change one torsion angle |
| CMembraneTopologyCreator | |
| CMinimalRotamer | |
| CMinMover | A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set |
| CMinMoverCreator | |
| CMinPackMover | Mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing |
| CMinPackMoverCreator | |
| CMissingDensityToJumpMover | |
| CModifyVariantTypeMover | Adds variant types to selected residues |
| CModifyVariantTypeMoverCreator | |
| CMonteCarloRecover | |
| CMonteCarloRecoverCreator | |
| CMonteCarloReset | |
| CMonteCarloResetCreator | |
| CMonteCarloTest | |
| CMonteCarloTestCreator | |
| CMSDMover | |
| CMSDMoverCreator | |
| CMutateResidue | A mover to mutate a single residue |
| CMutateResidueCreator | |
| CO2M_MutateMover | |
| CPackRotamersMover | A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing |
| CPackRotamersMoverCreator | |
| CPackRotamersMoverLazy | Mover that packs the side-chains using a rotamer library in a lazy fashion |
| CPackRotamersMoverLazyCreator | |
| CPDBReloadMover | |
| CPDBReloadMoverCreator | |
| CPeptideStapleMover | |
| CProlineFixMover | |
| CPSSM2BfactorMover | |
| CPSSM2BfactorMoverCreator | |
| CRandomOmegaFlipMover | |
| CRandomOmegaFlipMoverCreator | |
| CRandomTorsionMover | |
| CRandomTorsionMoverCreator | |
| CRepackSidechainsMover | A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() |
| CRepackSidechainsMoverCreator | |
| CRepeatPropagationMover | |
| CRepeatPropagationMoverCreator | |
| CReportEffectivePKA | Scale density map intensities to match a pose's |
| CReportEffectivePKACreator | |
| CRepulsiveOnlyMover | This mover replace designated residues with glycines, and then assigns a "REPLONLY" residue type to those glycines. Those "REPLONLY" residues will make only repulsive contributions to the overall energy |
| CResetBaselineMover | |
| CResetBaselineMoverCreator | |
| CResidueTypeConstraintMover | |
| CResidueTypeConstraintMoverCreator | |
| CResTypeFragmentMover | |
| CReturnSidechainMover | |
| CRingConformationMover | |
| CRotamerizeMover | Mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set |
| CRotamerTrialsMinMover | |
| CRotamerTrialsMinMoverCreator | |
| CRotamerTrialsMover | |
| CRotamerTrialsMoverCreator | |
| CSaneMinMover | |
| CSaneMinMoverCreator | |
| CScoreMover | |
| CScoreMoverCreator | |
| CSequenceProfileMover | |
| CSequenceProfileMoverCreator | |
| CSetReturningPackRotamersMover | |
| CSetTorsion | A mover to change one torsion angle |
| CSetTorsionCreator | |
| CShakeStructureMover | |
| CShearMover | A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified |
| CShearMoverCreator | |
| CShortBackrubMover | |
| CShortBackrubMoverCreator | |
| CSmallMover | A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified |
| CSmallMoverCreator | |
| CSmoothFragmentMover | |
| CSmoothSymmetricFragmentMover | A SymmetricFragmentMover that applies uniform sampling of fragments |
| CSuperimposeMover | Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O) |
| CSuperimposeMoverCreator | |
| CSwitchChainOrderMover | |
| CSwitchChainOrderMoverCreator | |
| CSwitchResidueTypeSetMover | A mover that switches a pose between residue type sets (e.g. centroid and fullatom) |
| CSwitchResidueTypeSetMoverCreator | |
| CSymmetricFragmentMover | A SymmetricFragmentMover that applies uniform sampling of fragments |
| CTailsScoreMover | |
| CTaskAwareMinMover | |
| CTaskAwareMinMoverCreator | |
| CTorsionDOFMover | TODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code) |
| CTorsionSetMover | |
| CTumble | |
| CTumbleCreator | |
| CUniformRotationMover | Uniform Rotation Mover |
| CUniformTranslationMover | Uniform Translation Mover |
| CUserDefinedGroupDiscriminator | |
| CVirtualRootMover | |
| CVirtualRootMoverCreator | |
| CWobbleMover | A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure |
| ►Nsparta | |
| CANN | |
| CChemicalShiftEvaluator | |
| CChemicalShiftEvaluatorCreator | Creator for the ChemicalShiftsEvaluatorCreator class |
| CCORdata | |
| CGDB | |
| CPDB | |
| CRingData | |
| ►CSparta | |
| CSpartaLib | { most of the original SPARTA class goes into SpartaLib – to be reused between different evaluators.. |
| ►Nss_prediction | |
| CSS_predictor | |
| ►Nstar | |
| CExtender | |
| CStarAbinitio | |
| ►Nstepwise | |
| ►Nlegacy | |
| ►Nmodeler | |
| ►Nprotein | |
| CStepWiseProteinMinimizer | |
| CStepWiseProteinPoseSetup | |
| ►Nrna | |
| CCluster_Member | |
| CRNA_AnalyticLoopCloser | The RNA de novo structure modeling protocol |
| CSlicedPoseWorkingParameters | |
| CStepWiseRNA_Clusterer | |
| CStepWiseRNA_Minimizer | |
| CStepWiseRNA_PoseSelection | |
| CStepWiseRNA_PoseSetup | |
| CStepWiseWorkingParametersSetup | |
| ►Nscreener | |
| CProteinAtrRepScreener | |
| CRNA_AtrRepScreener | |
| CSimplePoseSelection | |
| CSimpleRMSD_Screener | |
| ►Nmodeler | |
| ►Nalign | |
| CStepWiseClusterer | |
| CStepWiseLegacyClusterer | |
| CStepWiseLegacyClustererSilentBased | |
| CStepWisePoseAligner | |
| ►Noptions | |
| CStepWiseBasicModelerOptions | |
| CStepWiseModelerOptions | |
| CStepWiseProteinModelerOptions | |
| CStepWiseRNA_ModelerOptions | |
| ►Npacker | |
| CSideChainCopier | |
| CStepWiseMasterPacker | |
| CStepWisePacker | |
| ►Npolar_hydrogens | |
| CPolarHydrogenPacker | |
| ►Nprecomputed | |
| CPrecomputedLibraryMover | |
| ►Nprotein | |
| ►Nchecker | |
| CProteinAtrRepChecker | |
| ►Nloop_close | |
| CStepWiseProteinCCD_Closer | |
| CStepWiseProteinCCD_MultiPoseCloser | |
| CStepWiseProteinKIC_LoopBridger | |
| CInputStreamWithResidueInfo | |
| CMainChainTorsionSet | |
| CStepWiseProteinBackboneSampler | |
| ►Nrna | |
| ►Nbulge | |
| CBulgeApplyMover | |
| CBulgeUnApplyMover | |
| ►Nchecker | |
| CAtom_Bin | |
| CRNA_AtrRepChecker | |
| CRNA_BaseCentroidChecker | |
| CRNA_ChainClosableGeometryChecker | |
| CRNA_ChainClosureChecker | |
| CRNA_VDW_BinChecker | |
| CVDW_RepScreeninfo | |
| ►Nhelix | |
| CRNA_HelixAssembler | The RNA de novo structure modeling protocol |
| ►No2prime | |
| CO2PrimePacker | |
| ►Nphosphate | |
| CMultiPhosphateSampler | |
| CPhosphateMove | |
| CPhosphateMover | |
| ►Nrigid_body | |
| CBaseBin | |
| Ccompare_base_bin | |
| Ccompare_int_pair | |
| ►Nsugar | |
| CStepWiseRNA_VirtualSugarJustInTimeInstantiator | |
| CStepWiseRNA_VirtualSugarSampler | |
| CStepWiseRNA_VirtualSugarSamplerFromStringList | |
| CSugarInstantiateMover | |
| CSugarModeling | |
| CSugarVirtualizeMover | |
| CCombine_Tags_Info | |
| CFilterer_Count | |
| CInternalWorkingResidueParameter | |
| CJump_point | |
| Coutput_data_struct | |
| CResidue_info | |
| CStepWiseRNA_CombineLongLoopFilterer | |
| CStepWiseRNA_CountStruct | |
| CTorsion_Info | |
| ►Nworking_parameters | |
| CStepWiseBasicWorkingParameters | |
| CStepWiseWorkingParameters | |
| CStepWiseConnectionSampler | |
| CStepWiseMinimizer | |
| CStepWiseModeler | |
| ►Nmonte_carlo | |
| ►Nmover | |
| CAddMover | |
| CAddOrDeleteMover | |
| CDeleteMover | |
| CFromScratchMover | |
| CResampleMover | |
| CTransientCutpointHandler | |
| ►Noptions | |
| CStepWiseMonteCarloOptions | |
| ►Nrna | |
| CRNA_AddDeleteMonteCarlo | |
| CRNA_O2PrimeMover | |
| CRNA_TorsionMover | |
| CAttachment | |
| CStepWiseMonteCarlo | |
| CSWA_Move | |
| CSWA_MoveSelector | |
| ►Noptions | |
| CStepWiseBasicOptions | |
| ►Nsampler | |
| ►Ncopy_dofs | |
| CCopyDofStepWiseSampler | |
| CResidueAlternativeSet | |
| CResidueAlternativeStepWiseSampler | |
| CResidueAlternativeStepWiseSamplerComb | |
| CResidueListStepWiseSampler | |
| ►Ninput_streams | |
| CInputStreamStepWiseSampler | |
| ►Nprotein | |
| CProteinBetaAntiParallelStepWiseSampler | |
| CProteinFragmentStepWiseSampler | |
| CProteinMainChainStepWiseSampler | |
| ►Nrigid_body | |
| CEulerAngles | |
| CRigidBodyStepWiseSampler | |
| CRigidBodyStepWiseSamplerValueRange | |
| CRigidBodyStepWiseSamplerWithResidueAlternatives | |
| CRigidBodyStepWiseSamplerWithResidueList | |
| ►Nrna | |
| CRNA_ChiStepWiseSampler | |
| CRNA_KIC_Sampler | |
| CRNA_KinematicCloser | The RNA de novo structure modeling protocol |
| CRNA_MC_MultiSuite | |
| CRNA_MC_Sugar | |
| CRNA_MC_Suite | |
| CRNA_NucleosideStepWiseSampler | |
| CRNA_SugarStepWiseSampler | |
| CRNA_SuiteStepWiseSampler | |
| ►Nscreener | |
| CRNA_TorsionScreener | |
| CJumpStepWiseSampler | |
| CMC_Comb | |
| CMC_OneTorsion | |
| CMC_StepWiseSampler | |
| CNoOpStepWiseSampler | |
| CStepWiseSamplerAny | |
| CStepWiseSamplerBase | |
| CStepWiseSamplerComb | |
| CStepWiseSamplerOneTorsion | |
| CStepWiseSamplerOneValue | |
| CStepWiseSamplerOneValueComb | |
| CStepWiseSamplerSized | |
| CStepWiseSamplerSizedAny | |
| CStepWiseSamplerSizedComb | |
| ►Nscreener | |
| CAnchorSugarScreener | |
| CBaseBinMapUpdater | |
| CBaseCentroidScreener | |
| CBulgeApplier | |
| CCentroidDistanceScreener | |
| CFastForwardToNextResidueAlternative | |
| CFastForwardToNextRigidBody | |
| CIntegrationTestBreaker | |
| CNativeRMSD_Screener | |
| CO2PrimeScreener | |
| CPackScreener | |
| CPartitionContactScreener | |
| CPhosphateScreener | |
| CPoseSelectionScreener | |
| CProteinCCD_ClosureScreener | |
| CResidueContactScreener | |
| CRNA_ChainClosableGeometryResidueBasedScreener | |
| CRNA_ChainClosableGeometryScreener | |
| CRNA_ChainClosableGeometryStubBasedScreener | |
| CRNA_ChainClosureScreener | |
| CSampleApplier | |
| CScorer | |
| CStepWiseResiduePairScreener | |
| CStepWiseScreener | |
| CStubApplier | |
| CStubDistanceScreener | |
| CSugarInstantiator | |
| CTagDefinition | |
| CVDW_BinScreener | |
| ►Nsetup | |
| CStepWiseCSA_JobDistributor | |
| CStepWiseJobDistributor | |
| CStepWiseMonteCarloJobDistributor | |
| CStepWiseSampleAndScreen | |
| ►Nsurface_docking | |
| CCentroidRelaxMover | |
| CFullatomRelaxMover | |
| CSurfaceDockingProtocol | |
| CSurfaceOrientMover | |
| CSurfaceParameters | |
| CSurfaceVectorFallbackConfiguration | |
| CSurfaceVectorFallbackConfigurationCreator | |
| CSurfaceVectorLoader | SurfaceVectorLoader constructs a SurfaceParameters instance from data provided by the resource manager |
| CSurfaceVectorLoaderCreator | |
| CSurfaceVectorOptions | |
| CSurfaceVectorOptionsCreator | |
| ►Nsymmetric_docking | |
| ►Nmembrane | |
| CMPSymDockMover | |
| CMPSymDockMoverCreator | Mover Creator |
| CSymDockBaseProtocol | |
| CSymDockingHiRes | |
| CSymDockingLowRes | |
| CSymDockProtocol | Main Symmetric Docking protocol class |
| CSymDockProtocolCreator | |
| CSymFoldandDockMoveRbJumpMover | |
| CSymFoldandDockMoveRbJumpMoverCreator | |
| CSymFoldandDockRbTrialMover | |
| CSymFoldandDockRbTrialMoverCreator | |
| CSymFoldandDockSlideTrialMover | |
| CSymFoldandDockSlideTrialMoverCreator | |
| CSymInterfaceSidechainMinMover | |
| CSymRestrictTaskForDocking | |
| CSymSidechainMinMover | |
| ►Ntoolbox | |
| ►Nmatch_enzdes_util | |
| CAlignPoseToInvrotTreeMover | Small mover that takes an invrot tree |
| CAllowedSeqposForGeomCst | Simple helper class that holds a list of what sequence positions each geom cst is allowd to be at not sure about the ideal home of this class yet, the matcher task could use it too |
| CCovalentConnectionReplaceInfo | Helper class to allow for removal of covalent constraints |
| CCstResInteractions | |
| CEnzConstraintIO | |
| CEnzConstraintParameters | Class that holds all the parameters for one specific constraint |
| CEnzCstTemplateRes | Helper class for class EnzConstraintParameters, gathers information |
| CEnzCstTemplateResAtoms | Helper class for EnzCstTemplateRes, holds atom ids corresponding |
| CEnzCstTemplateResCache | |
| CEnzdesCacheableObserver | |
| CEnzdesCstCache | Simple class to store the pose specific enzdes constraint information in the actual pose |
| CEnzdesCstParamCache | |
| CEnzdesLoopInfo | |
| CEnzdesLoopsFile | Class to process an enzdes loops file |
| CEnzdesSeqRecoveryCache | |
| CExternalGeomSampler | The external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner |
| CGeomSampleInfo | Class that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB |
| CInvrotCollector | @ brief helper class for collecting all different definitions of invrots from a tree |
| CInvrotTarget | 'root' target against which the inverse rotamers are built abstract base class to allow for invrots being built against any sort of entity |
| CInvrotTree | |
| CInvrotTreeNode | |
| CInvrotTreeNodeBase | Abstract base class for an inverse rotamer tree node. Exists so that the target node (InvrotTreeTarget) and the different geom cst nodes (InvrotTreeNode) have a common base class. This is necessary so that a node can point at its parent node in a tree without having to worry about whether that is a target or a regular node |
| CLigandConformer | |
| CMatchConstraintFileInfo | |
| CMatchConstraintFileInfoList | Simple container class to contain several MatchConstraintFileInfo instances. this can also query the MatchConstraintFileInfos for common upstream restypes and put all their geomsamples into one list |
| CResInteractions | |
| CSingleResidueInvrotTarget | |
| CTheozymeInvrotTree | This class takes an EnzConstraintIO object and generates a 3D model of the theozyme in it, where inverse rotamers are generated for every block in the cstfile. Shit gets complicated when ambiguous interactions are specified and other residues are interacting (possibly in ambiguous fashion) with these ambiguous residues.. |
| ►Npose_metric_calculators | |
| CBuriedUnsatisfiedPolarsCalculator | |
| CCatPiCalculator | |
| CChargeCalculator | |
| CClashCountCalculator | |
| CDecomposeAndReweightEnergiesCalculator | |
| CEmptyVertexData | |
| CEnergiesData | |
| CFragQualCalculator | |
| CHPatchCalculator | |
| CInterGroupNeighborsCalculator | |
| CMetricValueGetter | |
| CNeighborhoodByDistanceCalculator | |
| CNeighborsByDistanceCalculator | |
| CNonlocalContactsCalculator | |
| CNumberHBondsCalculator | |
| CPackstatCalculator | |
| CPiPiCalculator | |
| CResidueDecompositionByChainCalculator | |
| CResidueDecompositionCalculator | |
| CRotamerBoltzCalculator | |
| CRotamerRecovery | |
| CSaltBridgeCalculator | |
| CSemiExplicitWaterUnsatisfiedPolarsCalculator | |
| CSequenceComparison | |
| CSurfaceCalculator | |
| ►Nrotamer_set_operations | |
| CAddGood2BPairEnergyRotamers | Implementation of rosetta 2.x style rotamer explosion builds a whole bunch of extra rotamers, but only adds them to the set if they score better than a cutoff with a given set of target residues |
| CRigidBodyMoveBaseRSO | |
| CRigidBodyMoveRSO | |
| CSpecialRotamerRSO | |
| ►Ntask_operations | |
| CAlignedThreadOperation | |
| CAlignedThreadOperationCreator | |
| CCrystalContactsOperation | |
| CCrystalContactsOperationCreator | |
| CDatabaseThread | |
| CDatabaseThreadCreator | |
| CDesignAroundOperation | |
| CDesignAroundOperationCreator | |
| CDockingNoRepack1 | |
| CDockingNoRepack2 | |
| CDsspDesignOperation | TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure |
| CDsspDesignOperationCreator | |
| CImportUnboundRotamersOperation | |
| CImportUnboundRotamersOperationCreator | |
| CInteractingRotamerExplosion | : taskop to oversample rotamers that make good interactions with a (set of) specified target residue(s) similar to Rosetta 2.x rotamer explosion |
| CInteractingRotamerExplosionCreator | |
| CInterfaceTaskOperation | |
| CJointSequenceOperation | |
| CJointSequenceOperationCreator | |
| CLimitAromaChi2_RotamerSetOperation | |
| CLimitAromaChi2Operation | |
| CLimitAromaChi2OperationCreator | |
| CLinkResidues | |
| CLinkResiduesCreator | |
| CModifyAnnealer | |
| CModifyAnnealerCreator | |
| CPreventChainFromRepackingOperation | |
| CPreventChainFromRepackingOperationCreator | |
| CPreventResiduesFromRepackingOperation | |
| CPreventResiduesFromRepackingOperationCreator | |
| CProteinCore | |
| CProteinCoreFilterCreator | |
| CProteinInterfaceDesignOperation | |
| CProteinInterfaceDesignOperationCreator | |
| CReadResfileFromDB | |
| CReadResfileFromDBCreator | |
| CRestrictByCalculatorsOperation | |
| CRestrictByCalculatorsOperationCreator | |
| CRestrictChainToRepackingOperation | |
| CRestrictChainToRepackingOperationCreator | |
| CRestrictConservedLowDdgOperation | Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking |
| CRestrictConservedLowDdgOperationCreator | |
| CRestrictIdentitiesAtAlignedPositionsOperation | |
| CRestrictIdentitiesAtAlignedPositionsOperationCreator | |
| CRestrictIdentitiesOperation | |
| CRestrictIdentitiesOperationCreator | |
| CRestrictInterGroupVectorOperation | |
| CRestrictInterGroupVectorOperationCreator | |
| CRestrictNativeResiduesOperation | |
| CRestrictNativeResiduesOperationCreator | |
| CRestrictNonSurfaceToRepackingOperation | |
| CRestrictNonSurfaceToRepackingOperationCreator | |
| CRestrictOperationsBase | |
| CRestrictResiduesToRepackingOperation | |
| CRestrictResiduesToRepackingOperationCreator | |
| CRestrictToAlignedSegmentsOperation | |
| CRestrictToAlignedSegmentsOperationCreator | |
| CRestrictToCDRH3Loop | |
| CRestrictToCDRH3LoopCreator | |
| CRestrictToInterface | |
| CRestrictToInterfaceCreator | |
| CRestrictToInterfaceOperation | |
| CRestrictToInterfaceOperationCreator | |
| CRestrictToInterfaceVectorOperation | |
| CRestrictToInterfaceVectorOperationCreator | |
| CRestrictToLoops | |
| CRestrictToLoopsAndNeighbors | 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 |
| CRestrictToLoopsAndNeighborsCreator | |
| CRestrictToLoopsCreator | |
| CRestrictToMoveMapChiOperation | A TaskOperation that accepts a movemap and restricts chi that are false to either packing or design. Does not turn anything on, just like the rest of the RestrictTo operations |
| CRestrictToNeighborhoodOperation | |
| CRestrictToNeighborhoodOperationCreator | |
| CRestrictToTerminiOperation | |
| CRestrictToTerminiOperationCreator | |
| CRetrieveStoredTaskOperation | |
| CRetrieveStoredTaskOperationCreator | |
| CSelectByDeltaScoreOperation | |
| CSelectByDeltaScoreOperationCreator | |
| CSelectByDensityFitOperation | |
| CSelectByDensityFitOperationCreator | |
| CSelectBySASAOperation | |
| CSelectBySASAOperationCreator | |
| CSelectResiduesWithinChainOperation | |
| CSelectResiduesWithinChainOperationCreator | |
| CSeqprofConsensusOperation | |
| CSeqprofConsensusOperationCreator | |
| CSetIGTypeOperation | |
| CSetIGTypeOperationCreator | |
| CSTMStoredTask | |
| CStoreCombinedStoredTasksMover | Mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls |
| CStoreCombinedStoredTasksMoverCreator | |
| CStoreCompoundTaskMover | |
| CStoreCompoundTaskMoverCreator | |
| CStoreTaskMover | Mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls |
| CStoreTaskMoverCreator | |
| CThreadSequenceOperation | |
| CThreadSequenceOperationCreator | |
| CAllowInsert | |
| CClusterBase | |
| CClusterOptions | |
| CClusterPhilStyle | |
| CCovalentResidueNetwork | Creates networks based on covalent connections between residues |
| CDecoySetEvaluation | |
| CDistanceResidueNetwork | Creates networks based on residue proximity in space |
| CDummyClass | |
| CGreedyKCenter | Greedy K-Center Clustering Algorithm |
| CIGLigandDesignEdgeUpweighter | |
| CInteratomicVarianceMatrix | |
| CKCluster | Basic class for performing a K-style Clustering algorithm |
| CKClusterData | Database of a K-style Clustering algorithm |
| CKClusterElement | |
| CKMedoid | Typical K-Medoids Clustering Algorithm |
| CNode | |
| COP_const_iterator | Const_iterator class for SilentFileData container |
| CResidueGroupIGEdgeUpweighter | |
| CResidueNetwork | Residuenetwork base class |
| CSelectResiduesByLayer | |
| CSF_Replica | |
| ►Ntopology_broker | |
| ►Nclaims | |
| CBBClaim | |
| CCutClaim | |
| CDofClaim | |
| CJumpClaim | |
| CLegacyRootClaim | |
| CSequenceClaim | |
| CSymmetryClaim | |
| ►Nweights | |
| CAbinitioMoverWeight | |
| CConstAbinitioMoverWeight | |
| CLargeFragWeight | |
| CSmallFragWeight | |
| CSmoothFragWeight | |
| CAsymFoldandDockClaimer | |
| CBasicJumpClaimer | |
| CClaimerMessage | |
| CCmdLineData | |
| CConstraintClaimer | |
| CConstraintEvaluatorWrapper | |
| CConstraintEvaluatorWrapperCreator | Creator for the ConstraintsEvaluatorWrapperCreator class |
| CCoordConstraintClaimer | |
| CCutBiasClaimer | |
| CDensityScoringClaimer | |
| CDisulfJumpClaimer | Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore |
| CEXCN_FailedBroking | |
| CEXCN_FilterFailed | |
| CEXCN_Input | |
| CEXCN_TopologyBroker | |
| CEXCN_Unknown | |
| CFibrilModelingClaimer | |
| CFoldandDockClaimer | |
| CFragmentClaimer | |
| CFragmentContainer | |
| CFragmentJumpClaimer | Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore |
| CLoopFragmentClaimer | |
| CMembraneTopologyClaimer | |
| CMetalloClaimer | |
| CPcsEnergyController | |
| CPseudocontactShiftEnergyController | |
| CPseudocontactShiftEnergyController_Ts1 | |
| CPseudocontactShiftEnergyController_Ts2 | |
| CPseudocontactShiftEnergyController_Ts3 | |
| CPseudocontactShiftEnergyController_Ts4 | |
| CRigidBodyRandomTMHMover | |
| ►CRigidChunkClaimer | Defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move |
| CCM_SuggestFixResidue | |
| CJumpCalculator | Helper class – computes if we have all jupms needed to rigidify the chosen chunk and generate more jumps if needed |
| CSequenceClaimer | |
| CSequenceNumberResolver | |
| CStartStructClaimer | |
| CSuggestValueMessage | |
| CSymmetryClaimer | |
| CTemplateFragmentClaimer | Hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates |
| CTemplateJumpClaimer | Hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates |
| CTMHTopologySamplerClaimer | |
| CTopologyBroker | |
| CTopologyClaimer | |
| CTopologyClaimerFactory | A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method |
| ►Ntrajectory | |
| CDbTrajectoryReader | |
| ►CDbTrajectoryWriter | |
| CFrame | |
| ►Nub_e2c | |
| Cubi_e2c_modeler | |
| ►Nunfolded_state_energy_calculator | |
| CUnfoldedStateEnergyCalculatorJobDistributor | |
| CUnfoldedStateEnergyCalculatorMover | |
| CUnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor | |
| ►Nviewer | |
| CConformationViewer | Observer that attaches to a Conformation and displays graphics |
| CGraphicsState | |
| CSilentObserver | |
| Ctriangle | |
| CtriangleIterator | |
| ►Nvip | |
| CVIP_Mover | |
| CVIP_Report | |
| ►Nwum | |
| CDatabaseEntryWorkUnit | |
| Cfind_SilentStructOPs | This little class is a predicate for finding silent structures in say a vector of silent structures |
| CMoverList | |
| CMPI_WorkUnitManager | |
| CMPI_WorkUnitManager_Slave | |
| CSilentStructStore | |
| Csort_SilentStructOPs | |
| CWorkUnit_MoverWrapper | This WorkUnit type can encapsulate any MoverOP. When registering this WOrkunit provide it with a MoverOP and then, when executed on the slaves, this workunit will run the mover On every single input structure and return the results |
| CWorkUnit_SilentStructStore | This WorkUnit type has structures in it. Most Workunits should derive from this one rather THe the Base class |
| CWorkUnit_Wait | |
| ►CWorkUnitBase | The base class for all work units |
| CWU_Header | This structure can contain any non-dynamicly allocated data. Any simple data types can be used here, ints, real, floats, char, etc. |
| CWorkUnitList | WOrkUnitList is a store for WorkUnitCOPs. THe purpose of this class is to store all the possible WorkUnits that a protocol might need. When needed these are cloned and then used. THis class acts like a library of WorkUnit blueprints |
| CWorkUnitManager | |
| CWorkUnitQueue | |
| CWorkUnitQueue_Swapped | |
| ►Nwum2 | |
| CEndPoint | |
| CStatusRequest | |
| CStatusResponse | |
| CWorkUnit | The base class for all work units, this is abstract |
| CWorkUnit_ElScripts | |
| CWorkUnit_Wait | WorkUnit that sleeps for X seconds |
| CWUQueue | |
| CLoopRebuild | The loop-rebuild protocol |
| CLoopRefine | Class LoopRefine for fullatom loop refinement |
| CRBSegmentRelaxImpl | |
| CAlternating | |
| CAn | |
| CAn | |
| CImplements | |
| CImplements | |
| CSimple | Associates fragment indices with Gunn scores |
| CTransformation | |
| CTrial | |
1.8.7