|
| file | AlignedThreadOperation.cc |
| |
| file | AlignedThreadOperation.fwd.hh |
| |
| file | AlignedThreadOperation.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | AlignedThreadOperationCreator.hh |
| |
| file | CrystalContactsOperation.cc |
| | Exclude crystal contacts from design.
|
| |
| file | CrystalContactsOperation.fwd.hh |
| | Exclude crystal contacts from design.
|
| |
| file | CrystalContactsOperation.hh |
| | Exclude crystal contacts from design.
|
| |
| file | CrystalContactsOperationCreator.hh |
| | Exclude crystal contacts from design.
|
| |
| file | DatabaseThread.cc |
| | picks a sequence from database by start and end position on the pose
|
| |
| file | DatabaseThread.fwd.hh |
| |
| file | DatabaseThread.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | DatabaseThreadCreator.hh |
| |
| file | DesignAroundOperation.cc |
| |
| file | DesignAroundOperation.fwd.hh |
| |
| file | DesignAroundOperation.hh |
| |
| file | DesignAroundOperationCreator.hh |
| |
| file | DsspDesignOperation.cc |
| | Design residues with selected amino acids depending on DSSP secondary structure assignment. All functionality here is included in the LayerDesign task operation, but this filter has significantly reduced overhead by avoiding slow SASA calculations.
|
| |
| file | DsspDesignOperation.fwd.hh |
| |
| file | DsspDesignOperation.hh |
| | Design residues with selected amino acids depending on DSSP secondary structure assignment. All functionality here is included in the LayerDesign task operation, but this filter has significantly reduced overhead by avoiding slow SASA calculations.
|
| |
| file | DsspDesignOperationCreator.hh |
| |
| file | ImportUnboundRotamersOperation.cc |
| | Import unbound (or native) rotamers into Rosetta!
|
| |
| file | ImportUnboundRotamersOperation.fwd.hh |
| | rotamer set operation forward declaration
|
| |
| file | ImportUnboundRotamersOperation.hh |
| | eliminate aromatic rotamers, of which chi2 are around 0, 180 degree.
|
| |
| file | ImportUnboundRotamersOperationCreator.hh |
| |
| file | InteractingRotamerExplosion.cc |
| |
| file | InteractingRotamerExplosion.fwd.hh |
| |
| file | InteractingRotamerExplosion.hh |
| | TaskOperation class that oversamples rotamers interacting with a certain target.
|
| |
| file | InteractingRotamerExplosionCreator.hh |
| |
| file | InterfaceTaskOperation.cc |
| | Base class for TaskOperations that will work with docking to define an interface.
|
| |
| file | InterfaceTaskOperation.fwd.hh |
| |
| file | InterfaceTaskOperation.hh |
| | Base class for TaskOperations that will work with docking to define an interface.
|
| |
| file | JointSequenceOperation.cc |
| | set designable residues to those observed in a set of structures
|
| |
| file | JointSequenceOperation.fwd.hh |
| |
| file | JointSequenceOperation.hh |
| | set every position to be designable to residues observed in a set of structures
|
| |
| file | JointSequenceOperationCreator.hh |
| |
| file | LayerOperations.cc |
| | operation defines either core, surface or periphery. It solely determines which residue to pack/design, does not define identities.
|
| |
| file | LayerOperations.hh |
| | select residues depending on layer: core, boundary, and surface and the layer are defined by accessible surface area of each residue, like nobu's just more general
|
| |
| file | LayerOperationsCreator.hh |
| |
| file | LimitAromaChi2Operation.cc |
| | eliminate aromatic rotamers, of which chi2 are around 0, 180 degree.
|
| |
| file | LimitAromaChi2Operation.fwd.hh |
| | rotamer set operation forward declaration
|
| |
| file | LimitAromaChi2Operation.hh |
| | eliminate aromatic rotamers, of which chi2 are around 0, 180 degree.
|
| |
| file | LimitAromaChi2OperationCreator.hh |
| |
| file | LinkResidues.cc |
| |
| file | LinkResidues.fwd.hh |
| |
| file | LinkResidues.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | LinkResiduesCreator.hh |
| |
| file | ModifyAnnealer.cc |
| | Task operation to set high and low temps for annealer as well as whether or not to do a quench step.
|
| |
| file | ModifyAnnealer.fwd.hh |
| | Task operation to set high and low temps for annealer as well as whether or not to do a quench step.
|
| |
| file | ModifyAnnealer.hh |
| | Task operation to set high and low temps for annealer as well as whether or not to do a quench step.
|
| |
| file | ModifyAnnealerCreator.hh |
| |
| file | PreventChainFromRepackingOperation.cc |
| |
| file | PreventChainFromRepackingOperation.fwd.hh |
| |
| file | PreventChainFromRepackingOperation.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | PreventChainFromRepackingOperationCreator.hh |
| |
| file | PreventResiduesFromRepackingOperation.cc |
| |
| file | PreventResiduesFromRepackingOperation.fwd.hh |
| |
| file | PreventResiduesFromRepackingOperation.hh |
| | TaskOperation class that prevents a vector of residues indices from repacking parsed as a string that is comma delimited ",".
|
| |
| file | PreventResiduesFromRepackingOperationCreator.hh |
| |
| file | ProteinCoreResFilter.cc |
| | TaskOperation class that finds an interface and leaves it mobile in the PackerTask.
|
| |
| file | ProteinCoreResFilter.hh |
| |
| file | ProteinCoreResFilterCreator.hh |
| |
| file | ProteinInterfaceDesignOperation.cc |
| |
| file | ProteinInterfaceDesignOperation.fwd.hh |
| |
| file | ProteinInterfaceDesignOperation.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | ProteinInterfaceDesignOperationCreator.hh |
| |
| file | ReadResfileFromDB.cc |
| |
| file | ReadResfileFromDB.fwd.hh |
| | Forward declaration of the ReadResfileFromDB class.
|
| |
| file | ReadResfileFromDB.hh |
| | read a refile indexed by the input structure tag from a supplied relational database
|
| |
| file | ReadResfileFromDBCreator.hh |
| |
| file | RestrictByCalculatorsOperation.cc |
| | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask.
|
| |
| file | RestrictByCalculatorsOperation.fwd.hh |
| | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask.
|
| |
| file | RestrictByCalculatorsOperation.hh |
| | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask.
|
| |
| file | RestrictByCalculatorsOperationCreator.hh |
| |
| file | RestrictChainToRepackingOperation.cc |
| |
| file | RestrictChainToRepackingOperation.fwd.hh |
| |
| file | RestrictChainToRepackingOperation.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | RestrictChainToRepackingOperationCreator.hh |
| |
| file | RestrictIdentitiesAtAlignedPositions.cc |
| |
| file | RestrictIdentitiesAtAlignedPositions.fwd.hh |
| |
| file | RestrictIdentitiesAtAlignedPositions.hh |
| | TaskOperation class that restricts the identities at positions aligned with those of another pdb with the positions observed in that pdb.
|
| |
| file | RestrictIdentitiesAtAlignedPositionsCreator.hh |
| |
| file | RestrictIdentitiesOperation.cc |
| | Restricts specified residue types to only repack, no design.
|
| |
| file | RestrictIdentitiesOperation.fwd.hh |
| |
| file | RestrictIdentitiesOperation.hh |
| | TaskOperation class that restricts a vector of Size defined residues to repacking when parsed, it takes in a string and splits by ",".
|
| |
| file | RestrictIdentitiesOperationCreator.hh |
| |
| file | RestrictInterGroupVectorOperation.cc |
| |
| file | RestrictInterGroupVectorOperation.fwd.hh |
| |
| file | RestrictInterGroupVectorOperation.hh |
| | restricts design to only those residues between two groups of structures
|
| |
| file | RestrictInterGroupVectorOperationCreator.hh |
| |
| file | RestrictNativeResiduesOperation.cc |
| | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed.
|
| |
| file | RestrictNativeResiduesOperation.fwd.hh |
| |
| file | RestrictNativeResiduesOperation.hh |
| | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed.
|
| |
| file | RestrictNativeResiduesOperationCreator.hh |
| |
| file | RestrictNonSurfaceToRepackingOperation.cc |
| |
| file | RestrictNonSurfaceToRepackingOperation.fwd.hh |
| |
| file | RestrictNonSurfaceToRepackingOperation.hh |
| | TaskOperation class that restrics buried and boundary positions to repacking leaving surface positions designable.
|
| |
| file | RestrictNonSurfaceToRepackingOperationCreator.hh |
| |
| file | RestrictOperationsBase.cc |
| | Base class for PoseMetricCalculator-using TaskOperations.
|
| |
| file | RestrictOperationsBase.fwd.hh |
| | Base class for PoseMetricCalculator-using TaskOperations.
|
| |
| file | RestrictOperationsBase.hh |
| | Base class for PoseMetricCalculator-using TaskOperations.
|
| |
| file | RestrictResiduesToRepackingOperation.cc |
| |
| file | RestrictResiduesToRepackingOperation.fwd.hh |
| |
| file | RestrictResiduesToRepackingOperation.hh |
| | TaskOperation class that restricts a vector of Size defined residues to repacking when parsed, it takes in a string and splits by ",".
|
| |
| file | RestrictResiduesToRepackingOperationCreator.hh |
| |
| file | RestrictToAlignedSegments.cc |
| |
| file | RestrictToAlignedSegments.fwd.hh |
| |
| file | RestrictToAlignedSegments.hh |
| |
| file | RestrictToAlignedSegmentsCreator.hh |
| |
| file | RestrictToCDRH3Loop.cc |
| |
| file | RestrictToCDRH3Loop.fwd.hh |
| | Forward declaration of the RestrictToCDRH3Loop class.
|
| |
| file | RestrictToCDRH3Loop.hh |
| | This class allows the selection for packing of the Antibody CDR-H3 loop by taking advantage of the PDB numbering schemes that are commonly used for Antibodies.
|
| |
| file | RestrictToCDRH3LoopCreator.hh |
| |
| file | RestrictToInterface.cc |
| | When passed to a PackerTask, pack/design is limited to the protein interface.
|
| |
| file | RestrictToInterface.fwd.hh |
| |
| file | RestrictToInterface.hh |
| | When passed to a PackerTask, pack/design is limited to the interface.
|
| |
| file | RestrictToInterfaceCreator.hh |
| |
| file | RestrictToInterfaceOperation.cc |
| | TaskOperation class that finds an interface and leaves it mobile in the PackerTask.
|
| |
| file | RestrictToInterfaceOperation.fwd.hh |
| | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask.
|
| |
| file | RestrictToInterfaceOperation.hh |
| | TaskOperation class that finds an interface and makes it mobile in the PackerTask.
|
| |
| file | RestrictToInterfaceOperationCreator.hh |
| |
| file | RestrictToInterfaceVectorOperation.cc |
| | TaskOperation class that finds an interface based on: core/pack/task/operation/util/interface_vector_calculate.hh and leaves it mobile in the PackerTask.
|
| |
| file | RestrictToInterfaceVectorOperation.fwd.hh |
| | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask.
|
| |
| file | RestrictToInterfaceVectorOperation.hh |
| | TaskOperation class that finds an interface based on InterfaceVectorDefinition and leaves it mobile in the PackerTask. Serves mostly to wrap InterfaceVectorDefinition into a TaskOperation. see src/core/pack/task/operation/util/interface_vector_calculate.hh.
|
| |
| file | RestrictToInterfaceVectorOperationCreator.hh |
| |
| file | RestrictToLoops.cc |
| |
| file | RestrictToLoops.fwd.hh |
| |
| file | RestrictToLoops.hh |
| |
| file | RestrictToLoopsAndNeighbors.cc |
| |
| file | RestrictToLoopsAndNeighbors.fwd.hh |
| | Forward declaration of the RestrictToLoopsAndNeighbors class.
|
| |
| file | RestrictToLoopsAndNeighbors.hh |
| | This class allows the selection for packing (and possibly design) of residues contained in a Loops object as well as the neighbors within a specified cutoff distance, with the default and maximum cutoff at 10.0 A.
|
| |
| file | RestrictToLoopsAndNeighborsCreator.hh |
| | Creator class for the RestrictToLoopsAndNeighbors TaskOperation.
|
| |
| file | RestrictToLoopsCreator.hh |
| |
| file | RestrictToMoveMapChiOperation.cc |
| |
| file | RestrictToMoveMapChiOperation.fwd.hh |
| |
| file | RestrictToMoveMapChiOperation.hh |
| | Makes it easier to use TF and MM in the same class.
|
| |
| file | RestrictToMoveMapChiOperationCreator.hh |
| |
| file | RestrictToNeighborhoodOperation.cc |
| | TaskOperation class that finds a neighborhood and leaves it mobile in the PackerTask.
|
| |
| file | RestrictToNeighborhoodOperation.fwd.hh |
| | Forward declaration of a TaskOperation class that finds a neighborhood; leaves it mobile in the PackerTask.
|
| |
| file | RestrictToNeighborhoodOperation.hh |
| | TaskOperation class that finds a neighborhood and makes it mobile in the PackerTask.
|
| |
| file | RestrictToNeighborhoodOperationCreator.hh |
| |
| file | RestrictToTerminiOperation.cc |
| | Restrict to packing only the residues at either or both termini.
|
| |
| file | RestrictToTerminiOperation.fwd.hh |
| | RestrictToTerminiOperation forward header.
|
| |
| file | RestrictToTerminiOperation.hh |
| | Restrict to packing only the residues at either or both termini.
|
| |
| file | RestrictToTerminiOperationCreator.hh |
| | RestrictToTerminiOperation class creator.
|
| |
| file | RetrieveStoredTaskOperation.cc |
| | Retrieves a stored task from the pose's CacheableData. Must be used in conjunction with the StoredTaskMover. Allows storage/retrieval of a task so that particular sets of residues can be stably addressed throughout the entirety of a RosettaScripts protocol.
|
| |
| file | RetrieveStoredTaskOperation.fwd.hh |
| |
| file | RetrieveStoredTaskOperation.hh |
| | Retrieves a stored task from the pose's CacheableData. Must be used in conjunction with the StoredTaskMover. Allows storage/retrieval of a task so that particular sets of residues can be stably addressed throughout the entirety of a RosettaScripts protocol.
|
| |
| file | RetrieveStoredTaskOperationCreator.hh |
| |
| file | SelectByDeltaScoreOperation.cc |
| |
| file | SelectByDeltaScoreOperation.fwd.hh |
| |
| file | SelectByDeltaScoreOperation.hh |
| |
| file | SelectByDeltaScoreOperationCreator.hh |
| |
| file | SelectByDensityFitOperation.cc |
| |
| file | SelectByDensityFitOperation.fwd.hh |
| |
| file | SelectByDensityFitOperation.hh |
| |
| file | SelectByDensityFitOperationCreator.hh |
| |
| file | SelectBySASAOperation.cc |
| |
| file | SelectBySASAOperation.fwd.hh |
| |
| file | SelectBySASAOperation.hh |
| |
| file | SelectBySASAOperationCreator.hh |
| |
| file | SelectResiduesWithinChain.cc |
| |
| file | SelectResiduesWithinChain.fwd.hh |
| |
| file | SelectResiduesWithinChain.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | SelectResiduesWithinChainCreator.hh |
| |
| file | SeqprofConsensusOperation.cc |
| | set designable residues to those observed in sequence profile
|
| |
| file | SeqprofConsensusOperation.fwd.hh |
| |
| file | SeqprofConsensusOperation.hh |
| | set every position to be designable to residues observed in sequence profile
|
| |
| file | SeqprofConsensusOperationCreator.hh |
| |
| file | SetIGTypeOperation.cc |
| | Task operation to set interaction graph type (linmem, lazy or double lazy)
|
| |
| file | SetIGTypeOperation.fwd.hh |
| | Task operation to set Interaction graph Type.
|
| |
| file | SetIGTypeOperation.hh |
| | Task operation to set interaction graph type (linear memory, lazy or double lazy)
|
| |
| file | SetIGTypeOperationCreator.hh |
| |
| file | STMStoredTask.cc |
| | CacheableData wrapper for PackerTask storage.
|
| |
| file | STMStoredTask.fwd.hh |
| |
| file | STMStoredTask.hh |
| |
| file | StoreCombinedStoredTasksMover.cc |
| | The StoreCombinedStoredTasksMover HAS BEEN DEPRECATED. It was used to combine several STMStoredTasks (protocols/toolbox/task_operations/STMStoredTask.cc), but has been replaced by the StoreCompoundTaskMover (protocols/toolbox/task_operations/StoreCompoundTaskMover.cc), which is much more flexible. It is being moved out of devel/matdes/ into protocols/toolbox/task_operations/ to support the publication King et al., Nature 2014.
|
| |
| file | StoreCombinedStoredTasksMover.fwd.hh |
| |
| file | StoreCombinedStoredTasksMover.hh |
| | Headers for StoreCombinedStoredTasksMover class – DEPRECATED (see .cc file)
|
| |
| file | StoreCombinedStoredTasksMoverCreator.hh |
| |
| file | StoreCompoundTaskMover.cc |
| | Combine tasks using boolean logic for residues that are packable or designable, assign new packing behavior to residues that match or do not match the specified criteria, and store the resulting task in the pose's cacheable data. TODO (Jacob): Add option to combine allowed amino acid sets.
|
| |
| file | StoreCompoundTaskMover.fwd.hh |
| | Combine tasks using boolean logic for residues that are packable or designable, as well as for residue specific AA sets, and store the resulting task in the pose's cacheable data.
|
| |
| file | StoreCompoundTaskMover.hh |
| | Combine tasks using boolean logic for residues that are packable or designable, as well as for residue specific AA sets, and store the resulting task in the pose's cacheable data.
|
| |
| file | StoreCompoundTaskMoverCreator.hh |
| | Combine tasks using boolean logic for residues that are packable or designable, as well as for residue specific AA sets, and store the resulting task in the pose's cacheable data.
|
| |
| file | StoreTaskMover.cc |
| | The StoreTaskMover allows you to create a PackerTask at some point during a RosettaScripts run and save it for access later during the same run. Can be useful for mutating/analyzing a particular set of residues using many different movers/filters.
|
| |
| file | StoreTaskMover.fwd.hh |
| |
| file | StoreTaskMover.hh |
| | Headers for StoreTaskMover class.
|
| |
| file | StoreTaskMoverCreator.hh |
| | This class will create instances of Mover StoreTaskMover for the MoverFactory.
|
| |
| file | ThreadSequenceOperation.cc |
| |
| file | ThreadSequenceOperation.fwd.hh |
| |
| file | ThreadSequenceOperation.hh |
| | TaskOperation class that restricts a chain to repacking.
|
| |
| file | ThreadSequenceOperationCreator.hh |
| |
1.8.7