Rosetta Protocols  2014.35
task_operations Directory Reference
Directory dependency graph for task_operations:
src/protocols/toolbox/task_operations

Files

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
 TaskOperation class that restricts a chain to repacking.
 
file  DesignAroundOperationCreator.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  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