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task_operations Directory Reference
Directory dependency graph for task_operations:
src/protocols/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  ConservativeDesignOperation.cc
 
file  ConservativeDesignOperation.fwd.hh
 
file  ConservativeDesignOperation.hh
 
file  ConservativeDesignOperationCreator.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  DsspDesignOperationTests.fwd.hh
 
file  ImportUnboundRotamersOperation.cc
 Import unbound (or native) rotamers into Rosetta!
 
file  ImportUnboundRotamersOperation.fwd.hh
 
file  ImportUnboundRotamersOperation.hh
 rotamer set operation forward declaration
 
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  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  LimitAromaChi2Operation.cc
 eliminate aromatic rotamers, of which chi2 are around 0, 180 degree. Chi2=0, 180 rotamers of aromatic residues ( PHE, TYR, HIS ) are not observed in nature very much, however Rosetta really like them. This is really pathology. For design purpose, we don't need them actually.
 
file  LimitAromaChi2Operation.fwd.hh
 
file  LimitAromaChi2Operation.hh
 rotamer set operation forward declaration
 
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  MutationSetDesignOperation.cc
 
file  MutationSetDesignOperation.fwd.hh
 
file  MutationSetDesignOperation.hh
 Sample a set of mutations each time packer is generated.
 
file  pHVariantTaskOperation.cc
 A TaskOp that enables sampling of protonation variants during repacking. The ionizable sidechains considered are ASP, GLU, LYS, TYR, and HIS. All other posiitons are restricted to repacking. The -pH_mode commandline option is still currently required to initially read the variants into the database.
 
file  pHVariantTaskOperation.fwd.hh
 During repacking, allow interchangeability of protonated and deprotonated variants.
 
file  pHVariantTaskOperation.hh
 
file  pHVariantTaskOperationCreator.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
 
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  PruneBuriedUnsatsOperation.cc
 Eliminate rotamers that contain a sidechain buried unsat and make no other sidechain h-bonds This is intended to speed up packing by eliminating useless polar rotamers. This can also help to reduce the number of buried unsats in designs because Rosetta can't pack them.
 
file  PruneBuriedUnsatsOperation.fwd.hh
 Forward declaration for PruneBuriedUnsatsOperation.
 
file  PruneBuriedUnsatsOperation.hh
 Eliminate rotamers that contain a sidechain buried unsat and make no other sidechain h-bonds This is intended to speed up packing by eliminating useless polar rotamers. This can also help to reduce the number of buried unsats in designs because Rosetta can't pack them.
 
file  PruneBuriedUnsatsOperationCreator.hh
 Creator for PruneBuriedUnsatsOperation.
 
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  ResfileCommandOperation.cc
 Applies the equivalent of a resfile line (without the resnums) to residues specified in a residue selector.
 
file  ResfileCommandOperation.fwd.hh
 Applies the equivalent of a resfile line (without the resnums) to residues specified in a residue selector.
 
file  ResfileCommandOperation.hh
 
file  ResfileCommandOperationCreator.hh
 
file  ResidueProbDesignOperation.cc
 
file  ResidueProbDesignOperation.fwd.hh
 
file  ResidueProbDesignOperation.hh
 Uses a probability distribution to sample allowed residues at a position, adding those types to the packer - only if they are designable.
 
file  ResidueProbDesignOperationCreator.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
 
file  RestrictIdentitiesAtAlignedPositionsCreator.hh
 
file  RestrictIdentitiesOperation.cc
 Restricts specified residue types to only repack, no design.
 
file  RestrictIdentitiesOperation.fwd.hh
 
file  RestrictIdentitiesOperation.hh
 
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
 
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 core::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  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/select/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/select/util/interface_vector_calculate.hh.
 
file  RestrictToInterfaceVectorOperationCreator.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
 
file  RestrictToTerminiOperation.fwd.hh
 Restrict to packing only the residues at either or both termini.
 
file  RestrictToTerminiOperation.hh
 
file  RestrictToTerminiOperationCreator.hh
 
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
 
file  SelectResiduesWithinChainCreator.hh
 
file  SeqprofConsensusOperation.cc
 set designable residues to those observed in sequence profile
 
file  SeqprofConsensusOperation.fwd.hh
 
file  SeqprofConsensusOperation.hh
 
file  SeqprofConsensusOperationCreator.hh
 
file  SequenceMotifTaskOperation.cc
 A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string.
 
file  SequenceMotifTaskOperation.fwd.hh
 A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string.
 
file  SequenceMotifTaskOperation.hh
 
file  SequenceMotifTaskOperationCreator.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/task_operations/STMStoredTask.cc), but has been replaced by the StoreCompoundTaskMover (protocols/task_operations/StoreCompoundTaskMover.cc), which is much more flexible. It is being moved out of devel/matdes/ into protocols/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
 
file  StoreCompoundTaskMover.hh
 
file  StoreCompoundTaskMoverCreator.hh
 
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