Rosetta 3.4
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
core::scoring::sc::_ATOM_RADIUS
protocols::moves::_BoolMover
core::scoring::sc::_DOT
core::scoring::sc::_PROBE
core::scoring::sc::_RESULTS
A
A
A
AOf residues
A
protocols::fldsgn::potentials::AACompositionEnergyAACompositionEnergy
protocols::fldsgn::potentials::AACompositionEnergyCreator
protocols::antibody2::Ab_Assemble_Templates
protocols::antibody2::Ab_CloseOneCDR_MoverCloses only one CDR onto a framework
protocols::antibody2::Ab_GraftOneCDR_MoverGrafts only one CDR onto a framework
protocols::antibody2::Ab_H3_cter_insert_moverH3 CDR, Fragment Insertion and CCD
protocols::antibody2::Ab_H3_perturb_ccd_build
protocols::antibody2::Ab_InfoAntibody2 definition
protocols::antibody2::Ab_LH_RepulsiveRamp_Mover
protocols::antibody2::Ab_LH_SnugFit_Mover
protocols::antibody2::Ab_ModelCDRH3
protocols::antibody2::Ab_Relax_a_CDR_FullAtom
protocols::antibody2::Ab_RelaxCDRs_MoverCloses only one CDR onto a framework
protocols::antibody2::Ab_TemplateInfoAntibody2 definition
core::util::ABEGOAbego elments
protocols::frag_picker::quota::ABEGO_SS_ConfigRead a config file for quota selector
protocols::frag_picker::quota::ABEGO_SS_MapSingle pool used by quota selector
protocols::frag_picker::quota::ABEGO_SS_PoolSingle pool used by quota selector
protocols::frag_picker::scores::ABEGO_SS_Score
core::fragment::picking_old::vall::eval::ABEGOEvalScores a fragment based on sum of secondary structure identity and sequence identity
core::util::ABEGOManagerManager for abego
protocols::simple_filters::AbinitioBaseFilter
protocols::topology_broker::weights::AbinitioMoverWeight
protocols::abinitio::AbrelaxApplicationApplication level code for Abrelax, Foldconstraints and JumpingFoldconstraints
protocols::abinitio::AbrelaxMover
protocols::jd2::archive::AbstractArchiveBaseTags 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
core::conformation::AbstractRotamerTrie
utility::pointer::access_ptr
core::scoring::packstat::Accumulator
protocols::match::downstream::ActiveSiteGrid
protocols::frag_picker::scores::AdaptiveScoreHistogram
protocols::match::AddAllPositionsMPMMPM that returns a vector of all protein positions in the pose i.e. allowing matching everywhere
protocols::domain_assembly::AddAssemblyConstraints
core::chemical::AddAtomAdd an atom to ResidueType
core::pack::task::operation::AddBehaviorRLT
core::pack::task::operation::AddBehaviorRLTCreator
core::chemical::AddBondAdd a bond to ResidueType
protocols::simple_moves::AddCavitiesMover
protocols::protein_interface_design::movers::AddChainBreakMover that sets a chainbreak in a specified position
protocols::protein_interface_design::movers::AddChainBreakCreator
core::chemical::AddChiAdd a chi angle to ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's, which often result in one or more extra chi angles
core::chemical::AddChiRotamerAdd a rotamer sample to a chi angle of the ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's
core::chemical::AddConnect
protocols::simple_moves::AddConstraintsToCurrentConformationMover
protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator
core::chemical::sdf::addedH
protocols::ligand_docking::AddHydrogen
protocols::ligand_docking::AddHydrogens
protocols::ligand_docking::AddHydrogensCreator
core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >Function declarations for the AdditionalBackgroundNodesInteractionGraph
protocols::enzdes::AddLigandMotifRotamers
protocols::enzdes::AddLigandMotifRotamersOperationCreator
protocols::enzdes::AddOrRemoveMatchCstsA simple wrapper to get the functionality in EnzConstraintIO into mover format
protocols::enzdes::AddOrRemoveMatchCstsCreator
core::chemical::AddPropertyAdd a property to ResidueType
protocols::enzdes::AddRigidBodyLigandConfs
protocols::enzdes::AddRigidBodyLigandConfsCreator
protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator
core::chemical::AdductDescription of optional single-atom residue adducts
protocols::protein_interface_design::AlaScan
protocols::simple_filters::AlaScan
protocols::simple_filters::AlaScanFilterCreator
protocols::comparative_modeling::Align_RmsdEvaluator
protocols::comparative_modeling::Align_RotamerEvaluator
core::sequence::Aligner
core::sequence::AlignerFactory
protocols::evaluation::AlignEvaluator
protocols::comparative_modeling::AlignmentCluster
protocols::comparative_modeling::AlignmentClustering
protocols::id::AlignmentIDUnique template identifier class
protocols::comparative_modeling::AlignmentSet
protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreatorCreator for the AlignRmsdTargetEvaluatorCreator class
core::pack::task::ALLAAALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask)
core::pack::task::ALLAAwcAllows repacking and designing to any canonical residue (default state of PackerTask)
core::pack::task::ALLAAxcALLAAxc allows repacking and designing to any canonical noncysteine residue
protocols::toolbox::AllowInsert
protocols::frag_picker::AllowPdbIdFilterAccepts a chunk based on the pdb id of the source protein
protocols::abinitio::AllResiduesChanged(helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values
Alternating
protocols::abinitio::AlternativePairings
protocols::frag_picker::scores::AmbigCSScoreScores a fragment by the root mean square deviation of Phi and Psi angles
core::scoring::constraints::AmbiguousConstraint
core::scoring::constraints::AmbiguousConstraintCreatorMover creator for the AmbiguousConstraint constraint
protocols::constraints_additional::AmbiguousMultiConstraint
core::scoring::constraints::AmbiguousNMRConstraint
core::scoring::constraints::AmbiguousNMRConstraintCreatorMover creator for the AmbiguousNMRConstraint constraint
core::scoring::constraints::AmbiguousNMRDistanceConstraint
core::scoring::constraints::AmbiguousNMRDistanceConstraintCreatorMover creator for the AmbiguousNMRDistanceConstraint constraint
core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
An
An
protocols::anchored_design::AnchorAnchor class provides for the "anchor" part of a scaffold in anchored interface design
protocols::swa::rna::Anchor_ribose_stub
protocols::anchored_design::AnchoredDesignMover
protocols::anchored_design::AnchoredPerturbMover
protocols::anchored_design::AnchoredRefineMover
protocols::anchored_design::AnchorMoversDataThis data class wraps all the data needed for the AnchoredDesign movers
core::scoring::constraints::AngleConstraintAn Angular Constraint
core::scoring::constraints::AngleConstraintCreatorMover creator for the AngleConstraint constraint
protocols::sparta::ANN
core::pack::annealer::AnnealerFactory
core::fragment::AnnotatedFragDataFragData that contains additional information
core::sequence::AnnotatedSequence
protocols::antibody::AntibodyAntibody definition
protocols::antibody::AntibodyModeler
protocols::cluster::APClusterPublic interface for doing affinity propagation clustering
core::pack::task::APOLAAPOLA is deprecated, it calls APOLAR to allow nonpolar residues and packing
core::pack::task::APOLARAPOLAR allows nonpolar residues and packing
core::chemical::AppendMainchainAtomAdd a mainchain atom after the last mainchain atom
core::pack::task::operation::AppendResidueRotamerSetApply rotamerSetOperation to only the rotamerSet for the given residue
core::pack::task::operation::AppendResidueRotamerSetCreator
core::pack::task::operation::AppendRotamerWhen a PackerTask is created by the Factory, the RotamerOperation will be given to it
core::pack::task::operation::AppendRotamerCreator
core::pack::task::operation::AppendRotamerSetWhen a PackerTask is created by the Factory, the RotamerSetOperation will be given to it
core::pack::task::operation::AppendRotamerSetCreator
protocols::enzdes::ApplyRandomStoredRBConfFor 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
protocols::jd2::archive::ArchiveBase
protocols::jd2::archive::ArchiveManagerArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY
protocols::mpi::ArchiveMasterBase
core::scoring::packstat::AreaAccumulator
core::optimization::ArmijoLineMinimization
core::graph::Array0< T >Class Array0 is a c-style array wrapper that does bounds checking in debug mode. It indexes from 0 just like regular c-arrays. Class Array0 does not manage it's own memory. It does not allocate memory if you want to make it larger, nor does it deallocate memory when you destroy it. Bounds checking only ensures that the user does not go outside of the memory Array0 thinks it's in charge of. If the user should happen to point the array0 at memory that has not been allocated, Array0 is not responsible for segmentation fault that will likely occur. Garbage in, garbage out
core::scoring::packstat::Array2D
core::graph::ArrayPool< T >
core::graph::ArrayPoolElement< T >
protocols::domain_assembly::AssembleLinkerMover
core::chemical::orbitals::AssignOrbitals
protocols::cluster::AssignToClustersMover
protocols::topology_broker::AsymFoldandDockClaimer
protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover
core::kinematics::tree::AtomKinematics Atom interface class
core::scoring::sc::Atom
core::conformation::AtomA simple object with atom's position and its chemical type
core::kinematics::tree::Atom_Kinematics Atom abstract base class
protocols::swa::rna::Atom_Bin
protocols::match::downstream::AtomAngleSecMatchRPERPE to figure out if three atoms are within a given angle atoms need to be set through the parent class add_at_ind function
protocols::features::AtomAtomPairFeatures
protocols::features::AtomAtomPairFeaturesCreatorCreator for the AtomAtomPairFeatures class
protocols::frag_picker::scores::AtomBasedConstraintsScoreA base class for all scoring methods that need atom coordinates
protocols::ligand_docking::AtomCountFilter
protocols::ligand_docking::AtomCountFilterCreator
protocols::match::downstream::AtomDihedralSecMatchRPERPE 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
protocols::match::downstream::AtomDistanceSecMatchRPERPE to figure out if two atoms are within a given distance atoms need to be set through the parent class add_at_ind function
protocols::match::downstream::AtomGeometrySecMatchRPEHelper class for GeometrySec abstract base class for distance, angle, and dihedral derived classes
core::conformation::AtomGraphEdgeData
core::conformation::AtomGraphVertexData
protocols::simple_filters::AtomicContactFilterDetects atomic (<4Ang) contacts between any two atoms of two residues
protocols::simple_filters::AtomicContactFilterCreator
protocols::simple_filters::AtomicDistanceFilterDetects atomic contacts between two atoms of two residues
protocols::simple_filters::AtomicDistanceFilterCreator
core::chemical::AtomICoorA basic class containing info of internal coordinates needed for building an atom within a ResidueType
core::id::AtomIDAtom identifier class. Defined by the atom number and the residue number
core::id::AtomID_Map< T >Map from Atom identifiers to contained values class
core::io::pdb::AtomInformationAtom_information contain information for individual atom. only fields that predent in file will be initialazed, other will have default value. That class basicaly reflect structure of 'ATOM' line in PDB file format
protocols::features::AtomInResidueAtomInResiduePairFeatures
protocols::features::AtomInResidueAtomInResiduePairFeaturesCreatorCreator for the AtomInResidueAtomInResiduePairFeatures class
core::scoring::AtomNeighborAtom-atom neighborlist object
core::optimization::AtomNode
core::scoring::constraints::AtomPairConstraint
core::scoring::constraints::AtomPairConstraintCreatorMover creator for the AtomPairConstraint constraint
protocols::frag_picker::scores::AtomPairConstraintsDataHolds data about a single distance constraint in the form AtomPairConstraintsScore needs
protocols::frag_picker::scores::AtomPairConstraintsScoreScores a fragment with a set of AtomPair constraints
core::scoring::etable::AtomPairEnergy
core::scoring::custom_pair_distance::AtomPairFuncList
core::scoring::packstat::AtomRadiusMap
core::scoring::custom_pair_distance::atoms_and_func_struct
core::kinematics::AtomTreeWrapper for a tree of kinematic Atoms
core::pack::scmin::AtomTreeCollectionA collection of ResidueAtomTreeCollection objects for an entire design task
core::import_pose::atom_tree_diffs::AtomTreeDiffAn object wrapper for reading atom_tree_diff files, complete with embedded reference structures
protocols::jobdist::AtomTreeDiffJobDistributorDistributor for use with atomtree_diff silent files
protocols::jd2::AtomTreeDiffJobInputter
protocols::jd2::AtomTreeDiffJobInputterCreator
protocols::jd2::AtomTreeDiffJobOutputter
protocols::jd2::AtomTreeDiffJobOutputterCreator
core::optimization::AtomTreeMinimizerHigh-level atom tree minimizer class
core::optimization::AtomTreeMultifuncAtom tree multifunction class
core::chemical::AtomTypeBasic atom type
core::chemical::AtomTypeDatabaseIO
core::chemical::sdf::atomTyper
core::chemical::AtomTypeSetSet of AtomTypes
protocols::features::AtomTypesFeatures
protocols::features::AtomTypesFeaturesCreatorCreator for the AtomTypesFeatures class
core::scoring::AtomVDW
core::kinematics::AtomWithDOFChangeSimple class for use in output-sensitive refold subroutine
protocols::qsar::scoring_grid::AtrGrid
protocols::qsar::scoring_grid::AtrGridCreator
core::pack::task::AUTOAUTO suggests that a packer can/should reconsider the design setting at a/each residue
core::chemical::AutomorphismIteratorEnumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations
protocols::rbsegment_relax::AutoRBMover
protocols::protein_interface_design::filters::AverageDegreeFilter
protocols::protein_interface_design::filters::AverageDegreeFilterCreator
protocols::loophash::BackboneDB
protocols::simple_moves::BackboneMover
protocols::enzdes::BackboneSampler
protocols::enzdes::BackboneSamplerCreator
protocols::loophash::BackboneSegment
core::scoring::constraints::BackboneStubConstraintThis constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location
core::pack::interaction_graph::BackgroundNode< V, E, G >A node which is not changing type or rotamer throughout a simulation
core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >An edge between a background node and a first class node
protocols::protein_interface_design::movers::BackrubDDMover
protocols::protein_interface_design::movers::BackrubDDMoverCreator
protocols::backrub::BackrubMoverClass for applying backrub moves to arbitrary protein segments
protocols::backrub::BackrubMoverCreator
protocols::backrub::BackrubSegmentClass for holind information about individual backrub segments
protocols::backrub::BackrubSidechainMover
protocols::backrub::BackrubSidechainMoverCreator
core::scoring::packing::Ball
protocols::swa::rna::Base_bin
core::scoring::rna::Base_pair
core::scoring::rna::Base_stack
core::fragment::BaseCacheUnit
protocols::jumping::BaseDisulfPairingLibrary
core::scoring::etable::BaseEtableEnergy< Derived >
protocols::jobdist::BaseJobDistributorCoordinates processing of jobs across multiple Rosetta processes
protocols::jumping::BaseJumpSetupVirtual base class: can create a set of jumps and cuts
protocols::jumping::BasePairingLibraryReturns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors
protocols::rna::BasePairType
core::scoring::dna::BasePartnerSilly vector1 wrapper class so we can derive from PoseCachedData
protocols::jobdist::BasicJobEach Job object describes a particular input to Rosetta
protocols::pack_daemon::BasicSimAnnealerRepacker
protocols::jd2::archive::BatchBatch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive
protocols::simple_filters::BatchEvaluator
protocols::jd2::BatchJobInputter
protocols::simple_filters::BatchNrEvaluator
core::scoring::etable::BB_BB_EnergyInvoker< Derived >
core::scoring::BB_Pos
protocols::fldsgn::topology::BB_Pos
protocols::topology_broker::BBClaim
protocols::simple_moves::BBConRotMover
protocols::loophash::BBData
core::pack::dunbrack::BBDepNRChiSample< P >P for precision
core::pack::dunbrack::BBDepSemiRotamericData< T >A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone dependent rotamers
protocols::loophash::BBExtraData
protocols::simple_moves::BBG8T3AMoverParticular gaussian mover from the original paper
protocols::simple_moves::BBGaussianMoverBasic class for implementing Gaussian Perturbation of bb
core::pack::dunbrack::BBIndNRChiSample< P >
core::pack::dunbrack::BBIndSemiRotamericData< T >A class to hold rotamer building data on the stack and yet have it accessible to derived classes when invoking base class functions. An alternative would have been to store mutable member data in the Library class itself. This option, however, is not thread safe. This data is used by the SemiRotamericSRDL class for when building backbone independent rotamers
core::fragment::BBTorsionAndAnglesSRFD
core::fragment::BBTorsionSRFD
protocols::forge::components::BDR
protocols::forge::components::BDRSegmentInfo
core::coarse::Rule::BeadAdder
core::coarse::Translator::BeadAtom
protocols::protein_interface_design::movers::BestHotspotCstMoverRemove all HotspotCst's from the pose except the best X
protocols::protein_interface_design::movers::BestHotspotCstMoverCreator
protocols::match::output::BestMatchesCollection
protocols::frag_picker::BestTotalScoreSelectorSelects a given number of fragments using a quota scheme
protocols::fldsgn::topology::BetaAlphaBetaMotif
protocols::fldsgn::topology::BetaAlphaBetaMotifSet
protocols::features::BetaTurnDetectionFeatures
protocols::features::BetaTurnDetectionFeaturesCreatorCreator for the BetaTurnDetectionFeatures class
protocols::frag_picker::scores::BFactorBFactor score counts identical residues
protocols::match::BfactorMPMRemoves 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
protocols::nonlocal::BiasedFragmentMover
core::scoring::constraints::BigBinConstraintConstraint on dihedral angle formed by 4 points
core::scoring::constraints::BigBinConstraintCreatorMover creator for the BigBinConstraint constraint
binary_function
BinaryExpression
core::io::silent::BinaryProteinSilentStructWhy this inheritance pathway? this makes no sense!
core::io::silent::BinaryProteinSilentStructCreatorCreator for the BinaryProteinSilentStruct class
core::io::silent::BinaryRNASilentStruct
core::io::silent::BinaryRNASilentStructCreatorCreator for the BinaryRNASilentStruct class
protocols::constraints_additional::BindingSiteConstraint
protocols::constraints_additional::BindingSiteConstraintCreatorMover creator for the BindingSiteConstraint constraint
protocols::protein_interface_design::filters::BindingStrainFilter
protocols::protein_interface_design::filters::BindingStrainFilterCreator
protocols::jd2::parser::BluePrint
protocols::fldsgn::BluePrintBDR
protocols::fldsgn::BluePrintBDRCreator
protocols::boinc::Boinc
protocols::boinc::BoincCurrentPoseObserver
protocols::jd2::BOINCJobDistributor
protocols::boinc::BoincSharedMemory
protocols::protein_interface_design::filters::BoltzmannFilter
protocols::protein_interface_design::filters::BoltzmannFilterCreator
core::scoring::methods::BondAngleDatabase
core::chemical::sdf::BondData
core::kinematics::tree::BondedAtomAtom which are bonded to its parentt, derived from Atom_
core::id::BondID
core::scoring::methods::BondLengthDatabase
core::fragment::picking_old::concepts::Book< Pages >Class demonstrating the Book concept
core::fragment::picking_old::concepts::Bookmark< PageConstIterator >Struct demonstrating Bookmark concept
protocols::match::Bool3DGrid
protocols::match::Bool3DGridKinemageWriter
protocols::frag_picker::BoundedCollector< StrictWeakOrdering >Keeps the N best fragments candidates for the final selection
protocols::frag_picker::BoundedCollector_CompareTotalScore
protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
core::scoring::constraints::BoundFunc
protocols::branch_angle::BranchAngleOptimizer
protocols::branch_angle::BranchCoef1Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors
protocols::branch_angle::BranchCoef2Class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors
protocols::branch_angle::BranchParam1Class to store bond angle energy parameters around a single atom atom with three bonded neighbors
protocols::branch_angle::BranchParam2Class to store bond angle energy parameters around a single atom atom with four bonded neighbors
core::optimization::BrentLineMinimization
protocols::forge::build::BridgeConnect two contiguous but disjoint sections of a Pose into one continuous section
protocols::kinmatch::BruteFunGroupTK
core::io::serialization::BUFFER
protocols::protein_interface_design::movers::BuildAlaPoseDesigns alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines
protocols::protein_interface_design::movers::BuildAlaPoseCreator
protocols::forge::build::BuildInstructionTracks modifications to be made and is capable of making residue length changes on a Pose
protocols::forge::build::BuildManagerContainer for managing BuildInstructions
protocols::motifs::BuildPosition
protocols::match::upstream::BuildSetA 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
protocols::match::BumpGrid
core::pack::rotamer_set::BumpSelector
core::scoring::methods::BurialEnergy
core::scoring::methods::BurialEnergyCreator
protocols::protein_interface_design::BuriedUnsatHbondFilterFilters based on an upper bound # of buried unsatisfied polar residues
protocols::simple_filters::BuriedUnsatHbondFilterFilters based on an upper bound # of buried unsatisfied polar residues
protocols::simple_filters::BuriedUnsatHbondFilterCreator
protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
core::scoring::disulfides::CaCbCb_Angle_Func
core::scoring::disulfides::CaCbCbCa_Dihedral_Func
core::id::CacheableAtomID_MapVectorAtomID_Map< xyzVector< Real > >
CacheableData
core::pose::datacache::CacheableDataType
core::pose::datacache::CacheableObserverBase class for Pose/Conformation observers that are stored in a Pose's DataCache
core::pose::datacache::CacheableObserverType
core::pose::datacache::CacheablePoseRawPtrPose *
core::sequence::CacheableSequenceProfile
core::fragment::CacheWrapper< T, XCacheUnit >
protocols::frag_picker::scores::CachingScoringMethod
protocols::seeded_abinitio::CAcstGenerator
protocols::seeded_abinitio::CAcstGeneratorCreator
core::pose::metrics::CalculatorFactory
protocols::simple_filters::CamShiftEvaluator
protocols::simple_filters::CamShiftEvaluatorCreatorCreator for the CamShiftEvaluatorCreator class
protocols::nonlocal::SmoothPolicy::Candidate
protocols::frag_picker::CandidatesCollectorA base class for collecting fragments
protocols::moves::CanonicalSamplingMover
protocols::canonical_sampling::CanonicalSamplingMover
core::scoring::carbon_hbonds::CarbonHBondEnergy
core::scoring::carbon_hbonds::CarbonHBondEnergyCreator
core::scoring::carbon_hbonds::CarbonHBondPotential
protocols::cartesian::CartesianAtom
core::scoring::methods::CartesianBondedEnergy
core::scoring::methods::CartesianBondedEnergyCreator
protocols::comparative_modeling::hybridize::CartesianHybridize
core::optimization::CartesianMinimizerHigh-level atom tree minimizer class
core::optimization::CartesianMinimizerMap
core::optimization::CartesianMultifuncAtom tree multifunction class
core::grid::CartGrid< T >
protocols::toolbox::pose_metric_calculators::CatPiCalculator
core::scoring::packstat::CavityBall
core::scoring::packstat::CavityBallCluster
core::scoring::disulfides::CB_Angle_Func
core::scoring::disulfides::Cb_Distance_FuncScore based on the distance between Cb
core::scoring::disulfides::CBSG_Dihedral_Func
protocols::loops::loop_closure::ccd::CcdLoopClosureMover
protocols::loops::loop_closure::ccd::CcdMover
protocols::rbsegment_relax::CCDMoveWrapper
protocols::antibody::CDRH3ModelerAb initio modeling of CDR H3 loop
protocols::antibody2::CDRH3Modeler2Ab initio modeling of CDR H3 loop
core::sequence::Cell
core::scoring::disulfides::Cen_Distance_Func
core::scoring::methods::CenHBEnergy
core::scoring::methods::CenHBEnergyCreator
core::scoring::CenHBPotential
core::scoring::CenListInfoKeep track of the cenlist information
core::scoring::methods::CenPairEnergy
core::scoring::methods::CenPairEnergyCreator
core::scoring::disulfides::CentroidDisulfideEnergy
core::scoring::disulfides::CentroidDisulfideEnergyComponentsStorage for Disulfide Energy Terms
core::scoring::disulfides::CentroidDisulfideEnergyContainer
core::scoring::disulfides::CentroidDisulfideEnergyCreator
core::scoring::disulfides::CentroidDisulfideNeighborConstIteratorJust a const version of CentroidDisulfideNeighborIterator
core::scoring::disulfides::CentroidDisulfideNeighborIteratorAn iterator over the disulfide bonds a residue forms
core::scoring::disulfides::CentroidDisulfidePotential
protocols::surface_docking::CentroidRelaxMover
core::scoring::constraints::ChainbreakDistFunc
core::scoring::methods::ChainbreakEnergyChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align
core::scoring::methods::ChainbreakEnergyCreator
core::util::ChainbreakUtil
protocols::simple_moves::ChainGroupDiscriminator
core::pack::task::operation::ChainIs
core::pack::task::operation::ChainIsCreator
core::pack::task::operation::ChainIsnt
core::pack::task::operation::ChainIsntCreator
core::pack::task::operation::ResiduePDBIndexIs::ChainPos
protocols::moves::ChangeFoldTreeMover
protocols::toolbox::pose_metric_calculators::ChargeCalculator
core::scoring::constraints::CharmmPeriodicFuncFunction of type y = 0.5 * k * (1 - cos(n * (x - x0) ) )
protocols::checkpoint::CheckPointer
core::chemical::ChemicalManagerClass managing different sets of atom_type_set and residue_type_set
protocols::sparta::ChemicalShiftEvaluator
protocols::sparta::ChemicalShiftEvaluatorCreatorCreator for the ChemicalShiftsEvaluatorCreator class
core::sequence::ChemicalShiftScoringScheme
core::sequence::ChemicalShiftSequence
core::sequence::ChemicalShiftSequenceCreator
core::pack::dunbrack::ChiSet
protocols::simple_filters::ChiWellRmsdEvaluator
protocols::simple_filters::ChiWellRmsdEvaluatorCreatorCreator for the ChiWellRmsdEvaluatorCreator class
protocols::nonlocal::Chunk
protocols::rna::ChunkSet
protocols::comparative_modeling::hybridize::ChunkTrialMover
core::scoring::packstat::Circle
core::scoring::constraints::CircularGeneral1D_FuncFunction that allows return of arbitrary FArrays -- this time circularized
core::scoring::constraints::CircularHarmonicFuncFunction that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints
protocols::fldsgn::CircularPermutation
protocols::fldsgn::CircularPermutationCreator
core::scoring::constraints::CircularPowerFuncGeneralization of CircularCircularPowerFunc -- other exponents allowed
core::scoring::constraints::CircularSigmoidalFuncFunction that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints
protocols::topology_broker::ClaimerMessage
protocols::toolbox::pose_metric_calculators::ClashCountCalculator
protocols::abinitio::ClassicAbinitio
protocols::simple_moves::ClassicFragmentMoverA FragmentMover that applies uniform sampling of fragments
protocols::qsar::scoring_grid::ClassicGrid
protocols::qsar::scoring_grid::ClassicGridCreator
protocols::match::downstream::ClassicMatchAlgorithmProduce 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
protocols::relax::ClassicRelaxA functor class which implements the classic Rosetta++ pose_relax protocol
protocols::relax::ClassicRelaxCreator
protocols::simple_moves::ClearConstraintsMover
protocols::simple_moves::ClearConstraintsMoverCreator
protocols::seeded_abinitio::CloseFold
protocols::seeded_abinitio::CloseFoldCreator
protocols::antibody::CloseOneMoverCloses only one CDR onto a framework
protocols::match::output::CloudPDBWriterOutput 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
protocols::cluster::Cluster
protocols::swa::rna::Cluster_Member
protocols::cluster::ClusterBase
protocols::toolbox::ClusterBase
protocols::toolbox::ClusterOptions
protocols::cluster::ClusterPhilStyle
protocols::toolbox::ClusterPhilStyle
protocols::cluster::ClusterPhilStyle_Loop
protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue
protocols::topology_broker::CmdLineData
core::coarse::CoarseEtable
core::scoring::etable::CoarseEtableEnergy
core::scoring::etable::CoarseEtableEnergyCreator
protocols::coarse_rna::CoarseRNA_DeNovoProtocolThe RNA de novo structure modeling protocol
protocols::coarse_rna::CoarseRNA_Fragments
protocols::coarse_rna::CoarseRNA_LoopCloserThe RNA de novo structure modeling protocol
core::pack::dunbrack::CoarseRotamer
core::pack::dunbrack::CoarseRotamerSet
core::pack::dunbrack::CoarseSingleResidueLibrary
protocols::simple_filters::COFilter
protocols::qsar::ColorGradient
protocols::swa::rna::Combine_Tags_Info
protocols::domain_assembly::CombineChainsMover
protocols::constraints_additional::CombinedConstraintEvaluator
protocols::constraints_additional::CombinedConstraintEvaluatorCreatorCreator for the CombinedConstraintsEvaluatorCreator class
protocols::filters::CombinedFilterUsed to combine multiple seperate filters into a single filter value
protocols::filters::CombinedFilterCreator
protocols::swa::rna::compare_base_bin
protocols::swa::rna::compare_int_pair
protocols::swa::rna::compare_test
protocols::frag_picker::CompareByScoreCombinationComparator based on the linear combination of some score components
protocols::frag_picker::CompareQueryPositionComparator based on a sequence position in a query
protocols::frag_picker::CompareScoreComponentComparator based on one of the score components calculated for fragments
protocols::jd2::CompareTags
protocols::frag_picker::CompareTotalScoreComparator based on the total score of fragments
core::sequence::CompassScoringScheme
protocols::ligand_docking::CompleteConnectionsFilter
protocols::filters::CompleteConnectionsFilter
protocols::ligand_docking::CompleteConnectionsFilterCreator
protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessageCompletionMessage(s) are send to the ArchiveManager whenever more than nr_notify decoys have been finished / or when the full batch is finished
protocols::frag_picker::CompositeFragmentSelectorSelects fragments by running several selectors
core::sequence::CompositeScoringScheme
core::sequence::CompositeSequence
core::sequence::CompositeSequenceCreator
protocols::moves::CompositionMover
protocols::filters::CompoundFilterUsed to define a compound logical statement involving other filters with AND, OR and XOR
protocols::filters::CompoundFilterCreator
protocols::ligand_docking::CompoundTranslate
protocols::ligand_docking::CompoundTranslateCreator
Computes
protocols::abinitio::ComputeTotalDistCst
core::conformation::ConformationA container of Residues and the kinematics to manage them
core::pose::signals::ConformationEventSignals a conformation change in a Pose
core::conformation::ConformationKinWriter
protocols::viewer::ConformationViewerObserver that attaches to a Conformation and displays graphics
core::scoring::constraints::ConformationXYZ
protocols::docking::ConformerSwitchMoverThis 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
protocols::docking::ConformerSwitchMoverCreator
core::conformation::signals::ConnectionEventSignal a change in the connection with a Conformation object, e.g. destruction or transfer
protocols::forge::build::ConnectRightInstruction to connect one Pose onto the right side of another
protocols::simple_moves::ConsensusDesignMoverThis 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
protocols::simple_moves::ConsensusDesignMoverCreator
protocols::simple_filters::ConservedPosMutationFilter
protocols::simple_filters::ConservedPosMutationFilterCreator
core::io::raw_data::RawFileData::const_iteratorConst_iterator class for RawFileData container
core::io::silent::SilentFileData::const_iteratorConst_iterator class for SilentFileData container
protocols::topology_broker::weights::ConstAbinitioMoverWeight
core::scoring::constraints::ConstantConstraintA Constant Constraint
core::scoring::constraints::ConstantFuncDerived class of class Func representing a Constant distribution with a user-specified mean and standard deviation
core::fragment::ConstantLengthFragSetA set of fragments that contains fragments of a constant length read in from a fragment file
core::fragment::ConstantLengthFragSetIterator_
core::scoring::constraints::ConstraintActually a *restraint*, like a virtual rubber band between a pair of atoms
protocols::topology_broker::ConstraintClaimer
core::scoring::constraints::ConstraintCreatorAbstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class
core::scoring::constraints::ConstraintEdge
protocols::optimize_weights::ConstraintedOptimizationWeightFunc
protocols::constraints_additional::ConstraintEvaluator
protocols::constraints_additional::ConstraintEvaluatorCreatorCreator for the ConstraintsEvaluatorCreator class
core::scoring::constraints::ConstraintFactory
protocols::forge::constraints::ConstraintFileRCG
protocols::simple_moves::ConstraintFragmentMover
protocols::abinitio::ConstraintFragmentSampler
core::scoring::constraints::ConstraintGraph
core::scoring::constraints::ConstraintIO
core::scoring::constraints::ConstraintNode
protocols::simple_moves::ConstrainToIdealMover
core::scoring::constraints::ConstraintRegistrator< T >This templated class will register an instance of an ConstraintCreator (class T) with the ConstraintFactory. It will ensure that no ConstraintCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
core::scoring::constraints::Constraints
core::scoring::constraints::ConstraintsEnergy
core::scoring::constraints::ConstraintsEnergyCreator
core::scoring::constraints::ConstraintSet
protocols::simple_moves::ConstraintSetMover
protocols::simple_moves::ConstraintSetMoverCreator
protocols::frag_picker::scores::ConstScoreConstScore adds a constant to the total score for each position
protocols::contact_map::ContactSimple class representing a contact between two atoms
protocols::frag_picker::Contact
protocols::frag_picker::ContactCounts
protocols::contact_map::ContactMap
protocols::contact_map::ContactMapCreator
protocols::simple_filters::ContactMapEvaluator
protocols::simple_filters::ContactMapEvaluatorCreatorCreator for the ContactMapEvaluatorCreator class
core::scoring::methods::ContactOrderEnergy
core::scoring::methods::ContactOrderEnergyCreator
protocols::contact_map::ContactPartnerSimple class that holds the information on an atom involved in a contact
core::scoring::methods::ContextDependentLRTwoBodyEnergy
core::scoring::methods::ContextDependentOneBodyEnergy
core::scoring::methods::ContextDependentTwoBodyEnergy
core::scoring::ContextGraph
core::scoring::ContextGraphFactory
core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator
core::scoring::methods::ContextIndependentLRTwoBodyEnergy
core::scoring::methods::ContextIndependentOneBodyEnergy
core::scoring::methods::ContextIndependentTwoBodyEnergy
protocols::filters::ContingentFilter
protocols::filters::ContingentFilterCreator
core::pack::rotamer_set::ContinuousRotamerSet
core::pack::rotamer_set::ContinuousRotamerSets
protocols::moves::mc_convergence_checks::ConvergenceCheck
core::optimization::ConvergenceTest
protocols::topology_broker::CoordConstraintClaimer
core::scoring::constraints::CoordinateConstraint
core::scoring::constraints::CoordinateConstraintCreatorMover creator for the CoordinateConstraint constraint
protocols::abinitio::CoordinateConstraintKC
protocols::seeded_abinitio::CoordinateCst
protocols::seeded_abinitio::CoordinateCstCreator
protocols::sparta::CORdata
protocols::fldsgn::filters::CoreDunbrackFilter
protocols::fldsgn::filters::CoreDunbrackFilterCreator
protocols::forge::build::CountFromLeftCount starting from interval().left in a BuildInstruction
core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
core::scoring::etable::count_pair::CountPairAll
core::scoring::etable::count_pair::CountPairCrossover3
core::scoring::etable::count_pair::CountPairCrossover4
core::scoring::etable::etrie::CountPairData_1_1
core::scoring::etable::etrie::CountPairData_1_2
core::scoring::etable::etrie::CountPairData_1_3
core::scoring::etable::etrie::CountPairDataGeneric
core::scoring::etable::count_pair::CountPairFactory
core::scoring::etable::count_pair::CountPairFunction
core::scoring::etable::count_pair::CountPairGeneric
core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >
core::scoring::etable::count_pair::CountPairIntraResC3
core::scoring::etable::count_pair::CountPairIntraResC4
core::scoring::etable::count_pair::CountPairNone
core::scoring::constraints::CountViolFunc
protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfoHelper class to allow for removal of covalent constraints
core::scoring::trie::CPDataCorrespondence
CrossoverBehavior
protocols::noesy_assign::CrossPeak
protocols::noesy_assign::CrossPeak3D
protocols::noesy_assign::CrossPeak4D
protocols::noesy_assign::CrossPeakInfoShared information about CrossPeak (one for each proton dimension)
protocols::noesy_assign::CrossPeakList
protocols::frag_picker::CS2ndShift
core::scoring::methods::CSD_TorsionEnergyA knowledge-based torsional potential for small molecules derived from the Cambridge Structural Database by KWK
core::chemical::CSDAtomTypeBasic "conformational" atom type derived from analysis of Cambridge Structure Database
core::chemical::CSDAtomTypeSetA set of CSDAtomTypes
protocols::frag_picker::scores::CSScoreScores a fragment by the root mean square deviation of Phi and Psi angles
protocols::frag_picker::CSTalosIO
core::scoring::constraints::CstEnergyContainer
core::scoring::constraints::CstMinimizationData
protocols::toolbox::match_enzdes_util::CstResInteractions
core::scoring::constraints::CstResNeighbConstIterator
core::scoring::constraints::CstResNeighbIterator
core::chemical::sdf::CtabBase
core::chemical::sdf::ctabV2000Parser
core::chemical::sdf::ctabV3000Parser
core::scoring::methods::CustomAtomPairEnergy
core::scoring::methods::CustomAtomPairEnergyCreator
protocols::frag_picker::CustomScoreSelectorSelects a given number of fragments using a quota scheme
protocols::topology_broker::CutBiasClaimer
protocols::topology_broker::CutClaim
protocols::moves::CycleMoverCycleMover iterates through its vector of Movers one at a time over many calls to apply()
protocols::moves::CyclicMoverA simple class for cycling between movers in consecutive calls to apply()
protocols::pack_daemon::DaemonSet
core::scoring::data_struct
core::scoring::data_structDa
core::scoring::data_structDaR
core::scoring::data_structR
protocols::wum::DatabaseEntryWorkUnit
protocols::features::DatabaseFilter
protocols::features::DatabaseJobInputter
protocols::features::DatabaseJobInputterCreator
protocols::features::DatabaseJobOutputter
protocols::features::DatabaseJobOutputterCreator
core::scoring::geometric_solvation::DatabaseOccSolEne
protocols::wum::DatabaseQueryWorkUnitManager< T >
protocols::canonical_sampling::mc_convergence_checks::DataBuffer
DataCache
protocols::jd2::parser::DataLoaderA class for loading arbitrary data into the XML parser's DataMap
protocols::jd2::parser::DataLoaderCreatorA class for creating new instances of DataLoaders for use in the XML Parser
protocols::jd2::parser::DataLoaderFactoryA factory for creating DataLoaders, which are able to load arbitrary data into the 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
protocols::jd2::parser::DataLoaderRegistrator< T >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
protocols::moves::DataMapGeneral-purpose store for any reference-count derived object
protocols::moves::DataMapObj< Ty >Templated class to make any data type compatible with ReferenceCounts and OPs. e.g., utility::pointer::owning_ptr< DataMapObj< bool > > stop; You can then place such constructs on the DataMap
protocols::cluster::DataPointData structure for one input data point for affinity propagation clustering
protocols::simple_moves::ddG
protocols::optimize_weights::DDGBindOptEData
protocols::simple_moves::ddGCreator
protocols::ddG::ddGData
protocols::protein_interface_design::DdgFilter
protocols::simple_filters::DdgFilter
protocols::simple_filters::DdgFilterCreator
protocols::ddg::ddGMover
protocols::optimize_weights::DDGMutationOptEData
core::scoring::interface::DDPlookup
core::scoring::interface::DDPscore
core::scoring::interface::DDPscoreCreator
protocols::jd2::archive::DebugArchive
core::pack::annealer::DebuggingAnnealer
protocols::jd2::DebugOut_MpiFileBuffer
protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
core::io::raw_data::DecoyFileData
protocols::toolbox::DecoySetEvaluation
core::io::raw_data::DecoyStruct
core::conformation::DefaultCubeHashUses default boost::hash combine to hash Cubes
protocols::seeded_abinitio::DefineMovableLoops
protocols::seeded_abinitio::DefineMovableLoopsCreator
core::chemical::DeleteAtomDelete an atom
core::chemical::DeletePropertyDelete a property from ResidueType Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM's (e.g. methylation)
protocols::protein_interface_design::filters::DeltaFilter
protocols::protein_interface_design::filters::DeltaFilterCreator
core::scoring::DenseEnergyContainer
protocols::pack_daemon::DenseIGRepacker
core::scoring::DenseNeighborConstIterator
core::scoring::DenseNeighborIterator
core::pack::interaction_graph::DensePDEdge
core::pack::interaction_graph::DensePDInteractionGraph
core::pack::interaction_graph::DensePDNode
protocols::topology_broker::DensityScoringClaimer
protocols::frag_picker::DenyPdbIdFilterDenies a chunk based on the pdb id of the source protein
core::optimization::DerivCheckDataPoint
core::sequence::DerivedSequenceMapping
core::scoring::DerivVectorPairA glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms
core::optimization::DescentDirectionAlgorithm
protocols::protein_interface_design::filters::DesignableResiduesFilter
protocols::protein_interface_design::filters::DesignableResiduesFilterCreator
protocols::toolbox::task_operations::DesignAroundOperation
protocols::toolbox::task_operations::DesignAroundOperationCreator
core::io::sequence_comparation::DesignContrastDesignContrast contains information for comparing the native protein sequence to designed protein sequence. And output the compare resultes to a special formated file which can be used for statistics calculations
protocols::protein_interface_design::movers::DesignMinimizeHbondsUsed 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
protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator
protocols::dna::DesignProteinBackboneAroundDNA
protocols::dna::DesignProteinBackboneAroundDNACreator
protocols::simple_moves::DesignRepackMoverPure virtual base class for movers which redesign and repack the interface
protocols::flxbb::DesignTask
protocols::flxbb::DesignTask_Layer
protocols::flxbb::DesignTask_Normal
protocols::enzdes::DesignVsNativeComparisonClass that holds a bunch of native poses and compares them
core::pose::signals::DestructionEventSpecial signal that the Pose is getting destroyed
protocols::enzdes::DetectProteinLigandInterfaceGiven 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
protocols::enzdes::DetectProteinLigandInterfaceOperationCreator
core::scoring::methods::dfire::DFIRE_Energy
core::scoring::methods::dfire::DFIRE_EnergyCreator
core::scoring::methods::dfire::DFIRE_Potential
core::optimization::DFPMinConvergedAbsolute
core::optimization::DFPMinConvergedFractional
protocols::optimize_weights::DGBindOptEDataScore a "bound" and an "unbound" structure, and minimize the squared error between the difference in their scores and the experimental delta_G of binding
protocols::enzdes::DiffAtomSasaFilter
protocols::enzdes::DiffAtomSasaFilterCreator
core::scoring::constraints::DihedralConstraintConstraint on dihedral angle formed by 4 points
core::scoring::constraints::DihedralConstraintCreatorMover creator for the DihedralConstraint constraint
protocols::frag_picker::scores::DihedralConstraintsScoreScores a fragment with a set of Dihedral constraints
core::scoring::constraints::DihedralPairConstraintConstraint on dihedral angle formed by 4 points
core::scoring::constraints::DihedralPairConstraintCreatorConstraint creator for DihedralPairConstraint
core::scoring::DimerPairing
protocols::fldsgn::topology::DimerPairing
protocols::fldsgn::topology::DimerPairings
core::scoring::methods::DirectReadoutEnergyImplementation of Kono and Sarai's knowledge-based protein-DNA interaction energy
core::scoring::methods::DirectReadoutEnergyCreator
core::scoring::dna::DirectReadoutPotential1st pass implementation of Kono + Sarai's protein-DNA interaction potential
core::pack::task::operation::DisallowIfNonnativeDisallowIfNonnative allows you to define what residues are NOT allowed in packing unless that residue is present in the input. Behaves like RestrictAbsentCanonicalAAS and NOTAA except will allow a resitricted residue at a position if it is there to begin with at the time of Task creation. Will do all residues unless otherwise defined by selection syntax below
core::pack::task::operation::DisallowIfNonnativeCreator
core::pack::task::operation::DisallowIfNonnativeRLT
core::pack::task::operation::DisallowIfNonnativeRLTCreator
protocols::genetic_algorithm::DiscreteRandomizer
core::graph::DisjointSets
core::scoring::methods::DistanceChainbreakEnergyDistanceChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how far apart their N and C atom are
core::scoring::methods::DistanceChainbreakEnergyCreator
core::scoring::custom_pair_distance::DistanceFunc
core::scoring::saxs::DistanceHistogram
protocols::noesy_assign::DistanceScoreMoverMaintains 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)
protocols::ligand_docking::DistributionMapA singleton class that returns a map of strings to enum types
core::scoring::disulfides::DisulfideAtomIndicesThis class is used by the *DisulfideEnergyContainer and the *DisulfidePotential classes to rapidly index into a residue that's known to form a disulfide. For the sake of computing derivatives, there are only three atoms that need to be readily available: CA, CB, and the atom which makes the disulfide bond, either SG or CEN. The DisulfideEnergyContainer is responsible for keeping the indices in one of these objects up-to-date with the residue it is meant to shadow
protocols::frag_picker::scores::DisulfideDistanceScores a fragment by the root mean square deviation of Phi and Psi angles
core::io::raw_data::DisulfideFileParses and stores a disulfide file
protocols::protein_interface_design::filters::DisulfideFilterFilters for structures which could form a disulfide bond across the docking interface
protocols::protein_interface_design::filters::DisulfideFilterCreator
protocols::frag_picker::scores::DisulfideIdentityDisulfideIdentity score counts identical residues
core::scoring::disulfides::DisulfideMatchingDatabase
core::scoring::disulfides::DisulfideMatchingEnergy
core::scoring::disulfides::DisulfideMatchingEnergyComponentsStorage for Disulfide Energy Terms
core::scoring::disulfides::DisulfideMatchingEnergyContainer
core::scoring::disulfides::DisulfideMatchingEnergyCreator
core::scoring::disulfides::DisulfideMatchingNeighborConstIteratorJust a const version of DisulfideMatchingNeighborIterator
core::scoring::disulfides::DisulfideMatchingNeighborIteratorAn iterator over the disulfide bonds a residue forms
core::scoring::disulfides::DisulfideMatchingPotential
protocols::protein_interface_design::movers::DisulfideMover
protocols::protein_interface_design::movers::DisulfideMoverCreator
protocols::topology_broker::DisulfJumpClaimerClaimer 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
core::scoring::disulfides::DisulfMinData
protocols::jumping::DisulfPairing
protocols::jumping::DisulfPairingLibrary
core::scoring::disulfides::DisulfResNeighbConstIterator
core::scoring::disulfides::DisulfResNeighbIterator
protocols::jumping::DisulfTemplate
protocols::frag_picker::DiversifyCrmsdByClusteringSelects fragments by running several selectors
protocols::frag_picker::DiversifyCrmsdSelectorSelects fragments by running several selectors
protocols::frag_picker::DiversifyDihedralsSelectorSelects fragments by running several selectors
protocols::enzdes::DiversifyStoredRBConfsUses a docking mover to diversiy the stored confs until they're all min_rms_ away from each other note: no scorefunction used here
protocols::simple_moves::DME_FilterMover
core::scoring::methods::DNA_BaseEnergy
core::scoring::methods::DNA_BaseEnergyCreator
core::scoring::dna::DNA_BasePotential
protocols::dna::DnaChains
protocols::dna::DnaDesignDefCommand-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience
protocols::dna::DnaInterfaceFinder
protocols::dna::DnaInterfaceMinMover
protocols::dna::DnaInterfaceMinMoverCreator
protocols::dna::DnaInterfaceMultiStateDesignWraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework
protocols::dna::DnaInterfaceMultiStateDesignCreator
protocols::dna::DnaInterfacePacker
protocols::dna::DnaInterfacePackerCreator
protocols::dna::DnaNeighbor
protocols::dna::DnaPosition
protocols::protein_interface_design::movers::DockAndRetrieveSidechains
protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator
protocols::protein_interface_design::DockDesignFilterFactory
protocols::jd2::DockDesignParserReading the xml file and generating the mover
protocols::docking::DockingEnsembleThis 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
protocols::docking::DockingEnsemblePrepackProtocol
protocols::docking::DockingHighRes
protocols::docking::DockingHighResFilterHigh-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given (2) interface_score must be negative
protocols::docking::DockingHighResLegacyThis mover does the high resolution refinement stage of the RosettaDock algorithm
protocols::docking::DockingInitialPerturbationThis mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options
protocols::docking::DockingLowRes
protocols::docking::DockingLowResFilterLow-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
protocols::toolbox::task_operations::DockingNoRepack1
core::pack::task::operation::DockingNoRepack1
protocols::toolbox::task_operations::DockingNoRepack2
core::pack::task::operation::DockingNoRepack2
protocols::docking::DockingPrepackProtocol
protocols::docking::DockingProtocolThis is the standard RosettaDock protocol
protocols::docking::DockingProtocolCreator
core::scoring::DockingScoreFunction
protocols::docking::DockingSlideIntoContactContrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently)
protocols::docking::DockMCMCycle
protocols::docking::DockMCMProtocol
protocols::docking::DockMinMover
protocols::docking::DockSetupMoverAllows docking using simulated or parallel tempering
protocols::docking::DockSetupMoverCreator
protocols::docking::DockTaskFactory
core::scoring::constraints::DOF_ConstraintThis isn't quite a standard constraint since it acts on DOF's directly rather than on XYZ coordinates
core::optimization::DOF_DataPoint
core::id::DOF_IDKinematics DOF identifier class
core::id::DOF_ID_Map< T >Map from Atom DOF identifiers to contained values class
core::id::DOF_ID_RangeKinematics DOF identifier (with range) class
core::optimization::DOF_Node
protocols::topology_broker::DofClaim
protocols::simple_moves::DOFHistogramRecorder
protocols::abinitio::DomainAssemblyInsert fragments in a linker region. Very similar to what's in looprelax_main
protocols::abinitio::DomainAssemblyCreator
core::pack::interaction_graph::DotSphereRepresents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA
protocols::pack_daemon::DoubleDenseIGRepacker
core::pack::interaction_graph::DoubleDensePDEdge
core::pack::interaction_graph::DoubleDensePDInteractionGraph
core::pack::interaction_graph::DoubleDensePDNode
protocols::abinitio::DoubleLayerKinematicAbinitio
core::pack::interaction_graph::DoubleLazyEdge
core::pack::interaction_graph::DoubleLazyInteractionGraphThe double lazy interaction graph is primarily useful for multistate design where one is interested in knowing at particular edge, all of the rotamer pair energies for a particular amino acid assignment. The double lazy interaction graph is lazy in two ways: first, in delaying the computation of rotamer pair energies until they are needed, and second, in delaying the allocation of memory for rotamer pair energies until that memory is needed. The DLIG will do one of two things once it allocates space for a block of rotamer pairs: 1) In its standard operating behavior, it will leave that space allocated until the graph is destroyed, which means that the energies it stores in that block will never be computed more than once; or 2) In its alternate operating behavior, the LMIG will deallocate some of those blocks to make sure that it never uses more than some maximum amount of memory on RPEs
core::pack::interaction_graph::DoubleLazyNode
core::fragment::DownJumpSRFD
protocols::match::downstream_hit
protocols::match::downstream::DownstreamAlgorithmA class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits
protocols::match::downstream::DownstreamBuilder
protocols::match::output::DownstreamCoordinateKinemageWriter
protocols::match::output::DownstreamRMSEvaluatorIn 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
core::sequence::DP_Matrix
core::sequence::DPScoringScheme
core::graph::DS_Node
core::scoring::dssp::Dssp
protocols::moves::DsspMover
protocols::moves::DsspMoverCreator
protocols::toolbox::DummyClass
protocols::protein_interface_design::movers::DumpPdbWhat you think this can now be assimilated into DumpPdbMover
protocols::protein_interface_design::movers::DumpPdbCreator
core::pack::dunbrack::DunbrackConstraint
core::pack::dunbrack::DunbrackConstraintCreatorMover creator for the DunbrackConstraint constraint
core::pack::dunbrack::DunbrackEnergy
core::pack::dunbrack::DunbrackEnergyCreator
core::pack::dunbrack::DunbrackRotamer< S, P >
core::pack::dunbrack::DunbrackRotamerMeanSD< S, P >A class who's size is known at compile time. A vector of these objects will occupy a perfectly contiguous region of memory, with no extra space allocated for pointers. These objects may be rapidly allocated and deallocated on the stack
core::pack::dunbrack::DunbrackRotamerSampleData
protocols::match::upstream::DunbrackSCSamplerBasic 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
protocols::pack_daemon::DynamicAggregateFunction
core::graph::Edge
core::kinematics::EdgeSingle edge of the fold_tree
core::pack::interaction_graph::EdgeBase
core::graph::EdgeListCustom edge list class. Returns const-iterators which only return Edge const *'s and non-const-iterators which can return either const or non-const Edge*'s. Manages its own memory using an unordered-object-pool for fast insertion and deletion of EdgeListElements. Implemented as a doubly linked list, though there's no practical way to start at the end of a list and work backward since decrementing the end iterator is not a valid operation
core::graph::EdgeListConstIteratorCustom Edge list const iterator class, which returns only const Edge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL's const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< Edge * > and a list< Edge const * >
core::graph::EdgeListElementAn extensible graph class
core::graph::EdgeListIteratorCustom Edge list (non-const) iterator class, which can return non-const Edge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL's const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< Edge * > and a list< Edge const * >
protocols::pockets::EggshellGrid@
core::optimization::EItemInner class for Genetic Algorithm, hold one population with some additional info
core::scoring::hackelec::ElecAtom
core::scoring::electron_density::ElecDensAllAtomCenEnergy
core::scoring::electron_density::ElecDensAllAtomCenEnergyCreator
core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator
core::scoring::electron_density::ElecDensCenEnergy
core::scoring::electron_density::ElecDensCenEnergyCreator
core::scoring::electron_density::ElecDensEnergy
core::scoring::electron_density::ElecDensEnergyCreator
core::scoring::electron_density::ElectronDensity
core::scoring::electron_density_atomwise::ElectronDensityAtomwise
core::chemical::ElementClass to describe Elements
core::chemical::ElementSetA set of Elements
core::chemical::sdf::elementToType
core::scoring::EMapVectorA vector for storing energy data, initially all values are 0
core::pack::task::EMPTYEMPTY disallows all canonical residues but leaves packing and designing unchanged (for noncanonicals)
protocols::toolbox::pose_metric_calculators::EmptyVertexData
core::scoring::EnergiesA cached energies object
protocols::toolbox::pose_metric_calculators::EnergiesData
protocols::simple_moves::EnergyCutRotamerTrialsMinMoverWrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant
protocols::simple_moves::EnergyCutRotamerTrialsMover
core::pose::metrics::EnergyDependentCalculator
core::scoring::EnergyEdge
core::fragment::picking_old::vall::eval::EnergyEvalScores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction
core::pose::signals::EnergyEventSignals an energy change in a Pose
core::scoring::EnergyGraphClass to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method
core::scoring::methods::EnergyMethodBase class for the energy method hierarchy
core::scoring::methods::EnergyMethodCreatorThe EnergyMethodCreator class's responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one
core::scoring::methods::EnergyMethodOptions
core::scoring::methods::EnergyMethodRegistrator< T >This templated class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
core::io::silent::EnergyNames
core::scoring::EnergyNode
protocols::protein_interface_design::EnergyPerResidueFilter
protocols::simple_filters::EnergyPerResidueFilter
protocols::simple_filters::EnergyPerResidueFilterCreator
protocols::cluster::EnsembleConstraints
protocols::cluster::EnsembleConstraints_Simple
protocols::scoring::methods::EnsembleEnergy
protocols::scoring::methods::EnsembleEnergyCreator
protocols::genetic_algorithm::Entity
protocols::pack_daemon::EntityCorrespondence
protocols::genetic_algorithm::EntityElementEntity element
protocols::genetic_algorithm::EntityElementCreatorEntity element creator
protocols::genetic_algorithm::EntityElementFactoryEntity element factory
protocols::genetic_algorithm::EntityElementRegistrator< T >
protocols::genetic_algorithm::EntityElementsEqual
protocols::pack_daemon::EntityFunc
protocols::pack_daemon::EntityFuncExpressionCreator
protocols::pack_daemon::EntityHistoryLT
protocols::genetic_algorithm::EntityRandomizer
Entry
core::scoring::methods::EnvEnergy
core::scoring::methods::EnvEnergyCreator
core::scoring::EnvPairPotential
core::scoring::methods::EnvSmoothEnergy
core::scoring::methods::EnvSmoothEnergyCreator
protocols::toolbox::match_enzdes_util::EnzConstraintIO
protocols::toolbox::match_enzdes_util::EnzConstraintParametersClass that holds all the parameters for one specific constraint
protocols::toolbox::match_enzdes_util::EnzCstTemplateResHelper class for class EnzConstraintParameters, gathers information
protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtomsHelper class for EnzCstTemplateRes, holds atom ids corresponding
protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
protocols::enzdes::EnzdesBaseProtocol
protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
protocols::toolbox::match_enzdes_util::EnzdesCstCacheSimple class to store the pose specific enzdes constraint information in the actual pose
protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
protocols::enzdes::EnzdesFixBBProtocol
protocols::enzdes::EnzdesFlexBBProtocol
protocols::enzdes::EnzdesFlexibleRegion
protocols::enzdes::EnzdesJobInputter
protocols::enzdes::EnzdesJobInputterCreator
protocols::enzdes::EnzdesJobOutputterFor now this class only writes a different scorefile than the default one written by the FileJobOutputter. the structure output format is pdb
protocols::enzdes::EnzdesJobOutputterCreator
protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
protocols::toolbox::match_enzdes_util::EnzdesLoopsFileClass to process an enzdes loops file
protocols::enzdes::EnzdesScorefileFilter
protocols::enzdes::EnzdesScorefileFilterCreator
protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
protocols::enzdes::EnzRepackMinimize
protocols::enzdes::EnzRepackMinimizeCreator
protocols::enzdes::EnzScoreFilter
protocols::enzdes::EnzScoreFilterCreator
core::scoring::etable::EtableJk Class definition for Etable
core::scoring::etable::etrie::EtableAtom
core::scoring::etable::EtableEnergy
core::scoring::etable::EtableEnergyCreator
core::scoring::constraints::EtableFuncClass for representing arbitrarily defined functions
core::scoring::etable::EtableOptions
protocols::swa::rna::Euler_angles
protocols::jd2::archive::EvaluatedArchiveTags 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
protocols::simple_filters::EvaluatedTrialMover
protocols::evaluation::EvaluatorCreatorThe Creator class is responsible for creating a particular mover class
protocols::evaluation::EvaluatorFactoryCreate Evaluator Reporters
protocols::evaluation::EvaluatorRegistrator< T >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
core::scoring::packstat::Event
core::pack::task::EXEX handles the various extrachi options
core::pack::task::EX_CUTOFFEX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers)
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator
core::scoring::ExcludedResPredicate
protocols::jd2::archive::EXCN_Archive
protocols::noesy_assign::EXCN_AssignmentNotFound
core::id::EXCN_AtomNotFound
EXCN_BadInput
protocols::loophash::EXCN_bbdb_Merge_Failed
protocols::moves::mc_convergence_checks::EXCN_Converged
protocols::moves::EXCN_Converged
protocols::loophash::EXCN_DB_IO_Failed
protocols::topology_broker::EXCN_FailedBroking
protocols::noesy_assign::EXCN_FileFormat
protocols::topology_broker::EXCN_FilterFailed
protocols::canonical_sampling::mc_convergence_checks::EXCN_Heat_Converged
protocols::topology_broker::EXCN_Input
protocols::loophash::EXCN_Invalid_Hashmap
core::kinematics::EXCN_InvalidFoldTree
protocols::loops::EXCN_Loop_not_closed
EXCN_Msg_Exception
protocols::loophash::EXCN_No_Extra_Data_To_Write
protocols::noesy_assign::EXCN_NoesyAssign
protocols::canonical_sampling::mc_convergence_checks::EXCN_Pool_Converged
protocols::topology_broker::EXCN_TopologyBroker
protocols::topology_broker::EXCN_Unknown
protocols::noesy_assign::EXCN_UnknownAtomname
protocols::noesy_assign::EXCN_UnknownResonance
protocols::loophash::EXCN_Wrong_DB_Format
protocols::cluster::ExemplarData structure for one similarity measurement (s_ik) for affinity propagation clustering
protocols::pack_daemon::ExpExpression
protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator
core::pack::interaction_graph::exposed_hydrophobic_data
Expression
ExpressionCreator
core::sequence::ExtendAlignerSW
core::import_pose::pose_stream::ExtendedPoseInputStream
protocols::simple_moves::ExtendedPoseMover
protocols::simple_moves::ExtendedPoseMoverCreator
protocols::star::Extender
core::fragment::picking_old::concepts::Extent< PageIter >Class demonstrating the Extent concept
core::fragment::picking_old::concepts::ExtentEvaluator< Bookmark, Ext >Class demonstrating ExtentEvaluator concept
protocols::simple_filters::ExternalEvaluator
protocols::toolbox::match_enzdes_util::ExternalGeomSamplerThe external geom sampler is a class that manages the data necessary to construct the coordinates of the three atoms in the downstream partner
core::pack::task::operation::ExtraChiCutoffExtraChiCutoff (correponding to flag "-extrachi_cutoff <float>" )
core::pack::task::operation::ExtraChiCutoffCreator
protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover
protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator
protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover
protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator
core::pack::task::operation::ExtraRotamersExtraRotamer for a residue. You know, -ex1, -ex2, all that
core::pack::task::operation::ExtraRotamersCreator
core::pack::task::operation::ExtraRotamersGeneric
core::pack::task::operation::ExtraRotamersGenericCreator
protocols::simple_filters::ExtraScoreEvaluatorCreatorCreator for the ExtraScoreEvaluatorCreator class
protocols::comparative_modeling::ExtraThreadingMover
core::scoring::methods::Fa_MbenvEnergy
core::scoring::methods::Fa_MbenvEnergyCreator
core::scoring::methods::Fa_MbsolvEnergy
core::scoring::methods::Fa_MbsolvEnergyCreator
core::scoring::constraints::FadeFunc
core::scoring::hbonds::FadeInterval
protocols::docking::FaDockingSlideIntoContactSlides docking partners together by monitoring fa_rep
protocols::filters::FalseFilter
protocols::filters::FalseFilterCreator
protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
protocols::surface_docking::FaSlideAwayFromSurfaceMoves the protein away from the surface
protocols::surface_docking::FaSlideIntoSurfaceSlides docking partners together by monitoring fa_rep
core::scoring::electron_density::FastDensEnergy
core::scoring::electron_density::FastDensEnergyCreator
protocols::pack_daemon::FASTER_IG_Repacker
core::pack::annealer::FASTERAnnealer
core::pack::interaction_graph::FASTEREdge
core::pack::interaction_graph::FASTERInteractionGraph
core::pack::interaction_graph::FASTERNode
protocols::loophash::FastGapMoverMover 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
protocols::moves::FastLinearFunc
protocols::relax::FastRelax
protocols::relax::FastRelaxCreator
core::scoring::saxs::FastSAXSEnergy
core::scoring::saxs::FastSAXSEnergyCreator
protocols::simple_moves::symmetry::FaSymDockingSlideTogetherSlides docking partners together by monitoring fa_rep
protocols::protein_interface_design::FavorNativeResidue
protocols::protein_interface_design::movers::FavorNativeResiduePreCycle
protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator
protocols::protein_interface_design::FavorNonNativeResidue
protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle
protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator
protocols::simple_moves::FavorSequenceProfile
protocols::simple_moves::FavorSequenceProfileCreator
protocols::swa::rna::FB_Pose_Data
protocols::features::FeaturesReporter
protocols::features::FeaturesReporterCreatorThe Creator class is responsible for creating a particular mover class
protocols::features::FeaturesReporterFactoryCreate Features Reporters
protocols::features::FeaturesReporterRegistrator< T >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
protocols::topology_broker::FibrilModelingClaimer
core::io::pdb::FieldData type Class to represent one field in PDB file
protocols::checkpoint::FileBuffer
core::io::pdb::FileDataFileData class. Hold data created from PDB file
protocols::jd2::FileJobOutputter
protocols::jd2::FileSystemJobDistributor
protocols::filters::Filter
protocols::filters::FilterCollectionWrapper-class that contains a vector1 of Filters
protocols::filters::FilterCreatorAbstract base class for a Filter factory; the Creator class is responsible for creating a particular filter class
protocols::swa::rna::Filterer_Count
protocols::filters::FilterFactory
protocols::moves::FilterMover
protocols::filters::FilterRegistrator< T >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
protocols::protein_interface_design::filters::FilterScanFilter
protocols::protein_interface_design::filters::FilterScanFilterCreator
protocols::flxbb::FilterStructs
protocols::flxbb::FilterStructs_Packstat
protocols::flxbb::FilterStructs_TotalCharge
protocols::ligand_docking::FinalMinimizer
protocols::ligand_docking::FinalMinimizerCreator
protocols::wum::find_SilentStructOPsThis little class is a predicate for finding silent structures in say a vector of silent structures
protocols::pockets::FingerprintBase
protocols::pockets::FingerprintMultifuncAtom tree multifunction class
core::pack::interaction_graph::FirstClassEdge< V, E, G >
core::pack::interaction_graph::FirstClassNode< V, E, G >
protocols::genetic_algorithm::FitnessFunction
core::pack::task::FIX_HIS_TAUTOMERFIX_HIS_TAUTOMER: when a histidine is present when the PackerTask is initialized, this flag will fix its tautomer (whether its hydrogen is on ND1 or NE2. Does nothing if not histidine at initialization (meaning if it mutates to histidine later this flag will have no effect)
core::pack::annealer::FixbbCoupledRotamerSimAnnealer
core::pack::annealer::FixbbLinkingRotamerSimAnnealer
core::pack::rotamer_set::FixbbRotamerSets
core::pack::annealer::FixbbSimAnnealer
core::pack::interaction_graph::FixedBBEdge
core::pack::interaction_graph::FixedBBInteractionGraph
core::pack::interaction_graph::FixedBBNode
protocols::canonical_sampling::FixedTemperatureController
protocols::abinitio::FixTemplateJumpSetup
core::scoring::constraints::FlatHarmonicFunc
protocols::flexpack::interaction_graph::FlexbbEdge
protocols::flexpack::interaction_graph::FlexbbIGFactory
protocols::flexpack::interaction_graph::FlexbbInteractionGraph
protocols::flexpack::interaction_graph::FlexbbNode
protocols::flexpack::rotamer_set::FlexbbRotamerSet
protocols::flexpack::rotamer_set::FlexbbRotamerSets
protocols::flexpack::annealer::FlexbbSimAnnealer
protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex
protocols::flexpack::FlexPacker
protocols::flexpep_docking::FlexPepDockingAbInitio
protocols::flexpep_docking::FlexPepDockingFlags
protocols::flexpep_docking::FlexPepDockingLowRes
protocols::flexpep_docking::FlexPepDockingPoseMetrics
protocols::flexpep_docking::FlexPepDockingProtocol
protocols::flexpep_docking::FlexPepDockingProtocolCreator
protocols::swa::rna::FloatingBaseChainClosureJobParameter
protocols::flxbb::FlxbbDesign
protocols::flxbb::FlxbbDesignCreator
protocols::flxbb::FlxbbDesignPack
protocols::topology_broker::FoldandDockClaimer
protocols::abinitio::FoldConstraintsExtension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles()
core::kinematics::FoldTreeThe FoldTree is a residue-based treelike representation of a molecule
protocols::loops::FoldTreeFromLoops
protocols::loops::FoldTreeFromLoopsCreator
protocols::comparative_modeling::hybridize::FoldTreeHybridize
core::scoring::saxs::FormFactor
core::scoring::saxs::FormFactorManagerSelects a given number of fragments using a quota scheme
protocols::frag_picker::scores::FourAtomsConstraintDataHolds data about a single four-body constraint in the form usefull for InterbondAngleScore and DihedralConstraintsScore classes
core::scoring::constraints::FourPointsFuncA simple class that represents the coordinates of four points, pretending that they all belong to residue 1. The residue() method is not implemented and cause a utility_exit
core::fragment::FragCache< T >
core::fragment::FragData
core::fragment::FragFactory
core::fragment::FragID
core::fragment::FragID_Iterator
protocols::rbsegment_relax::FragInsertAndAlignMoverPerforms a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'
protocols::frag_picker::scores::FragmentAllAtomCrmsdScores a fragment by its crmsd to the given reference structure
protocols::frag_picker::FragmentCandidateVector candidate says which X-mer from vall fits to a query sequence
protocols::topology_broker::FragmentClaimer
protocols::frag_picker::FragmentComparatorBase
protocols::simple_moves::FragmentCost
protocols::frag_picker::scores::FragmentCrmsdScores a fragment by its crmsd to the given reference structure
protocols::frag_picker::scores::FragmentCrmsdResDepthScores a fragment by its crmsd to the given reference structure
protocols::frag_picker::scores::FragmentDMEScores a fragment by its DME to the given reference structure
core::fragment::FragmentIO
protocols::rna::FragmentLibrary
core::fragment::picking_old::FragmentLibraryManagerSingleton class for accessing fragment libraries
protocols::simple_moves::FragmentMoverAbstract base class for FragmentMovers
protocols::frag_picker::FragmentPickerThe core of the fragment picking machinery
protocols::jd2::parser::FragmentReader
core::fragment::FragmentRmsd
protocols::abinitio::FragmentSampler
protocols::frag_picker::scores::FragmentScoreManagerHolds particular score components, weights and calculates the total score for a fragment candidate
protocols::frag_picker::scores::FragmentScoreMapHolds all small scores (score components) for a given fragment
protocols::frag_picker::scores::FragmentScoringMethodFragment candidate score
protocols::frag_picker::FragmentSelectingRuleSelects a given number of fragments just by selecting the best ones
protocols::toolbox::pose_metric_calculators::FragQualCalculator
protocols::fldsgn::filters::FragQualFilter
protocols::fldsgn::filters::FragQualFilterCreator
core::fragment::FragSetThe FragSet: (Interface Definition -- Virtual BaseClass )
core::fragment::FragSetCollection
protocols::jd2::parser::FragSetLoaderA class for loading arbitrary data into the XML parser's DataMap
protocols::jd2::parser::FragSetLoaderCreator
core::fragment::FragStore< T >
core::fragment::FrameFrame couples a list of FragData-instances to a certain alignment frame, i.e., position in sequence space A frame may be continous, i.e., its fragment data will be applied to all residues between start() and end() or ( in a specialized version inheriting this interface) may contain a loose list of sequence positions
core::fragment::FrameIterator
core::fragment::FrameIteratorWorker_
core::fragment::FrameList
core::fragment::FrameListIterator_
core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator
core::scoring::disulfides::FullatomDisulfideEnergy
core::scoring::disulfides::FullatomDisulfideEnergyComponents
core::scoring::disulfides::FullatomDisulfideEnergyContainer
core::scoring::disulfides::FullatomDisulfideEnergyCreator
core::scoring::disulfides::FullatomDisulfidePotential
protocols::surface_docking::FullatomRelaxMover
protocols::rna::FullAtomRNA_Fragments
protocols::match::upstream::FullChiSampleSet
core::scoring::constraints::FuncFunc is an abstract base class representing a function used to define constraints, in which func(r) gives the constraint score for the given value r
core::optimization::func_1d
core::scoring::constraints::FuncFactory
protocols::kinmatch::FunGroupTK
G
core::optimization::GA_Minimizer
protocols::cluster::GatherPosesMover
core::scoring::rna::Gaussian_parameter
core::scoring::constraints::GaussianFuncDerived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation
core::scoring::methods::GaussianOverlapEnergy
core::scoring::methods::GaussianOverlapEnergyCreator
protocols::rbsegment_relax::GaussianRBSegmentMover
protocols::sparta::GDB
core::scoring::methods::GenBornEnergy
core::scoring::methods::GenBornEnergyCreator
core::scoring::GenBornPoseInfo
core::scoring::GenBornPotential
core::scoring::GenBornResidueInfo
core::scoring::GenBornRotamerSetInfo
core::pose::signals::GeneralEventSignals a general change in a Pose
core::conformation::signals::GeneralEventSignals a general change in a Conformation
protocols::enzdes::GenerateStoredRBConfsGenerates 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
protocols::comparative_modeling::GenericJobInputter
protocols::comparative_modeling::GenericJobInputterCreator
protocols::moves::GenericMonteCarloMover
protocols::moves::GenericMonteCarloMoverCreator
core::scoring::etable::etrie::GenericResidueConnectionData
core::coarse::GenericRule
protocols::genetic_algorithm::GeneticAlgorithm
protocols::moves::GeometricFuncRamps 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 );
core::scoring::geometric_solvation::GeometricSolEnergy
core::scoring::geometric_solvation::GeometricSolEnergyCreator
protocols::features::GeometricSolvationFeatures
protocols::features::GeometricSolvationFeaturesCreatorCreator for the GeometricSolvationFeatures class
protocols::match::downstream::GeometrySecMatchRPEHolds a list of AtomGeometrySecMatchRPEs, that get evaluated in sequence when an instance of this class is asked to evaluate two residues
protocols::toolbox::match_enzdes_util::GeomSampleInfoClass that stores information of one geometric parameter line of the .cst file i.e. angleA or torsionB
protocols::frag_picker::GrabAllCollectorKeeps all fragments candidates for the final selection
protocols::antibody::GraftMoverGrafts a series of CDR onto a framework
protocols::antibody::GraftOneMoverGrafts only one CDR onto a framework
core::graph::GraphA Graph with constant time edge insertion and deletion. Extensible
protocols::viewer::GraphicsState
protocols::toolbox::GreedyKCenterGreedy K-Center Clustering Algorithm
protocols::simple_moves::GreedyOptMutationMover
protocols::simple_moves::GreedyOptMutationMoverCreator
protocols::simple_moves::GreenPacker
protocols::qsar::scoring_grid::GridBase
protocols::qsar::scoring_grid::GridCreatorAbstract class fora mover factory. The creator class is responsible for creating a particular mover class
protocols::qsar::scoring_grid::GridFactory
core::scoring::geometric_solvation::GridInfo
protocols::qsar::scoring_grid::GridManager
protocols::qsar::scoring_grid::GridRegistrator< T >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
protocols::scoring::methods::pcs::GridSearchIterator
protocols::scoring::methods::pcs2::GridSearchIterator
protocols::scoring::methods::pcs2::GridSearchIteratorCA
protocols::simple_moves::GroupDiscriminatorInterface 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
protocols::forge::build::GrowLeftInstruction to create an n-side extension
protocols::ligand_docking::GrowLigand
protocols::ligand_docking::GrowLigandCreator
protocols::seeded_abinitio::GrowPeptides
protocols::seeded_abinitio::GrowPeptidesCreator
protocols::forge::build::GrowRightInstruction to create a c-side extension
protocols::simple_moves::GunnCost
protocols::frag_picker::scores::GunnCost
protocols::frag_picker::scores::GunnCostScoreScores a fragment by its crmsd to the given reference structure
protocols::simple_moves::GunnTuple
protocols::frag_picker::scores::GunnTuple
core::scoring::hackaro::HackAroEnergy
core::scoring::hackaro::HackAroEnergyCreator
core::scoring::hackelec::HackElecEnergy
core::scoring::hackelec::HackElecEnergyAroAll
core::scoring::hackelec::HackElecEnergyAroAllCreator
core::scoring::hackelec::HackElecEnergyAroAro
core::scoring::hackelec::HackElecEnergyAroAroCreator
core::scoring::hackelec::HackElecEnergyCreator
core::scoring::Hairpin
core::scoring::Hairpins
protocols::canonical_sampling::HamiltonianExchange
protocols::canonical_sampling::HamiltonianExchangeCreator
core::scoring::constraints::HarmonicFunc
protocols::match::downstream::hash_upstream_hit
protocols::qsar::scoring_grid::HbaGrid
protocols::qsar::scoring_grid::HbaGridCreator
core::scoring::hbonds::hbtrie::HBAtom
core::scoring::hbonds::hbtrie::HBCountPairFunction
core::scoring::hbonds::hbtrie::HBCPData
protocols::qsar::scoring_grid::HbdGrid
protocols::qsar::scoring_grid::HbdGridCreator
core::scoring::hbonds::HBEvalTuple
core::scoring::hbonds::HBond
protocols::ligand_docking::HBondAcceptorFilter
protocols::ligand_docking::HBondAcceptorFilterCreator
core::scoring::hbonds::HBondDatabase
core::scoring::hbonds::HBondDerivs
protocols::ligand_docking::HBondDonorFilter
protocols::ligand_docking::HBondDonorFilterCreator
core::scoring::hbonds::HBondEnergy
core::scoring::hbonds::HBondEnergyCreator
protocols::features::HBondFeatures
protocols::features::HBondFeaturesCreatorCreator for the HBondFeatures class
core::scoring::hbonds::HBondOptions
protocols::features::HBondParameterFeatures
protocols::features::HBondParameterFeaturesCreatorCreator for the HBondParameterFeatures class
core::scoring::hbonds::HBondResidueMinDataA class to hold data for the HBondEnergy class used in score and derivative evaluation
core::scoring::hbonds::HBondResPairMinData
core::scoring::hbonds::HBondSet
protocols::protein_interface_design::HbondsToResidueFilterReturns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class
protocols::protein_interface_design::filters::HbondsToResidueFilterReturns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class
protocols::protein_interface_design::filters::HbondsToResidueFilterCreator
core::scoring::hbonds::HBondTypeManager
protocols::abinitio::hConvergenceCheck
protocols::canonical_sampling::mc_convergence_checks::Heat_ConvergenceCheck
protocols::ligand_docking::HeavyAtomFilter
protocols::filters::HeavyAtomFilter
protocols::ligand_docking::HeavyAtomFilterCreator
protocols::features::helixAssembly::HelicalFragment
protocols::rbsegment_relax::HelicalGaussianMover
protocols::simple_moves::HelicalPeptideLengthMover
core::scoring::Helices
protocols::fldsgn::topology::Helix
protocols::features::helixAssembly::HelixBundleFeatures
protocols::features::helixAssembly::HelixBundleFeaturesCreatorCreator for the HelixBundleFeatures class
protocols::fldsgn::filters::HelixKinkFilter
protocols::fldsgn::filters::HelixKinkFilterCreator
protocols::fldsgn::topology::HelixPairing
protocols::fldsgn::filters::HelixPairingFilter
protocols::fldsgn::filters::HelixPairingFilterCreator
protocols::fldsgn::topology::HelixPairingSet
protocols::nonlocal::HelixRotate
protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
protocols::ligand_docking::HighResDocker
protocols::ligand_docking::HighResDockerCreator
core::pack::interaction_graph::history_queue_structFor storing three peices of associated data describing the recent history structure on a LinearMemNode
protocols::match::Hit
protocols::match::HitHasherThis 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
protocols::match::HitNeighborFinder
core::scoring::packing::HolesEnergy
core::scoring::packing::HolesEnergyCreator
core::scoring::packing::HolesEnergyRes
protocols::simple_filters::HolesFilter
protocols::simple_filters::HolesFilterCreator
core::scoring::packing::HolesParams
core::scoring::packing::HolesParamsRes
core::scoring::packing::HolesResultResult class holding the three scores and the per-atom scores
protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator
protocols::protein_interface_design::movers::HotspotHasherMover
protocols::protein_interface_design::movers::HotspotHasherMoverCreator
protocols::hotspot_hashing::HotspotStub
protocols::hotspot_hashing::HotspotStubSet
core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode)
core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable
protocols::toolbox::pose_metric_calculators::HPatchCalculator
core::pack::interaction_graph::HPatchEdge< V, E, G >Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast
core::pack::interaction_graph::HPatchEnergyDefines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A
core::pack::interaction_graph::HPatchEnergyCreator
core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >Defines the interaction graph that will keep track of changes to the hpatch score
core::pack::interaction_graph::HPatchNode< V, E, G >Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph
protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
protocols::fldsgn::potentials::sspot::HSPairPotentialSecondary structure scoring cut from classic rosetta structure.h/structure.cc
protocols::fldsgn::topology::HSSTriplet
protocols::fldsgn::filters::HSSTripletFilter
protocols::fldsgn::filters::HSSTripletFilterCreator
protocols::fldsgn::topology::HSSTripletSet
core::scoring::packstat::HTL_EventX
protocols::comparative_modeling::hybridize::HybridizeFoldtreeDynamic
protocols::comparative_modeling::hybridize::HybridizeProtocol
protocols::comparative_modeling::hybridize::HybridizeProtocolCreator
core::scoring::methods::HybridVDW_Energy
core::scoring::methods::HybridVDW_EnergyCreator
protocols::frag_picker::scores::HydrophobicityProfileSimilarityScores a fragment by its hydrophobicity similarity
protocols::frag_picker::scores::HydrophobicitySimilarityScores a fragment by its hydrophobicity similarity
core::chemical::ICoorAtomIDAtom 's ID in internal coordinates in a ResidueType
core::chemical::orbitals::ICoorOrbitalData
protocols::idealize::IdealizeMoverMover 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
protocols::idealize::IdealizeMoverCreator
core::fragment::picking_old::vall::eval::IdentityEvalScores a fragment based on sum of secondary structure identity and sequence identity
core::conformation::signals::IdentityEventSignals a change in residue identity in a Conformation
core::scoring::constraints::IdentityFunc
protocols::moves::IfMover
protocols::moves::IfMoverCreator
core::pack::task::IGEdgeReweightContainerClass that interfaces to containers holding IGedge weights between individual residues of the task
core::pack::task::IGEdgeReweighterHelper class for IGEdgeReweightContainer
protocols::toolbox::IGLigandDesignEdgeUpweighter
protocols::comparative_modeling::IgnoreSubsetConstraintSet
Implements
Implements
protocols::scoring::ImplicitFastClashCheck
core::pack::task::operation::IncludeCurrent
core::pack::task::operation::IncludeCurrentCreator
core::fragment::IndependentBBTorsionSRFDA version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD)
protocols::loops::loop_mover::IndependentLoopMover
core::pack::task::operation::InitializeExtraRotsFromCommandline
core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator
core::pack::task::operation::InitializeFromCommandline
core::pack::task::operation::InitializeFromCommandlineCreator
protocols::jd2::InnerJob
protocols::jd2::InnerMultiThreadingJob
protocols::swa::InputStreamWithResidueInfo
protocols::comparative_modeling::hybridize::InsertChunkMover
protocols::pack_daemon::InSetExpressionReturns "true" if the expression ex evaluates to one of a set of indicated values
core::pack::interaction_graph::InteractionGraphBase
core::pack::interaction_graph::InteractionGraphFactory
protocols::toolbox::InteratomicVarianceMatrix
protocols::frag_picker::scores::InterbondAngleScoreScores a fragment with a set of Dihedral constraints
protocols::scoring::methods::InterchainEnvEnergy
protocols::scoring::methods::InterchainEnvEnergyCreator
protocols::scoring::methods::InterchainPairEnergy
protocols::scoring::methods::InterchainPairEnergyCreator
protocols::scoring::InterchainPotential
protocols::ligand_docking::ligand_options::InterfaceFor each residue is it in the interface, a mobile region or a non-mobile region?
protocols::scoring::Interface
protocols::analysis::InterfaceAnalyzerMover
protocols::analysis::InterfaceAnalyzerMoverCreator
protocols::ligand_docking::InterfaceBuilder
protocols::ligand_docking::InterfaceBuilderLoaderA class for loading InterfaceBuilders into the XML parser's DataMap
protocols::ligand_docking::InterfaceBuilderLoaderCreator
core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
protocols::protein_interface_design::filters::InterfaceHolesFilter
protocols::protein_interface_design::filters::InterfaceHolesFilterCreator
protocols::ligand_docking::ligand_options::InterfaceInfoInfo for each residue- is it part of the interface and if so, what ligands is it near
protocols::scoring::InterfaceInfoKeep track of the interface information
core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
protocols::protein_interface_design::movers::InterfaceRecapitulationMoverPure virtual base class for movers which redesign and repack the interface
protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator
core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
protocols::protein_interface_design::InterfaceSasaFilter
protocols::simple_filters::InterfaceSasaFilter
protocols::simple_filters::InterfaceSasaFilterCreator
protocols::ligand_docking::InterfaceScoreCalculator
protocols::ligand_docking::InterfaceScoreCalculatorCreator
protocols::docking::InterfaceSidechainMinMover
protocols::toolbox::task_operations::InterfaceTaskOperation
protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator
protocols::flxbb::InterlockAroma
protocols::flxbb::InterlockAromaCreator
protocols::fldsgn::filters::InterlockingAromaFilter
protocols::fldsgn::filters::InterlockingAromaFilterCreator
protocols::swa::rna::InternalWorkingResidueParameter
protocols::jumping::IntervalTwo numbers, i.e., jump start end residue, or cut-regions..
protocols::forge::build::IntervalSimple struct defining a closed interval of residues [left, right] where left <= right
protocols::forge::constraints::InverseRotamersRCGRemodelConstraintGenerator 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
protocols::moves::InvGeometricFuncRamps 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 );
core::scoring::etable::count_pair::Invoker
core::pack::interaction_graph::InvRotamerDotsUsed to determine whether the overlap between two atoms is buried or exposed
protocols::motifs::IRCollection
core::scoring::IsProteinCAPredicate
protocols::moves::IteratedConvergenceMoverA 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
protocols::moves::IteratedConvergenceMoverCreator
protocols::abinitio::IterativeAbrelax
protocols::abinitio::IterativeBase
protocols::abinitio::IterativeCentroid
protocols::abinitio::IterativeFullatom
protocols::optimize_weights::IterativeOptEDriver
protocols::pack_daemon::IterativeVectorExpression
iterator
core::io::raw_data::RawFileData::iteratorIterator class for RawFileData container
core::io::silent::SilentFileData::iteratorIterator class for SilentFileData container
protocols::frag_picker::scores::JCouplingScores a fragment by the JCouplings
protocols::frag_picker::JCouplingIO
JDtestmoverLocal mover for testing purposes
core::optimization::JJH_Minimizer
protocols::jd2::Job
protocols::features::JobDataFeatures
protocols::features::JobDataFeaturesCreatorCreator for the JobDataFeatures class
protocols::jd2::JobDistributor
protocols::jd2::JobDistributorFactory
protocols::jd2::JobInputter
protocols::jd2::JobInputterCreatorAbstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class
protocols::jd2::JobInputterFactory
protocols::jd2::JobInputterRegistrator< T >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
protocols::jd2::JobOutputter
protocols::jd2::JobOutputterCreatorAbstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class
protocols::jd2::JobOutputterFactory
protocols::jd2::JobOutputterRegistrator< T >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
protocols::toolbox::task_operations::JointSequenceOperation
protocols::toolbox::task_operations::JointSequenceOperationCreator
protocols::simple_filters::JScoreEvaluator
protocols::simple_filters::JScoreEvaluatorCreatorCreator for the JScoreEvaluatorCreator class
core::kinematics::JumpObject which makes rigid-body transformation with translational and rotational perturbation
protocols::swa::rna::Jump_point
core::kinematics::tree::JumpAtomAtom who are connected to its parent via rigid-body transformation "Jump"
protocols::topology_broker::JumpClaim
protocols::topology_broker::JumpClaimerClaimer 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
protocols::jumping::JumpSetup::JumpDef
protocols::jumping::ResiduePairJumpSetup::JumpDef
protocols::simple_filters::JumpEvaluator
core::id::JumpID
protocols::abinitio::JumpingFoldConstraints
protocols::abinitio::JumpingFoldConstraintsWrapper
core::fragment::JumpingFrameJumpingFrame, so far there is nothing special about JumpingFrames. but I think we might want to have additionally information like the start and end residues that belong to a certain jump_nr.! okay: right now I require that the creator of a JumpingFrame sets start to the start-residue of the jump
protocols::simple_filters::JumpNrEvaluator
protocols::simple_filters::JumpNrEvaluatorCreatorCreator for the JumpNrEvaluatorCreator class
protocols::moves::JumpOutMover
protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverClass for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator
protocols::jumping::JumpSample
protocols::jumping::JumpSelector
protocols::jumping::JumpSetup
protocols::jumping::JumpsFromAllPairings
protocols::jumping::JumpSelector::JumpWeightDef
core::scoring::constraints::KarplusFuncFunction that evaluates a J-coupling from dihedral angles in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints
protocols::toolbox::KClusterBasic class for performing a K-style Clustering algorithm
protocols::toolbox::KClusterDataDatabase of a K-style Clustering algorithm
protocols::toolbox::KClusterElement
protocols::abinitio::KinematicAbinitio
protocols::abinitio::KinematicControl
protocols::loops::loop_closure::kinematic_closure::KinematicMoverA mover class for performing kinematic loop closure on a peptide segment
protocols::loops::loop_closure::kinematic_closure::KinematicPerturberPure 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
protocols::abinitio::KinematicTaskControl
protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
protocols::kinmatch::KinFunGroupTK
protocols::toolbox::KMedoidTypical K-Medoids Clustering Algorithm
core::scoring::constraints::KofNConstraint
core::scoring::constraints::KofNConstraintCreatorMover creator for the KofNConstraint constraint
core::scoring::electron_density::KromerMann
protocols::kinmatch::KRSQuery
core::sequence::L1ScoringScheme
protocols::frag_picker::LAMBEGO_IO
protocols::frag_picker::scores::LAMBEGO_SimilarityScores a fragment by torsion bin similarity
protocols::topology_broker::weights::LargeFragWeight
protocols::flxbb::LayerDesignOperation
protocols::flxbb::LayerDesignOperationCreator
core::pack::interaction_graph::LazyEdge
core::pack::interaction_graph::LazyInteractionGraph
core::pack::interaction_graph::LazyNode
protocols::jd2::LazySilentFileJobInputter
protocols::jd2::LazySilentFileJobInputterCreator
core::import_pose::pose_stream::LazySilentFilePoseInputStream
protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
core::optimization::lbfgs_iteration_data
protocols::loophash::LeapIndexThe 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
core::scoring::packstat::LeeRichards
protocols::loophash::LegacyLeapIndex
core::conformation::signals::LengthEventSignals a change in length of residues in a Conformation
core::pose::datacache::LengthEventCollectorCacheable observer that keeps track of what length events occured
core::fragment::picking_old::vall::gen::LengthGenDefault constant length fragment Vall ExtentGenerator
core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >Librarian template for sorting through and extracting desired fragments
core::fragment::picking_old::concepts::Library< Books >Class demonstrating the Library concept
protocols::ligand_docking::Ligand_info
protocols::ligand_docking::LigandArea
protocols::ligand_docking::LigandAreaLoader
protocols::ligand_docking::LigandAreaLoaderCreator
protocols::ligand_docking::LigandBaseProtocolShared functionality for protocols that dock ligands
protocols::toolbox::match_enzdes_util::LigandConformer
protocols::match::downstream::LigandConformerBuilder
protocols::ligand_docking::LigandDesign
protocols::ligand_docking::LigandDesignCreator
protocols::ligand_docking::LigandDockMain
protocols::ligand_docking::LigandDockProtocol
protocols::motifs::LigandMotifSearch
protocols::enzdes::LigBurialFilter
protocols::enzdes::LigBurialFilterCreator
protocols::enzdes::LigDSasaFilter
protocols::enzdes::LigDSasaFilterCreator
protocols::enzdes::LigInterfaceEnergyFilter
protocols::enzdes::LigInterfaceEnergyFilterCreator
protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
protocols::toolbox::task_operations::LimitAromaChi2Operation
protocols::toolbox::task_operations::LimitAromaChi2OperationCreator
protocols::match::output::LimitHitsPerRotamerFilter
core::util::LineStruct
core::scoring::methods::LinearChainbreakEnergyLinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align
core::scoring::methods::LinearChainbreakEnergyCreator
protocols::moves::LinearFunc
core::pack::interaction_graph::LinearMemEdge
core::pack::interaction_graph::LinearMemNode
core::pack::interaction_graph::LinearMemoryInteractionGraph
core::scoring::constraints::LinearPenaltyFunction
core::optimization::LineMinimizationAlgorithm
protocols::forge::remodel::LineObject
core::scoring::methods::LK_BallEnergy
core::scoring::methods::LK_BallEnergyCreator
core::scoring::methods::LK_CosThetaEnergy
core::scoring::methods::LK_CosThetaEnergyCreator
core::scoring::methods::LK_hack
core::scoring::methods::LK_hackCreator
core::scoring::methods::LK_SigmoidalFunc
core::scoring::methods::LKB_ResidueInfo
core::scoring::methods::LKB_ResiduesInfo
protocols::pack_daemon::LnExpression
protocols::simple_moves::LoadUnboundRotMover
protocols::simple_moves::LoadUnboundRotMoverCreator
core::scoring::constraints::LocalCoordinateConstraint
core::scoring::constraints::LocalCoordinateConstraintCreatorMover creator for the LocalCoordinateConstraint constraint
protocols::loophash::LocalInserter
protocols::loophash::LocalInserter_SimpleMin
protocols::simple_moves::LoggedFragmentMover
core::scoring::methods::LongRangeTwoBodyEnergy
protocols::loops::LoopSingle loop definition
protocols::fldsgn::topology::Loop
protocols::loops::Loop_ltUsed to sort Loops by start-res
protocols::analysis::LoopAnalyzerMover
protocols::features::LoopAnchorFeatures
protocols::features::LoopAnchorFeaturesCreatorCreator for the LoopAnchorFeatures class
protocols::loops::loop_closure::ccd::LoopClosure
protocols::protein_interface_design::movers::LoopFinder
protocols::protein_interface_design::movers::LoopFinderCreator
protocols::topology_broker::LoopFragmentClaimer
protocols::loophash::LoopHashLibrary
protocols::loophash::LoopHashMapLoop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates
protocols::loophash::LoopHashMoverWrapper
protocols::loophash::LoopHashMoverWrapperCreator
protocols::loophash::LoopHashSampler
protocols::abinitio::LoopJumpFoldCst
protocols::protein_interface_design::movers::LoopLengthChangeDesigns alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines
protocols::protein_interface_design::movers::LoopLengthChangeCreator
protocols::loops::loop_mover::LoopMoverThe loop-rebuild protocol
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD
protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCDCreatorCreator for the LoopMover_Perturb_CCDCreator class
protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreatorCreator for the LoopMover_Perturb_KICCreator class
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDLoopMover utilizing fragment insertion, ccd loop closure, and minimization
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreatorCreator for the LoopMover_Perturb_QuickCCD_MovesCreator class
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreatorCreator for the LoopMover_Perturb_QuickCCDCreator class
protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub
protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreatorCreator for the LoopMover_Refine_BackrubCreator class
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreatorCreator for the LoopMover_Refine_CCDCreator class
protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreatorCreator for the LoopMover_Perturb_KICCreator class
protocols::loop_build::LoopMover_SlidingWindowLoopMover utilizing fragment insertion, ccd loop closure, and minimization
protocols::loop_build::LoopMover_SlidingWindowCreatorCreator for the LoopMover_SlidingWindowCreator class
protocols::loops::LoopMoverFactoryCreate LoopMover Reporters
protocols::protein_interface_design::movers::LoopMoverFromCommandLine
protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator
protocols::protein_interface_design::movers::LoopOverEssentially the same as the WhileMover but allows parsing and cloning. Will be removed at a future point. This should now be incorporated into WhileMover
protocols::protein_interface_design::movers::LoopOverCreator
protocols::LoopRebuildThe loop-rebuild protocol
protocols::LoopRefineClass LoopRefine for fullatom loop refinement
protocols::comparative_modeling::LoopRelaxMover
protocols::comparative_modeling::LoopRelaxMoverCreator
protocols::comparative_modeling::LoopRelaxThreadingMover
protocols::protein_interface_design::movers::LoopRemodel
protocols::protein_interface_design::movers::LoopRemodelCreator
protocols::antibody::LoopRlxMoverCloses only one CDR onto a framework
protocols::simple_filters::LoopRmsdEvaluator
protocols::loops::Loops
protocols::loops::LoopsFileIO
core::scoring::packstat::LR_AtomData
core::scoring::packstat::LR_MP_AtomData
core::scoring::LREnergyContainer
protocols::swa::MainChainTorsionSet
protocols::swa::protein::MainChainTorsionSet
protocols::frag_picker::scores::MakeABEGO_SS_ScoreMaker class that produces a new ABEGO_SS_Score object
protocols::frag_picker::scores::MakeAmbigCSScoreMaker class that produces a new AmbigCSScore object
protocols::frag_picker::scores::MakeAtomPairConstraintsScoreMaker class that produces a new AtomPairConstraintsScore object
protocols::frag_picker::scores::MakeBFactorMaker class that produces a new BFactor object
protocols::frag_picker::scores::MakeConstScoreMaker class that produces a new ConstScore object
protocols::frag_picker::scores::MakeCSScoreMaker class that produces a new CSScore object
protocols::frag_picker::scores::MakeDihedralConstraintsScoreMaker class that produces a new DihedralConstraintsScore object
protocols::frag_picker::scores::MakeDisulfideDistanceMatker class that produces a new DisulfideDistance object
protocols::frag_picker::scores::MakeDisulfideIdentityMaker class that produces a new DisulfideIdentity object
protocols::frag_picker::scores::MakeFragmentAllAtomCrmsdMaker class that produces a new FragmentAllAtomCrmsd object
protocols::frag_picker::scores::MakeFragmentCrmsdMaker class that produces a new FragmentCrmsd object
protocols::frag_picker::scores::MakeFragmentCrmsdResDepthMaker class that produces a new FragmentCrmsdResDepth object
protocols::frag_picker::scores::MakeFragmentDMEMaker class that produces a new FragmentDME object
protocols::frag_picker::scores::MakeFragmentScoringMethodFragment candidate
protocols::frag_picker::scores::MakeGunnCostScoreMaker class that produces a new GunnCostScore object
protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarityMaker class that produces a new HydrophobicityProfileSimilarity object
protocols::frag_picker::scores::MakeHydrophobicitySimilarityMaker class that produces a new HydrophobicitySimilarity object
protocols::frag_picker::scores::MakeInterbondAngleScoreMaker class that produces a new InterbondAngleScore object
protocols::frag_picker::scores::MakeJCouplingMatker class that produces a new JCoupling object
protocols::frag_picker::scores::MakeLAMBEGO_SimilarityMaker class that produces a new TorsionBin object
protocols::frag_picker::scores::MakeMidPhiOutMatker class that produces a new MidPhiOut object
protocols::frag_picker::scores::MakeMidPsiOutMatker class that produces a new MidPsiOut object
protocols::frag_picker::scores::MakePartialSecondarySimilarityMaker class that produces a new PartialSecondarySimilarity object
protocols::frag_picker::scores::MakePCS_FragDistanceMatker class that produces a new PCS_FragDistance object
protocols::frag_picker::scores::MakePhiMaker class that produces a new Phi object
protocols::frag_picker::scores::MakePhiPsiRmsdMatker class that produces a new PhiPsiRmsd object
protocols::frag_picker::scores::MakePhiPsiSquareWellMatker class that produces a new PhiPsiSquareWell object
protocols::simple_moves::MakePolyXMover
protocols::simple_moves::MakePolyXMoverCreator
protocols::frag_picker::scores::MakeProfileScore
protocols::frag_picker::scores::MakeProfileScoreBlosum62
protocols::frag_picker::scores::MakeProfileScoreDistWeight
protocols::frag_picker::scores::MakeProfileScoreL1
protocols::frag_picker::scores::MakeProfileScoreStructL1
protocols::frag_picker::scores::MakeProfileScoreSubMatrix
protocols::frag_picker::scores::MakeProlinePhiScoreMaker class that produces a new ProlinePhiScore object
protocols::frag_picker::scores::MakePsiMaker class that produces a new Psi object
protocols::frag_picker::scores::MakeRamaScoreMaker class that produces a new RamaScore object
protocols::frag_picker::scores::MakeRDCScoreMaker class that produces a new RDCScore object
protocols::frag_picker::scores::MakeScoreEValuator
protocols::frag_picker::scores::MakeSecondaryIdentityMaker class that produces a new SecondaryIdentity object
protocols::frag_picker::scores::MakeSecondarySimilarityMaker class that produces a new SecondarySimilarity object
protocols::frag_picker::scores::MakeSequenceIdentityMaker class that produces a new SequenceIdentity object
protocols::frag_picker::scores::MakeSolventAccessibilityMaker class that produces a new SolventAccessibility object
protocols::frag_picker::scores::MakeTalosSSSimilarityMaker class that produces a new TalosSSSimilarity object
protocols::frag_picker::scores::MakeTorsionBinSimilarityMaker class that produces a new TorsionBin object
core::fragment::MapCacheUnit< T >
protocols::protein_interface_design::movers::MapHotspot
protocols::protein_interface_design::movers::MapHotspotCreator
protocols::match::match_dspos1Describe a match as n_geometric_constraint upstream residue conformations and one positioning of the downstream partner ( "dspos1" = 1 downstrem position)
protocols::match::match_lite_equals
protocols::match::match_lite_hasher
protocols::match::output::MatchCollisionFilter
protocols::match::output::MatchConsolidator
protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoListSimple 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
protocols::match::MatchCounterClass for counting the number of matches given a particular discretization level
protocols::match::Matcher
protocols::match::MatcherMover
protocols::match::MatcherMoverCreator
protocols::match::MatcherOutputStats
protocols::match::MatcherTask
protocols::match::output::MatchEvaluator
protocols::match::output::MatchFilter
protocols::match::output::MatchGrouper
protocols::match::output::MatchOutputter
protocols::match::MatchOutputTracker
protocols::match::MatchPositionModifierBase class for objects that modify the match positions based on some criterion
protocols::match::output::MatchProcessor
core::sequence::MatrixScoringScheme
protocols::constraints_additional::MaxSeqSepConstraintSet
core::sequence::MCAligner
protocols::moves::MCShowMover
protocols::cartesian::MD_Angle
protocols::cartesian::MD_Bond
protocols::cartesian::MD_HarmonicDihedral
protocols::medal::MedalExchangeMover
protocols::medal::MedalMover
core::scoring::etable::MembEtableJk Class definition for Etable
core::scoring::Membrane_FAEmbed
core::scoring::Membrane_FAPotential
protocols::abinitio::MembraneAbinitio
core::scoring::methods::MembraneCbetaEnergy
core::scoring::methods::MembraneCbetaEnergyCreator
core::scoring::methods::MembraneCenPairEnergy
core::scoring::methods::MembraneCenPairEnergyCreator
protocols::rigid::MembraneCenterPerturbationMoverPerturb the pose along membrane normal
core::scoring::MembraneEmbed
core::scoring::methods::MembraneEnvEnergy
core::scoring::methods::MembraneEnvEnergyCreator
core::scoring::methods::MembraneEnvPenalties
core::scoring::methods::MembraneEnvPenaltiesCreator
core::scoring::methods::MembraneEnvSmoothEnergy
core::scoring::methods::MembraneEnvSmoothEnergyCreator
protocols::jumping::MembraneJump
core::scoring::methods::MembraneLipo
core::scoring::methods::MembraneLipoCreator
protocols::rigid::MembraneNormalPerturbationMoverRotation pose around membrane center, perturb the membrane normal vector relative to the pose
core::scoring::MembranePotential
protocols::simple_moves::MembraneTopologyA mover to change one torsion angle
core::scoring::MembraneTopology
protocols::topology_broker::MembraneTopologyClaimer
protocols::simple_moves::MembraneTopologyCreator
protocols::topology_broker::MetalloClaimer
core::scoring::methods::MetalloPlacementEnergy
protocols::evaluation::MetaPoseEvaluator
core::import_pose::pose_stream::MetaPoseInputStream
protocols::multistate_design::MetricCalculatorFitnessFunction
protocols::canonical_sampling::MetricRecorder
protocols::canonical_sampling::MetricRecorderCreator
protocols::toolbox::pose_metric_calculators::MetricValueGetter
protocols::canonical_sampling::MetropolisHastingsMover
protocols::canonical_sampling::MetropolisHastingsMoverCreator
protocols::frag_picker::scores::MidPhiOutScores a fragment by the root mean square deviation of Phi and Psi angles
protocols::frag_picker::scores::MidPsiOutScores a fragment by the root mean square deviation of Psi and Psi angles
core::optimization::symmetry::MinDebug
protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
protocols::flexpack::interaction_graph::MinimalistFlexbbNode
protocols::simple_moves::MinimalRotamer
core::scoring::MinimizationEdge
core::scoring::MinimizationGraphClass to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity
core::scoring::MinimizationNode
protocols::ligand_docking::MinimizeBackbone
protocols::ligand_docking::MinimizeBackboneCreator
protocols::ligand_docking::MinimizeLigand
core::optimization::MinimizerSimple low-level minimizer class
core::optimization::MinimizerMap
core::kinematics::MinimizerMapBase
core::optimization::MinimizerOptions
protocols::enzdes::MinimizeStoredRBConfsRotamer 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
core::pose::MiniPose
protocols::relax::MiniRelax
protocols::simple_moves::MinMoverA 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
protocols::simple_moves::MinMoverCreator
core::scoring::constraints::MinMultiHarmonicFunc
protocols::simple_moves::MinPackMoverMover 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
protocols::simple_moves::MinPackMoverCreator
protocols::simple_filters::MinValueEvaluator< T >
protocols::frag_picker::quota::missing_fraction_sorter_biggest_first
protocols::simple_moves::MissingDensityToJumpMover
core::scoring::constraints::MixtureFuncDerived class of class Func representing a Mixture of several distinct functions. The function is of the form ln( g(r) / h(r) ), where g(r) is a mixture of a Gaussian and Exponential distributions, and h(r) is a Gaussian distribution. See methods and implementation for more information
core::chemical::MMAtomTypeBasic MM atom type
core::chemical::MMAtomTypeSetA set of MMAtomTypes
core::scoring::methods::MMBondAngleEnergy
core::scoring::methods::MMBondAngleEnergyCreator
core::scoring::mm::MMBondAngleLibrary
core::scoring::mm::MMBondAngleResidueTypeParam
core::scoring::mm::MMBondAngleResidueTypeParamSet
core::scoring::mm::MMBondAngleScoreCalculates scores of mm bond angle paramater sets given an angle
core::scoring::methods::MMBondLengthEnergy
core::scoring::methods::MMBondLengthEnergyCreator
core::scoring::mm::MMBondLengthLibrary
core::scoring::mm::MMBondLengthScore
core::scoring::mm::mmtrie::MMEnergyTableAtom
core::scoring::methods::MMLJEnergyInter
core::scoring::methods::MMLJEnergyInterCreator
core::scoring::methods::MMLJEnergyIntra
core::scoring::methods::MMLJEnergyIntraCreator
core::scoring::mm::MMLJEnergyTableBlah
core::scoring::mm::MMLJLibraryA class to maintain a set of MM LJ paramaters
core::scoring::mm::MMLJScoreCalculates scores of mm lj paramater sets given two mm atom types, the path distance of the 2 atoms and actual distance between the two atoms
core::scoring::methods::MMTorsionEnergy
core::scoring::methods::MMTorsionEnergyCreator
core::scoring::mm::MMTorsionLibraryA class to maintain a set of MM torsion paramaters
core::scoring::mm::MMTorsionScoreCalculates scores of mm torsion paramater sets given an angle
protocols::enzdes::ModifyStoredRBConfsVirtual base class that has some common functionality
core::chemical::sdf::MolData
protocols::cartesian::MolecularDynamics
core::chemical::sdf::MolFileParser
core::chemical::sdf::MolWriter
protocols::moves::MonteCarloThis 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
protocols::moves::MonteCarloExceptionConverge
protocols::jd2::parser::MonteCarloLoaderThe MonteCarloLoader will create named MonteCarlo objects and load them into the DataMap
protocols::jd2::parser::MonteCarloLoaderCreator
protocols::moves::MonteCarloRecover
protocols::moves::MonteCarloRecoverCreator
protocols::moves::MonteCarloTest
protocols::moves::MonteCarloTestCreator
protocols::moves::MonteCarloUtilMCResetMover applies a monte carlo reset
protocols::motifs::Motif
protocols::motifs::MotifDnaPacker
protocols::motifs::MotifDnaPackerCreator
protocols::motifs::MotifHit
protocols::motifs::MotifLibrary
protocols::motifs::MotifSearch
protocols::filters::MoveBeforeFilterApply a sub-mover prior to calculating a filter value
protocols::filters::MoveBeforeFilterCreator
core::kinematics::MoveMapA class specifying DOFs to be flexible or fixed
protocols::ligand_docking::MoveMapBuilder
protocols::ligand_docking::MoveMapBuilderLoaderA class for loading MoveMapBuilders into the XML parser's DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder
protocols::ligand_docking::MoveMapBuilderLoaderCreator
protocols::rigid::MovePoseToMembraneCenterMoverMove pose into a membrane
protocols::moves::Mover: A mover is an object that can apply a conformational change to a pose
protocols::loophash::Mover_LoopHashRefine
protocols::moves::MoverContainer
protocols::moves::MoverCreatorAbstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class
protocols::moves::MoverFactory
protocols::wum::MoverList
protocols::moves::MoverRegistrator< T >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
protocols::moves::MoverStatistics
protocols::loophash::MPI_LoopHashRefine
protocols::loophash::MPI_LoopHashRefine_Emperor
protocols::loophash::MPI_LoopHashRefine_Master
protocols::wum::MPI_Relax
protocols::wum::MPI_WorkUnitManager
protocols::wum::MPI_WorkUnitManager_Slave
protocols::jd2::archive::MPIArchiveJobDistributorJobDistributor for the iterative ArchiveManager/Archive Framework
protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
protocols::jd2::MpiFileBuffer
protocols::jd2::MPIFileBufJobDistributor
protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
protocols::jd2::MPIMultiCommJobDistributor
protocols::pack_daemon::MPIMultistateFitnessFunction
protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
protocols::jd2::MPIWorkPartitionJobDistributor
protocols::jd2::MPIWorkPoolJobDistributor
core::scoring::constraints::MultiConstraint
core::scoring::constraints::MultiConstraintCreatorMover creator for the MultiConstraint constraint
core::pack::annealer::MultiCoolAnnealer
core::optimization::MultifuncMultifunction interface class
protocols::rna::MultipleDomainMoverThe RNA de novo structure modeling protocol
core::scoring::packstat::MultiProbePerSphereAccumulator
core::scoring::packstat::MultiProbePoseAccumulator
protocols::multistate_design::MultiStateAggregateFunction
protocols::pack_daemon::MultistateAggregateFunction
protocols::multistate_design::MultiStateEntity
protocols::multistate_design::MultiStateFitnessFunction
protocols::pack_daemon::MultistateFitnessFunction
protocols::multistate_design::MultiStatePacker
protocols::canonical_sampling::MultiTemperatureTrialCounter
protocols::jd2::MultiThreadingJob
protocols::comparative_modeling::MultiThreadingMover
protocols::pmut_scan::Mutant
protocols::simple_moves::MutateResidueA mover to mutate a single residue
protocols::simple_moves::MutateResidueCreator
protocols::pmut_scan::MutationData
protocols::fldsgn::MyAtom
core::id::NamedAtomIDAtom identifier class
core::scoring::constraints::NamedAtomPairConstraint
protocols::constraints_additional::NamedAtomPairConstraintCreatorThis class can be used to replace the standard AtomPairConstraintsCreator; see BrokerMain.cc for an example
core::id::NamedStubID
core::pack::task::NATAANATAA allows repacking but no sequence changes (all rotamers are of the original residue)
protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyNatbiasSecondaryStructureEnergy
protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator
protocols::fldsgn::potentials::sspot::NatbiasSheetPotential
protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotentialSecondary structure scoring cut from classic rosetta structure.h/structure.cc
protocols::simple_filters::NativeEvaluatorCreatorCreator for the NativeEvaluatorCreator class
core::pack::task::NATRONATRO disables packing and designing at a position, the residue will be totally unchanged
core::scoring::symmetry::NBListCache
core::pack::task::NCNC handles explicit allowance of noncanonical residue types
core::chemical::NCAARotLibPathSet the path to a rotamer library for an NCAA that is not in dunbrack
core::scoring::disulfides::NCaCaC_Dihedral_Func
protocols::fldsgn::NcontactsCalculator
protocols::fldsgn::filters::NcontactsFilter
protocols::fldsgn::filters::NcontactsFilterCreator
core::graph::NegSpaceElement< T >NegSpaceElement represents a single element in the singly-linked list of negative space in an array pool
protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
core::scoring::NeighborList
protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
protocols::protein_interface_design::NeighborTypeFilter
protocols::simple_filters::NeighborTypeFilter
protocols::simple_filters::NeighborTypeFilterCreator
protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
core::pack::task::NO_ADDUCTSNO_ADDUCTS will disable adducts, assuming they exist This command exists because if adducts exist, then they are enabled by default for all residues
core::graph::Node
core::pack::interaction_graph::NodeBase
protocols::noesy_assign::NoesyModule
core::fragment::NonContinuousFrameJumpingFrame is a discontinuous frame i.e, the SRFDs stored in the FragData objects can be applied to residues anywhere a 5 7 9 Frame of a FragData containing three BBTorsionSRFDs would change torsions of 5 7 9 a 5 32 2 Frame of a FragData containing two BBTorsionSRFD and on JumpSRFD would change torsions of 5 and 32 and the RT of jump_nr 2 note that in the latter case the 2 is not coding for a residue number!
noncopyable
protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
protocols::frag_picker::nonlocal::NonlocalFrags
protocols::frag_picker::nonlocal::NonlocalPairNonlocal fragment pair
protocols::pockets::NonPlaidFingerprint
core::scoring::constraints::NonResidueTypeConstraintThis class favors a particular residue identity at a particular position by reducing its res_type energy
protocols::jd2::NoOutputJobOutputter
protocols::jd2::NoOutputJobOutputterCreator
core::pack::task::operation::NoRepackDisulfidesPrevent disulfides from being repacked; assume disulfides info in Pose is up-to-date
core::pack::task::operation::NoRepackDisulfidesCreator
core::pack::task::NOTAANOTAA disallows residues specified in a following string, and allows packing
protocols::pack_daemon::NPDPropCalculator
protocols::pack_daemon::NPDPropCalculatorCreator
protocols::forge::constraints::NtoC_RCG
protocols::protein_interface_design::movers::NullDesignMoverDoes absolutely nothing. useful as if you want to havea final filter without making a move. this can now be assimilated with NullMover
protocols::moves::NullMover
protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
core::optimization::NumDerivCheckData
core::optimization::NumericalDerivCheckResult
protocols::match::NumNeighborsMPMRemoves 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
core::scoring::nv::NVlookup
core::scoring::nv::NVscore
core::scoring::nv::NVscoreCreator
core::sequence::NWAligner
core::pose::datacache::ObserverCacheA DataCache storing Pose/Conformation observers derived from core::pose::datacache::CacheableObserver
core::scoring::constraints::Obsolet_NamedAtomPairConstraint
core::scoring::geometric_solvation::OccludedHbondSolEnergy
core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator
core::scoring::geometric_solvation::OccludedHbondSolEnergyCreator
protocols::match::OccupiedSpaceHashThis class keeps track of the active voxels "up until now" with 64 hashes
core::scoring::packstat::Octree2D
core::scoring::constraints::OffsetPeriodicBoundFuncVariant of the bound func that is periodic
core::scoring::OmegaTether
core::scoring::methods::OmegaTetherEnergy
core::scoring::methods::OmegaTetherEnergyCreator
core::scoring::methods::OneBodyEnergy
core::scoring::electron_density::OneGaussianScattering
core::scoring::OneToAllEnergyContainer
core::scoring::OneToAllNeighborConstIterator
core::scoring::OneToAllNeighborIterator
core::pack::interaction_graph::OnTheFlyEdge
core::pack::interaction_graph::OnTheFlyInteractionGraph
core::pack::interaction_graph::OnTheFlyNode
protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >Const_iterator class for SilentFileData container
core::pack::task::operation::OperateOnCertainResidues
core::pack::task::operation::OperateOnCertainResiduesCreator
core::pack::task::operation::OptCysHGRun optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides()
core::pack::task::operation::OptCysHGCreator
protocols::optimize_weights::OptEData
protocols::optimize_weights::OptEMultifuncOptE mode multifunction class
protocols::optimize_weights::OptEPositionData
protocols::optimize_weights::OptEPositionDataFactory
protocols::optimize_weights::OptEVariableExpression
core::pack::task::operation::OptHRun optH; disallowed positions may be set to prevent optimization for those residues
core::pack::task::operation::OptHCreator
core::chemical::orbitals::OrbInfo
core::scoring::orbitals::OrbitalsAssigned
protocols::features::OrbitalsFeatures
protocols::features::OrbitalsFeaturesCreatorCreator for the OrbitalsFeatures class
core::scoring::orbitals::OrbitalsLookup
core::scoring::orbitals::OrbitalsScore
core::scoring::orbitals::OrbitalsScoreCreator
core::scoring::orbitals::OrbitalsStatistics
core::chemical::orbitals::OrbitalType
core::chemical::orbitals::OrbitalTypeMapper
core::chemical::orbitals::OrbitalTypeSet
core::conformation::orbitals::OrbitalXYZCoords
core::scoring::packstat::OrderCavBallOnR
core::scoring::packstat::OrderCavBallOnRmAnb
core::scoring::packstat::OrderCavBallOnRmE
core::scoring::packstat::OrderCavBallOnX
core::scoring::packstat::OrderCBC
core::fragment::OrderedFragSet
core::fragment::OrderedFragSetIterator_
protocols::simple_moves::symmetry::OrderedSequentialSymmetrySlider
core::scoring::packstat::OrderSphereOnID
core::scoring::packstat::OrderSphereOnX
protocols::match::upstream::OriginalBackboneBuildPoint
protocols::flexpack::interaction_graph::OTFFlexbbEdge
protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
protocols::flexpack::interaction_graph::OTFFlexbbNode
protocols::flexpack::OtherContextScoreFunction
protocols::swa::rna::output_data_struct
protocols::rotamer_recovery::RRReporterSQLite::OutputLevel
protocols::match::output::OutputWriter
utility::pointer::owning_ptr
core::scoring::P_AA
core::scoring::methods::P_AA_Energy
core::scoring::methods::P_AA_EnergyCreator
core::scoring::methods::P_AA_pp_Energy
core::scoring::methods::P_AA_pp_EnergyCreator
protocols::pack_daemon::PackDaemon
core::pack::dunbrack::PackedDunbrackRotamer< S, P >
protocols::simple_filters::PackerNeighborGraphFilter
core::pack::task::PackerTaskTask class that gives instructions to the packer
core::pack::task::PackerTask_PackerTask controls what rotameric (including sequence) changes the packer is allowed to make
core::scoring::packstat::PackingScore
core::scoring::packstat::PackingScoreResData
protocols::multistate_design::PackingState
protocols::simple_moves::PackRotamersMoverA 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
protocols::simple_moves::PackRotamersMoverCreator
protocols::simple_moves::PackRotamersMoverLazyMover that packs the side-chains using a rotamer library in a lazy fashion
protocols::simple_moves::PackRotamersMoverLazyCreator
protocols::toolbox::pose_metric_calculators::PackstatCalculator
core::scoring::methods::PackStatEnergy
core::scoring::methods::PackStatEnergyCreator
protocols::simple_filters::PackStatFilter
protocols::simple_filters::PackStatFilterCreator
protocols::analysis::PackStatMover
core::scoring::methods::PairEnergy
core::scoring::methods::PairEnergyCreator
core::scoring::PairEPotential
protocols::features::PairFeatures
protocols::features::PairFeaturesCreatorCreator for the PairFeatures class
core::scoring::dssp::Pairing
protocols::jumping::PairingLibrary
protocols::abinitio::PairingStatEntry
protocols::abinitio::PairingStatistics
protocols::jumping::PairingTemplate
core::sequence::PairScoringScheme
protocols::simple_filters::PalesEvaluator
protocols::simple_filters::PalesEvaluatorCreatorCreator for the PalesEvaluatorCreator class
protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator
protocols::canonical_sampling::ParallelTempering
protocols::canonical_sampling::ParallelTemperingCreator
protocols::rosetta_scripts::ParsedProtocol
protocols::rosetta_scripts::ParsedProtocolCreator
protocols::jd2::Parser
protocols::protein_interface_design::ParserJobInputter
protocols::protein_interface_design::ParserJobInputterCreator
protocols::frag_picker::scores::PartialSecondarySimilarityScores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms
If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster
protocols::comparative_modeling::PartialThreadingMover
core::optimization::ParticleSimple data container for PSO algorithm
core::optimization::ParticleSwarmMinimizerParticle Swarm Optimization engine
protocols::multistate_design::PartitionAggregateFunction
core::chemical::PatchA class patching basic ResidueType to create variant types, containing multiple PatchCase
core::chemical::PatchCaseA single case of a patch, eg proline Nterminus is a case of NtermProteinFull
protocols::protein_interface_design::PatchdockReader
protocols::canonical_sampling::PatchOperation
core::chemical::PatchOperationA single operation that needs to be applied in a residue patch
core::scoring::electron_density::PattersonCorrEnergy
core::scoring::electron_density::PattersonCorrEnergyCreator
protocols::evaluation::PCA
protocols::abinitio::PcaEvaluator
protocols::pockets::PCluster@
protocols::pockets::PClusterSet@
protocols::scoring::methods::pcs::PCS_data
protocols::scoring::methods::pcs::PCS_data_inputPCS_data_input contain all the input information for the PCS. This includes all the information from the .npc files
protocols::scoring::methods::pcs::PCS_data_input_manager
protocols::scoring::methods::pcs::PCS_data_per_lanthanides
protocols::scoring::methods::pcs::PCS_Energy
protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
protocols::scoring::methods::pcs::PCS_file_dataPCS_file_data contain all the information of a .npc file one per lanthanide
protocols::frag_picker::scores::PCS_FragDistanceScores a fragment by the root mean square deviation of Phi and Psi angles
protocols::scoring::methods::pcs::PCS_line_dataPCS_line_data class: hold a line of the input file information (.npc format) One PCS_line_data per line in the input file
protocols::scoring::methods::pcs::PCS_tensor
protocols::scoring::methods::pcs2::PcsDataCenter
protocols::scoring::methods::pcs2::PcsDataCenterManager
protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
protocols::scoring::methods::pcs2::PcsDataLanthanide
protocols::scoring::methods::pcs2::PcsEnergy
protocols::topology_broker::PcsEnergyController
protocols::scoring::methods::pcs2::PcsEnergyCreator
protocols::scoring::methods::pcs2::PcsEnergyParameter
protocols::scoring::methods::pcs2::PcsEnergyParameterManager
protocols::scoring::methods::pcs2::PcsGridSearchParameter
protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
protocols::scoring::methods::pcs2::PcsInputCenterPcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set
protocols::scoring::methods::pcs2::PcsInputCenterManager
protocols::scoring::methods::pcs2::PcsInputFilePcsInputFile contain all the information of a .npc file one per lanthanide
protocols::scoring::methods::pcs2::PcsInputLinePcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file
protocols::scoring::methods::pcs2::PcsTensor
protocols::sparta::PDB
core::io::pdb::PDB_DReaderPDB Reader it self, D - for dynamic approch of type handling
protocols::features::PdbDataFeatures
protocols::features::PdbDataFeaturesCreatorCreator for the PdbDataFeatures class
protocols::moves::PDBDumpMover
protocols::frag_picker::PdbIdChunkFilter
core::pose::PDBInfoMaintains pdb residue & atom information inside a Pose
protocols::jd2::PDBJobInputter
protocols::jd2::PDBJobInputterCreator
protocols::jd2::PDBJobOutputter
protocols::jd2::PDBJobOutputterCreator
protocols::dna::PDBOutput
core::import_pose::pose_stream::PDBPoseInputStream
core::pose::PDBPoseMapPDBPoseMap can be queried with PDB information (chain, sequence position) and returns a pose's resid position. Useful for handing input/output in terms of PDB positions. Can be tucked into the pose for repeated access, or generated just-in-time for a single use. Basically a wrapper class for std::map
core::import_pose::PDBSilentStruct
core::import_pose::PDBSilentStructCreatorCreator for the PDBSilentStruct class
protocols::canonical_sampling::PDBTrajectoryRecorder
protocols::canonical_sampling::PDBTrajectoryRecorderCreator
protocols::match::output::PDBWriter
protocols::scoring::methods::saxs::PDDFEnergy
protocols::scoring::methods::saxs::PDDFEnergyCreator
protocols::simple_filters::PDDFScoreFilter
core::pack::interaction_graph::PDEdge
core::pack::interaction_graph::PDInteractionGraph
core::pack::interaction_graph::PDNode
protocols::noesy_assign::PeakAssignmentFast access to assignments that are stored in CrossPeak -- similar to FragID
protocols::noesy_assign::PeakAssignmentParameters
protocols::noesy_assign::PeakAssignmentResidueMapFast access to assignments by residue number
protocols::noesy_assign::PeakCalibrator
protocols::noesy_assign::PeakCalibratorMap
protocols::noesy_assign::PeakFileFormat
protocols::noesy_assign::PeakFileFormat_Base
protocols::noesy_assign::PeakFileFormat_Sparky
protocols::noesy_assign::PeakFileFormat_xeasy
protocols::noesy_assign::PeakFileFormat_xpk
core::scoring::PeptideBondedEnergyContainer
core::scoring::PeptideBondedNeighborConstIterator
core::scoring::PeptideBondedNeighborIterator
core::scoring::methods::PeptideBondEnergyPeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment
core::scoring::methods::PeptideBondEnergyCreator
protocols::protein_interface_design::movers::PeptideStapleDesignMoverIntroduces a peptide staple (ala G. Verdine) to the pose
protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator
protocols::simple_moves::PeptideStapleMover
core::scoring::constraints::PeriodicBoundFuncVariant of the bound func that is periodic
core::scoring::constraints::PeriodicFuncFunction of type y = ( k * cos(n * (x - x0) ) ) + C
protocols::rotamer_recovery::PerNativeRRReporterHuman
core::scoring::packstat::PerSphereAccumulator
protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverClass for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator
protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverClass for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator
core::scoring::methods::pHEnergy
core::scoring::methods::pHEnergyCreator
protocols::frag_picker::scores::PhiScores a fragment by its predicted phi similarity
protocols::frag_picker::scores::PhiPsiRmsdScores a fragment by the root mean square deviation of Phi and Psi angles
protocols::frag_picker::scores::PhiPsiSquareWellScores a fragment by the root mean square deviation of Phi and Psi angles
protocols::frag_picker::PhiPsiTalosIO
core::pack::task::PIKAAPIKAA allows residues specifed in a following string and packing
core::pack::task::PIKNAPIKNA allows nucleic acid residues specifed in a following string
core::pack::task::PIKRNAPIKRNA allows nucleic acid residues specifed in a following string
protocols::toolbox::pose_metric_calculators::PiPiCalculator
protocols::protein_interface_design::movers::PlacementAuctionMover
protocols::protein_interface_design::movers::PlacementAuctionMoverCreator
protocols::protein_interface_design::movers::PlacementMinimizationMoverSimple rb-minimization in a bb-stub constraint biased forcefield. Note that this mover is dependent on a placement mover for setting its stubsets
protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator
protocols::protein_interface_design::movers::PlaceOnLoop
protocols::protein_interface_design::movers::PlaceOnLoopCreator
protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverChoose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria
protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator
protocols::protein_interface_design::movers::PlaceStubMoverChoose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria
protocols::protein_interface_design::movers::PlaceStubMoverCreator
protocols::pockets::PlaidFingerprint
protocols::jobdist::PlainPdbJobDistributorDistributor for use with plain old PDB files. Use is strongly discouraged in production environments!
protocols::jobdist::PlainRawJobDistributorDistributor for use with raw files
protocols::jobdist::PlainSilentFileJobDistributorDistributor for use with silent files
protocols::optimize_weights::PNatAAOptEPositionData
protocols::optimize_weights::PNatAAOptERotamerData
protocols::optimize_weights::PNatLigPoseOptEData
protocols::optimize_weights::PNatRotOptEPositionData
protocols::optimize_weights::PNatRotOptERotamerData
protocols::optimize_weights::PNatStructureOptEData
protocols::pockets::PocketConstraintThis constraint favors creating a pocket suitable for a small-molecule
protocols::pockets::PocketConstraintCreatorMover creator for the PocketConstraint constraint
protocols::pockets::PocketGrid@
core::scoring::packstat::Point
core::conformation::PointGraphEdgeData
core::conformation::PointGraphVertexData
protocols::pmut_scan::PointMutScanDriver
core::scoring::packstat::PointPair
core::scoring::methods::PoissonBoltzmannEnergy
core::scoring::methods::PoissonBoltzmannEnergyCreator
core::scoring::PoissonBoltzmannPotential
core::pack::task::POLARPOLAR allows polar residues and packing
protocols::qsar::scoring_grid::polarizGrid
protocols::qsar::scoring_grid::polarizGridCreator
protocols::nonlocal::Policy
protocols::nonlocal::PolicyFactory
core::scoring::hbonds::Polynomial_1d
Polynomial_1d
pool
protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck
protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
protocols::canonical_sampling::mc_convergence_checks::PoolData
protocols::simple_filters::PoolEvaluatorCreatorCreator for the PoolEvaluatorCreator class
core::pose::PoseA molecular system including residues, kinematics, and energies
protocols::swa::rna::pose_data_struct2
core::scoring::packing::PoseBalls
core::scoring::packing::PoseBallsLite
protocols::features::PoseCommentsFeatures
protocols::features::PoseCommentsFeaturesCreatorCreator for the PoseCommentsFeatures class
protocols::moves::PoseCondition
protocols::features::PoseConformationFeatures
protocols::features::PoseConformationFeaturesCreatorCreator for the PoseConformationFeatures class
protocols::evaluation::PoseEvaluator
protocols::swa::PoseFilter
protocols::swa::PoseFilter_RMSD_Screen
protocols::enzdes::PoseFoundResiduesCombinationHelper class to process and output the different found poses
core::import_pose::pose_stream::PoseInputStream
protocols::jd2::PoseInputStreamJobInputter
protocols::jd2::PoseInputStreamJobInputterCreator
protocols::match::output::PoseInserter
protocols::match::output::PoseMatchOutputWriterHelper class for the MatcherMover that will put a match into a supplied pose
core::pose::metrics::PoseMetricCalculator
core::pose::metrics::PoseMetricContainerContainer for managing PoseMetricCalculators
protocols::simple_filters::PoseMetricEvaluator< T >
core::import_pose::pose_stream::PoseOutputStream
core::scoring::packstat::PosePackData
core::pose::datacache::PositionConservedResiduesStore
core::io::PositionDdGInfo::PositionDdGInfoSmall helper class that stores the ddGs for mutations at a given position. camel case gets weird when trying to write words containing ddG..
protocols::genetic_algorithm::PositionSpecificRandomizerDifferent set of choices at each position in Entity's traits
protocols::dna::PositionTypeBasic struct for remembering position/type information before/during/after design
protocols::domain_assembly::PostDockAssemblyScorer
protocols::multistate_design::PosType
protocols::multistate_design::PosTypeCreator
protocols::pack_daemon::PowExpression
protocols::flexpack::interaction_graph::PrecomputedFlexbbInteractionGraph
core::pack::interaction_graph::PrecomputedPairEnergiesEdge
core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
core::pack::interaction_graph::PrecomputedPairEnergiesNode
protocols::enzdes::PredesignPerturbMover
protocols::enzdes::PredesignPerturbMoverCreator
core::scoring::Predicate
protocols::simple_filters::PredictedBurialEvaluator
protocols::simple_filters::PredictedBurialFnEvaluatorCreatorCreator for the PredictedBurialFnEvaluatorCreator class
protocols::protein_interface_design::movers::PrepackMover
protocols::protein_interface_design::movers::PrepackMoverCreator
core::chemical::PrependMainchainAtomAdd a mainchain atom before the first mainchain atom
core::pack::task::operation::PreserveCBeta
core::pack::task::operation::PreserveCBetaCreator
protocols::toolbox::task_operations::PreventChainFromRepackingOperation
protocols::toolbox::task_operations::PreventChainFromRepackingOperationCreator
core::pack::task::operation::PreventRepackingPreventRepacking allows you to prevent repacking (NATRO behavior) through the Factory. Useful if you do not know the residue numbers when the resfile is created. Note that this is unlike RestrictToRepacking; you have to specify which residues. If PreventRepacking worked on the entire Task you'd have a do-nothing task
core::pack::task::operation::PreventRepackingCreator
core::pack::task::operation::PreventRepackingRLT
core::pack::task::operation::PreventRepackingRLTCreator
protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation
protocols::toolbox::task_operations::PreventResiduesFromRepackingOperationCreator
core::pack::dunbrack::ProbSortClass
protocols::match::output::ProcessorFactory
core::scoring::methods::ProClosureEnergy
core::scoring::methods::ProClosureEnergyCreator
protocols::moves::ProfilerMover
protocols::frag_picker::scores::ProfileScoreFragment candidate
protocols::frag_picker::scores::ProfileScoreBlosum62Fragment candidate
protocols::frag_picker::scores::ProfileScoreDistWeightFragment candidate
protocols::frag_picker::scores::ProfileScoreL1Fragment candidate
protocols::frag_picker::scores::ProfileScoreStructL1Fragment candidate
protocols::frag_picker::scores::ProfileScoreSubMatrixFragment candidate
core::sequence::ProfSimScoringScheme
protocols::simple_moves::ProlineFixMover
protocols::frag_picker::scores::ProlinePhiScoreProlinePhiScore score counts identical residues
protocols::features::ProteinBackboneAtomAtomPairFeatures
protocols::features::ProteinBackboneAtomAtomPairFeaturesCreatorCreator for the ProteinBackboneAtomAtomPairFeatures class
protocols::match::upstream::ProteinBackboneBuildPoint
protocols::features::ProteinBackboneTorsionAngleFeatures
protocols::features::ProteinBackboneTorsionAngleFeaturesCreatorCreator for the ProteinBackboneTorsionAngleFeatures class
protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
protocols::toolbox::task_operations::ProteinInterfaceDesignOperationCreator
protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverWraps protein-interface specific considerations around the general multistate design / genetic algorithm framework
protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator
protocols::enzdes::ProteinLigandInterfaceUpweighterClass to alter a packer task to speficially upweight the protein-ligand interaction energies
protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator
protocols::features::ProteinResidueConformationFeatures
protocols::features::ProteinResidueConformationFeaturesCreatorCreator for the ProteinResidueConformationFeatures class
protocols::features::ProteinRMSDFeatures
protocols::features::ProteinRMSDFeaturesCreatorCreator for the ProteinRMSDFeatures class
protocols::match::upstream::ProteinSCSampler
protocols::features::ProteinSilentReport
core::io::silent::ProteinSilentStruct_SinglePrecCreatorCreator for the ProteinSilentStruct_SinglePrec class
core::io::silent::ProteinSilentStruct_Template< T >
core::io::silent::ProteinSilentStructCreatorCreator for the ProteinSilentStruct class
protocols::match::upstream::ProteinUpstreamBuilder
protocols::abinitio::Protocol
protocols::features::ProtocolFeatures
protocols::features::ProtocolFeaturesCreatorCreator for the ProtocolFeatures class
core::conformation::PseudoBond
core::conformation::PseudoBondCollection
protocols::topology_broker::PseudocontactShiftEnergyController
protocols::scoring::methods::pcs::PseudocontactShiftEnergyCreator
protocols::frag_picker::scores::PsiScores a fragment by its predicted psi similarity
protocols::optimize_weights::PSSMOptEPositionData
protocols::frag_picker::scores::PValuedFragmentScoreManagerHolds particular score components, weights and calculates the total score for a fragment candidate
core::scoring::methods::PyContextIndependentOneBodyEnergy
core::scoring::methods::PyContextIndependentTwoBodyEnergy
core::scoring::methods::PyEnergyMethodRegistratorThis class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
protocols::moves::PyMolMover
protocols::moves::PyMolObserver
protocols::qsar::qsarCreator
protocols::qsar::qsarMap
protocols::qsar::qsarMover
protocols::qsar::qsarOptData
protocols::qsar::qsarOptFunc
protocols::qsar::qsarPoint
protocols::pack_daemon::QuickRepacker
protocols::frag_picker::quota::quota_limits_sorter_biggest_first
protocols::frag_picker::quota::quota_limits_sorter_smallest_first
protocols::frag_picker::quota::QuotaCollectorA base class for collecting fragments
protocols::frag_picker::quota::QuotaConfigRead a config file for quota selector
protocols::frag_picker::QuotaDebug
protocols::frag_picker::quota::QuotaPoolSingle pool used by quota selector
protocols::frag_picker::quota::QuotaSelectorSelects a given number of fragments using a quota scheme
protocols::features::RadiusOfGyrationFeatures
protocols::features::RadiusOfGyrationFeaturesCreatorCreator for the RadiusOfGyrationFeatures class
core::scoring::Ramachandran
core::scoring::Ramachandran2B
core::scoring::methods::RamachandranEnergy
core::scoring::methods::RamachandranEnergy2B
core::scoring::methods::RamachandranEnergy2BCreator
core::scoring::methods::RamachandranEnergyCreator
protocols::frag_picker::scores::RamaScoreRamaScore score counts identical residues
protocols::moves::RampingFunc
protocols::moves::RampingMover
protocols::ligand_docking::RandomConformerMoverReplace the residue at the given position with a randomly selected conformer from its rotamer library
protocols::ligand_docking::RandomConformers
protocols::ligand_docking::RandomConformersCreator
protocols::moves::RandomMoverRandomMover picks a random move and applies it
protocols::moves::RandomMoverCreator
protocols::protein_interface_design::movers::RandomMutationDesigns alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines
protocols::protein_interface_design::movers::RandomMutationCreator
protocols::jumping::RandomSheetBuilderSelect jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++
protocols::simple_moves::symmetry::RandomSymmetrySlider
protocols::loops::RationalLoopComparatorOrders loops by start position
protocols::simple_moves::rational_mc::RationalMonteCarlo
core::io::raw_data::RawFileDataAbstract base class for classes that writes different types of silent-files that contain a mixture of Struct objects which are expected to be uniquely identified by some sort of string-based tag
core::io::raw_data::RawStruct
protocols::rbsegment_relax::RB_lt
protocols::rbsegment_relax::RBResidueRangeRB residue range
protocols::rbsegment_relax::RBSegmentRigid-body segments in a protein
protocols::rbsegment_relax::RBSegmentMoverPerforms a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'
protocols::rbsegment_relax::RBSegmentRelax
core::scoring::RDC
core::scoring::RDC_Rohl
protocols::simple_filters::RdcEvaluatorCreatorCreator for the RdcEvaluatorCreator class
protocols::frag_picker::scores::RDCScoreScores a fragment by its crmsd to the given reference structure
protocols::simple_filters::RdcSelectEvaluatorCreatorCreator for the RdcSelectEvaluatorCreator class
protocols::simple_filters::RdcTargetEvaluatorCreatorCreator for the RdcTargetEvaluatorCreator class
core::pack::task::operation::ReadResfile
core::pack::task::operation::ReadResfileAndObeyLengthEventsWritten by flo, feb 2011 class that can apply a resfile to a pose that had its length changed at some point in a protocol. A LengthEventCollector must be set in the pose's observer cache for this to work properly
core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator
core::pack::task::operation::ReadResfileCreator
protocols::toolbox::task_operations::ReadResfileFromDB
protocols::toolbox::task_operations::ReadResfileFromDBCreator
protocols::comparative_modeling::RecoverSideChainsMover
core::chemical::RedefineChiRedefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTM's
utility::pointer::ReferenceCount
utility::pointer::ReferenceCountMI
core::scoring::methods::ReferenceEnergy
core::scoring::methods::ReferenceEnergyCreator
protocols::nonlocal::Region
protocols::simple_filters::RegionalConnections
protocols::forge::build::RelativeConnectRightVersion of ConnectRight instruction that depends upon results from another BuildInstruction
protocols::protein_interface_design::filters::RelativePoseFilter
protocols::protein_interface_design::filters::RelativePoseFilterCreator
protocols::protein_interface_design::filters::RelativeSegmentFilterReturns the residues aligned to a segment on the input pdb to the source pdb
protocols::protein_interface_design::filters::RelativeSegmentFilterCreator
protocols::forge::build::RelativeSequencePositionComputes a position wrt values in given BuildInstruction
protocols::relax::RelaxProtocolBase
protocols::relax::RelaxScriptCommand
core::pose::RemarkInfo
core::pose::Remarks
protocols::forge::remodel::RemodelAccumulator
protocols::forge::remodel::RemodelConstraintGeneratorPure virtual base class
protocols::forge::remodel::RemodelData
protocols::forge::remodel::RemodelDesignMover
protocols::forge::remodel::RemodelEnzdesCstModule
protocols::forge::remodel::RemodelLoopMoverLoop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++
protocols::forge::remodel::RemodelLoopMoverCreator
protocols::forge::remodel::RemodelMover
protocols::forge::remodel::RemodelMoverCreator
protocols::forge::remodel::RemodelRotamerLinks
protocols::forge::remodel::RemodelRotamerLinksCreator
protocols::match::RemoveNorCTermMPMAdded by olga and flo 1/2011 class to exclude positions at the n and c termini of proteins from matching
protocols::qsar::RenderGridsToKinemage
protocols::qsar::RenderGridsToKinemageCreator
protocols::enzdes::RepackLigandSiteWithoutLigandMoverClass 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
protocols::protein_interface_design::movers::RepackMinimizeOne round of design/repacking followed by interface sc/bb and rigid-body minimization
protocols::protein_interface_design::movers::RepackMinimizeCreator
protocols::simple_moves::RepackSidechainsMoverA protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains()
protocols::simple_moves::RepackSidechainsMoverCreator
protocols::enzdes::RepackWithoutLigandFilter
protocols::enzdes::RepackWithoutLigandFilterCreator
protocols::moves::RepeatMoverA Mover that repeats an input Mover a user-specified number of times
protocols::qsar::scoring_grid::RepGrid
protocols::qsar::scoring_grid::RepGridCreator
protocols::moves::ReplicaExchangeMC
core::pack::task::operation::ReplicateTask
core::pack::task::operation::ReplicateTaskCreator
protocols::features::Report
protocols::protein_interface_design::ReportPSSMDifferences
protocols::protein_interface_design::ReportSequenceDifferences
protocols::features::ReportToDB
protocols::features::ReportToDBCreator
protocols::simple_moves::RepulsiveOnlyMoverThis 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
core::scoring::custom_pair_distance::resatom_and_func_struct
core::chemical::ResConnIDThe ResConnID could more properly be called the ResidueConnector. It stores the data necessary to describe how one ResidueConnection on a conformation::Residue is connected to the rest of the structure (Pose), by listing the other Residue's index and the ResidueConnection index
core::pack::task::ResfileCommandAbstract/interface class for Resfile reader command objects
core::pack::task::ResfileContents
core::pack::task::ResfileReaderException
core::pack::task::operation::ResFilter
core::pack::task::operation::ResFilterCreatorThe ResFilterCreator class's responsibilities are to create on demand a new ResFilter class. The ResFilterCreator must register itself with the ResFilterFactory at load time (before main() begins) so that the ResFilterFactory is ready to start creating ResFilters by the time any protocol requests one
core::pack::task::operation::ResFilterFactory
core::pack::task::operation::ResFilterRegistrator< T >This templated class will register an instance of an ResFilterCreator (class T) with the ResFilterFactory. It will ensure that no ResFilter creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
protocols::moves::ResId
core::scoring::ResidualDipolarCouplingResidualDipolarCouplings are mainly handled by this class related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy -- an energy method which triggers computations handled by this class
core::scoring::ResidualDipolarCoupling_Rohl
core::scoring::methods::ResidualDipolarCouplingEnergy
core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
core::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator
core::scoring::methods::ResidualDipolarCouplingEnergyCreator
protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegmentsCreator
protocols::scoring::ResidualDipolarCouplingRigidSegmentsResidualDipolarCouplingRigidSegmentss are mainly handled by this class related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingRigidSegmentsEnergy -- an energy method which triggers computations handled by this class
core::conformation::ResidueInstance Residue class, used for placed residues and rotamers
protocols::swa::rna::Residue_info
core::pack::scmin::ResidueAtomTreeCollectionThe conformation::Residues and kinematics::AtomTrees for a single collection of rotamers (e.g. a RotamerSet). Each chemical::ResidueType gets its own residue/atomtree pair. A particular AtomTree/Residue pair can be set as "active" and manipulated by setter and getters for either the coordinates of the Residues or the chi dihedrals of the AtomTree
core::pack::scmin::ResidueAtomTreeCollectionMomentoClass to save the state for a ResidueAtomTreeCollection
protocols::features::ResidueBurialFeatures
protocols::features::ResidueBurialFeaturesCreatorCreator for the ResidueBurialFeatures class
protocols::protein_interface_design::ResidueBurialFilter
protocols::simple_filters::ResidueBurialFilter
protocols::simple_filters::ResidueBurialFilterCreator
protocols::features::ResidueConformationFeatures
protocols::features::ResidueConformationFeaturesCreatorCreator for the ResidueConformationFeatures class
core::chemical::ResidueConnectionA simple class marking atoms at inter-residue connections
core::scoring::constraints::ResidueConstraints
core::kinematics::ResidueCoordinateChangeListThe AtomTree is responsible for informing the conformation of which residues have had either internal (DOF) or external (xyz) coordinate changes so that the Conformation may shuttle O(k) -- output sensitive -- data from the AtomTree to the Residue objects it manages
core::chemical::ResidueDatabaseIO
protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator
protocols::protein_interface_design::ResidueDistanceFilter
protocols::simple_filters::ResidueDistanceFilter
protocols::simple_filters::ResidueDistanceFilterCreator
core::conformation::ResidueFactoryCollection of functions making a single residue
protocols::comparative_modeling::features::ResidueFeature
protocols::comparative_modeling::features::ResidueFeatureFactory
protocols::features::ResidueFeatures
protocols::features::ResidueFeaturesCreatorCreator for the ResidueFeatures class
protocols::toolbox::ResidueGroupIGEdgeUpweighter
core::pack::task::operation::ResidueHasProperty
core::pack::task::operation::ResidueHasPropertyCreator
core::pack::task::operation::ResidueIndexIs
core::pack::task::operation::ResidueIndexIsCreator
core::pack::task::operation::ResidueIndexIsnt
core::pack::task::operation::ResidueIndexIsntCreator
core::io::pdb::ResidueInformationIntermediate format for easy construction of core::conformation::Residue objects. Subset of data from "ATOM" lines that is shared by all atoms in a residue
protocols::match::output::ResidueKinemageWriter
core::conformation::ResidueKinWriter
core::pack::task::operation::ResidueLacksProperty
core::pack::task::operation::ResidueLacksPropertyCreator
core::pack::task::ResidueLevelTask
core::pack::task::ResidueLevelTask_Residue-level task class; contained within PackerTask
core::conformation::ResidueMatcher
core::pack::task::operation::ResidueName3Is
core::pack::task::operation::ResidueName3IsCreator
core::pack::task::operation::ResidueName3Isnt
core::pack::task::operation::ResidueName3IsntCreator
core::scoring::ResidueNblistData
core::scoring::ResidueNeighborConstIterator
core::scoring::ResidueNeighborIterator
protocols::jumping::ResiduePairJump
protocols::jumping::ResiduePairJumpSetup
protocols::jumping::ResiduePairJumpSingleSingle residue component of a ResiduePairJump class
core::scoring::ResiduePairNeighborList
core::scoring::constraints::ResiduePairXYZ
core::pack::task::operation::ResiduePDBIndexIs
core::pack::task::operation::ResiduePDBIndexIsCreator
core::pack::task::operation::ResiduePDBIndexIsnt
core::pack::task::operation::ResiduePDBIndexIsntCreator
protocols::features::ResidueScoresFeatures
protocols::features::ResidueScoresFeaturesCreatorCreator for the ResidueScoresFeatures class
protocols::features::ResidueSecondaryStructureFeatures
protocols::features::ResidueSecondaryStructureFeaturesCreatorCreator for the ResidueSecondaryStructureFeatures class
core::chemical::ResidueSelectorA class picking out a subset of ResidueType by multiple criteria
core::chemical::ResidueSelectorSingleA base class for defining a ResidueSelector by a single criterion
protocols::protein_interface_design::ResiduesInInterfaceFilter
protocols::simple_filters::ResiduesInInterfaceFilter
protocols::simple_filters::ResiduesInInterfaceFilterCreator
protocols::ligand_docking::ResidueTorsionRestraintsManages harmonic restraints on torsions, so they can be turned off for packing
core::chemical::ResidueTypeSilly demo class -- what would the most familiar residue look like?
core::scoring::constraints::ResidueTypeConstraintThis class favors a particular residue identity at a particular position by reducing its res_type energy
core::scoring::constraints::ResidueTypeLinkingConstraintThis class favors a particular residue identity at a particular position by reducing its res_type energy
core::chemical::ResidueTypeSetA collection of ResidueType defined
protocols::features::ResidueTypesFeatures
protocols::features::ResidueTypesFeaturesCreatorCreator for the ResidueTypesFeatures class
protocols::forge::remodel::ResidueVicinityInfoSmall helper class for the ResidueVicinityRCG
protocols::forge::remodel::ResidueVicinityRCGRemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions
core::scoring::constraints::ResidueXYZ
protocols::toolbox::match_enzdes_util::ResInteractions
core::pack::task::operation::ResLvlTaskOperation
core::pack::task::operation::ResLvlTaskOperationCreatorThe ResLvlTaskOperationCreator class's responsibilities are to create on demand a new ResLvlTaskOperation class. The ResLvlTaskOperationCreator must register itself with the ResLvlTaskOperationFactory at load time (before main() begins) so that the ResLvlTaskOperationFactory is ready to start creating ResLvlTaskOperations by the time any protocol requests one
core::pack::task::operation::ResLvlTaskOperationFactory
core::pack::task::operation::ResLvlTaskOperationRegistrator< T >This templated class will register an instance of an ResLvlTaskOperationCreator (class T) with the ResLvlTaskOperationFactory. It will ensure that no ResLvlTaskOperation creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
protocols::abinitio::ResolutionSwitcher
protocols::noesy_assign::Resonance
protocols::noesy_assign::ResonanceList
core::scoring::custom_pair_distance::RespairInteractions
core::scoring::ResPairMinimizationData
core::scoring::ResRangePredicate
core::scoring::etable::ResResEnergyInvoker< Derived >
core::scoring::ResSingleMinimizationData
core::pack::task::operation::RestrictAbsentCanonicalAAS
core::pack::task::operation::RestrictAbsentCanonicalAASCreator
core::pack::task::operation::RestrictAbsentCanonicalAASRLT
core::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator
protocols::toolbox::task_operations::RestrictByCalculatorsOperation
protocols::toolbox::task_operations::RestrictByCalculatorsOperationCreator
protocols::toolbox::task_operations::RestrictChainToRepackingOperation
protocols::toolbox::task_operations::RestrictChainToRepackingOperationCreator
protocols::toolbox::task_operations::RestrictConservedLowDdgOperationTask 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
protocols::toolbox::task_operations::RestrictConservedLowDdgOperationCreator
protocols::dna::RestrictDesignToProteinDNAInterface
protocols::dna::RestrictDesignToProteinDNAInterfaceCreator
protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation
protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperationCreator
protocols::toolbox::task_operations::RestrictOperationsBase
protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
protocols::toolbox::task_operations::RestrictResiduesToRepackingOperationCreator
core::pack::task::operation::RestrictResidueToRepackingRestrictResidueToRepacking
core::pack::task::operation::RestrictResidueToRepackingCreator
protocols::toolbox::task_operations::RestrictToCDRH3Loop
protocols::toolbox::task_operations::RestrictToCDRH3LoopCreator
protocols::toolbox::task_operations::RestrictToInterface
core::pack::task::operation::RestrictToInterface
protocols::toolbox::task_operations::RestrictToInterfaceCreator
protocols::toolbox::task_operations::RestrictToInterfaceOperation
protocols::toolbox::task_operations::RestrictToInterfaceOperationCreator
protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
protocols::toolbox::task_operations::RestrictToInterfaceVectorOperationCreator
protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
protocols::toolbox::task_operations::RestrictToNeighborhoodOperationCreator
core::pack::task::operation::RestrictToRepacking
core::pack::task::operation::RestrictToRepackingCreator
core::pack::task::operation::RestrictToRepackingRLT
core::pack::task::operation::RestrictToRepackingRLTCreator
core::pack::task::operation::RestrictYSDesignRestrictYSDesign restricts positions to a binary Tyr/Ser alphabet
core::pack::task::operation::RestrictYSDesignCreator
protocols::dna::ResTypeSequence_lt
protocols::simple_moves::ReturnSidechainMover
protocols::dna::Reversion
protocols::protein_interface_design::Revert
core::scoring::methods::RG_Energy
core::scoring::methods::RG_Energy_Fast
core::scoring::methods::RG_Energy_FastCreator
core::scoring::rna::RG_Energy_RNA
core::scoring::rna::RG_Energy_RNACreator
core::scoring::methods::RG_MinData
protocols::simple_filters::RGFilter
protocols::rigid::RigidBodyDofPerturbMoverDoes 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
protocols::rigid::RigidBodyDofRandomizeMover
protocols::rigid::RigidBodyDofRandomTransMover
protocols::rigid::RigidBodyDofSeqPerturbMoverDoes 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
protocols::rigid::RigidBodyDofSeqRandomizeMover
protocols::rigid::RigidBodyDofSeqTransMover
protocols::rigid::RigidBodyDofTransMover
protocols::rigid::RigidBodyMotionMover
protocols::rigid::RigidBodyMoverRigid-body random translate/rotate around centroid of downstream side of a jump
protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO
protocols::rigid::RigidBodyPerturbMover
protocols::rigid::RigidBodyPerturbNoCenterMoverDoes 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
protocols::rigid::RigidBodyPerturbNoCenterMoverCreator
protocols::rigid::RigidBodyRandomizeMover
protocols::swa::RigidBodySampler
protocols::rigid::RigidBodySpinMover
protocols::rigid::RigidBodyTransMover
protocols::topology_broker::RigidChunkClaimerDefines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers --- here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued --- in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates ) e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree
protocols::match::downstream::RigidLigandBuilder
protocols::ligand_docking::RigidSearchMoverAn optimized mover for Monte Carlo trial of rigid body perturbations
protocols::sparta::RingData
core::scoring::methods::RMS_Energy
core::scoring::methods::RMS_EnergyCreator
protocols::simple_filters::RmsdEvaluator
protocols::simple_filters::RmsdEvaluatorCreatorCreator for the RmsdEvaluatorCreator class
protocols::protein_interface_design::filters::RmsdFilter
protocols::protein_interface_design::filters::RmsdFilterCreator
protocols::simple_filters::RmsdTargetEvaluatorCreatorCreator for the RmsdTargetEvaluatorCreator class
protocols::frags::RMSVallData
protocols::swa::rna::RNA_AnalyticLoopCloserThe RNA de novo structure modeling protocol
core::scoring::rna::RNA_AtomVDW
core::scoring::rna::RNA_BaseBaseEnergy
core::scoring::rna::RNA_BulgeEnergy
core::scoring::rna::RNA_BulgeEnergyCreator
core::scoring::rna::RNA_CentroidInfoKeep track of RNA centroid information inside the pose
protocols::rna::RNA_ChunkLibrary
core::scoring::rna::RNA_DataBackboneEnergy
core::scoring::rna::RNA_DataBackboneEnergyCreator
core::scoring::rna::RNA_DataInfoKeep track of RNA centroid information inside the pose
protocols::rna::RNA_DataReader
core::scoring::rna::RNA_Datum
protocols::rna::RNA_DeNovoProtocolThe RNA de novo structure modeling protocol
core::scoring::rna::RNA_FA_Stack
core::scoring::rna::RNA_FilteredBaseBaseInfoKeep track of RNA centroid information inside the pose
core::scoring::rna::RNA_FittedTorsionInfo
protocols::rna::RNA_FragmentMoverThe RNA de novo structure modeling protocol
protocols::rna::RNA_Fragments
core::scoring::rna::RNA_FullAtomStackingEnergy
core::scoring::rna::RNA_FullAtomStackingEnergyCreator
core::scoring::rna::RNA_FullAtomVDW_BasePhosphate
core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator
protocols::rna::RNA_HelixAssemblerThe RNA de novo structure modeling protocol
protocols::rna::RNA_JumpLibrary
core::scoring::rna::RNA_LJ_BaseEnergy
core::scoring::rna::RNA_LJ_BaseEnergyCreator
protocols::rna::RNA_LoopCloserThe RNA de novo structure modeling protocol
protocols::swa::rna::RNA_LoopCloseSampler
core::scoring::rna::RNA_LowResolutionPotential
protocols::rna::RNA_MinimizerThe RNA de novo structure modeling protocol
protocols::rna::RNA_Pairing
protocols::rna::RNA_PairingTemplate
core::scoring::rna::RNA_PairwiseLowResolutionEnergy
core::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator
core::scoring::rna::RNA_RawBaseBaseInfoKeep track of RNA centroid information inside the pose
protocols::rna::RNA_RelaxerThe RNA de novo structure modeling protocol
core::chemical::rna::RNA_ResidueType
core::scoring::rna::RNA_ScoringInfoKeep track of RNA centroid, useful atom, base-base info inside the pose
protocols::rna::RNA_SecStructInfoKeep track of RNA centroid information inside the pose
core::io::silent::RNA_SilentStruct
core::io::silent::RNA_SilentStructCreatorCreator for the RNA_SilentStruct class
protocols::rna::RNA_StructureParameters
core::scoring::rna::RNA_SugarCloseEnergy
core::scoring::rna::RNA_SugarCloseEnergyCreator
core::scoring::rna::RNA_TorsionEnergy
core::scoring::rna::RNA_TorsionEnergyCreator
core::scoring::rna::RNA_TorsionPotential
core::scoring::rna::RNA_VDW_Energy
core::scoring::rna::RNA_VDW_EnergyCreator
core::scoring::hackelec::RNAHackElecEnergy
core::scoring::hackelec::RNAHackElecEnergyCreator
protocols::rigid::RollMover
protocols::rigid::RollMoverCreator
protocols::topology_broker::RootClaim
core::pack::annealer::RotamerAssigningAnnealer
protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
protocols::simple_filters::RotamerBoltzmannWeight
protocols::features::RotamerBoltzmannWeightFeatures
protocols::features::RotamerBoltzmannWeightFeaturesCreatorCreator for the RotamerBoltzmannWeightFeatures class
protocols::simple_filters::RotamerBoltzmannWeightFilterCreator
core::pack::dunbrack::RotamerBuildingDataSimple class for passing data around in virtual function calls of the rotamer creating process. Derived classes will be simple containers for interpolated rotameric data that 1) has to be available to the derived class when building rotamers and 2) cannot be stored as member data in the derived class in a thread-safe manner. Derived classes of the RotamerBuildingData can be declared on the stack, passed into the RotamericSingleResidueDunbrackLibrary::build_chi_sets function, and then in the (virtual) chisamples_for_rotamer function, the derived classes may be downcast
core::pack::dunbrack::RotamerConstraintThis class favors a particular rotamer at a particular position by reducing its Dunbrack energy
core::pack::rotamer_set::RotamerCouplings
core::scoring::trie::RotamerDescriptor< AT, CPDAT >
core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT >
protocols::dna::RotamerDNAHBondFilter
core::pack::interaction_graph::RotamerDotsHandles sphere-sphere overlap calculations for the HPatchInteractionGraph
core::pack::interaction_graph::RotamerDotsCacheA lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes
core::pack::interaction_graph::RotamerDotsRadiusDataA singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class
protocols::RotamerDump::RotamerDumpMoverMover for dumping interaction graph information. The information is appended to the current job
core::pack::task::operation::RotamerExplosionRotamer explosion for a residue
core::pack::task::operation::RotamerExplosionCreator
core::pack::dunbrack::RotamericData< T >
core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
core::pack::dunbrack::RotamerLibrary
core::pack::dunbrack::RotamerLibraryScratchSpace
core::pack::rotamer_set::RotamerLinks
core::pack::rotamer_set::RotamerOperationRotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation
protocols::rotamer_recovery::RotamerRecovery
protocols::toolbox::pose_metric_calculators::RotamerRecovery
protocols::rotamer_recovery::RotamerRecoveryFactoryCreate Rotamer_Recovery Reporters
protocols::features::RotamerRecoveryFeatures
protocols::features::RotamerRecoveryFeaturesCreatorCreator for the RotamerRecoveryFeatures class
protocols::rotamer_recovery::RotamerRecoveryMover
protocols::rotamer_recovery::RotamerRecoveryMoverCreator
protocols::rotamer_recovery::RotamerRecoveryRegistrator< T >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
core::pack::rotamer_set::RotamerSet
core::pack::rotamer_set::RotamerSet_Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" -- the rotamer present on the input pose before packing began
core::conformation::RotamerSetBase
core::pack::rotamer_set::RotamerSetFactory
core::pack::rotamer_set::RotamerSetOperation
core::pack::rotamer_set::RotamerSets
core::pack::rotamer_set::RotamerSetsBase
core::pack::rotamer_set::RotamerSubsetContainer for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It's main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the "rot_to_pack" vector)
protocols::pack_daemon::RotamerSubsetRepacker
core::pack::rotamer_set::RotamerSubsets
protocols::simple_moves::RotamerTrialsMinMover
protocols::simple_moves::RotamerTrialsMinMoverCreator
protocols::simple_moves::RotamerTrialsMover
protocols::simple_moves::RotamerTrialsMoverCreator
core::scoring::trie::RotamerTrie< AT, CPDATA >
core::scoring::trie::RotamerTrieBase
protocols::ligand_docking::Rotate
protocols::ligand_docking::Rotate_info
protocols::ligand_docking::RotateCreator
protocols::rigid::RotateJumpAxisMover
protocols::ligand_docking::Rotates
protocols::ligand_docking::RotatesCreator
protocols::MakeRotLib::RotData
protocols::simple_filters::RPF_ScoreEvaluator
protocols::rotamer_recovery::RRComparerThe comparison functionality for the rotamer recovery test
protocols::rotamer_recovery::RRComparerAutomorphicRMSD
protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator
protocols::rotamer_recovery::RRComparerCreatorThe Creator class is responsible for creating a particular mover class
protocols::rotamer_recovery::RRComparerRotBins
protocols::rotamer_recovery::RRComparerRotBinsCreator
protocols::rotamer_recovery::RRProtocolThe protocol to run to compute the rotamer recovery the rotamer recovery test
protocols::rotamer_recovery::RRProtocolCreatorThe Creator class is responsible for creating a particular mover class
protocols::rotamer_recovery::RRProtocolMinPack
protocols::rotamer_recovery::RRProtocolMinPackCreator
protocols::rotamer_recovery::RRProtocolMover
protocols::rotamer_recovery::RRProtocolMoverCreator
protocols::rotamer_recovery::RRProtocolReferenceStructure
protocols::rotamer_recovery::RRProtocolReferenceStructureCreator
protocols::rotamer_recovery::RRProtocolRTMin
protocols::rotamer_recovery::RRProtocolRTMinCreator
protocols::rotamer_recovery::RRReporterThe reporting functionality for the rotamer recovery test
protocols::rotamer_recovery::RRReporterCreatorThe Creator class is responsible for creating a particular mover class
protocols::rotamer_recovery::RRReporterHumanThe reporting functionality for the rotamer recovery test in a human readable format
protocols::rotamer_recovery::RRReporterHumanCreator
protocols::rotamer_recovery::RRReporterSimple
protocols::rotamer_recovery::RRReporterSimpleCreator
protocols::rotamer_recovery::RRReporterSQLite
protocols::rotamer_recovery::RRReporterSQLiteCreator
core::kinematics::RTRotation + translation class
core::scoring::disulfides::RT_helper
core::pack::RTMin
core::coarse::Rule
core::coarse::RuleSet
core::scoring::methods::SA_Energy
core::scoring::methods::SA_EnergyCreator
protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
protocols::features::SaltBridgeFeatures
protocols::features::SaltBridgeFeaturesCreatorCreator for the SaltBridgeFeatures class
protocols::match::output::SameChiBinComboGrouper
protocols::match::output::SameRotamerComboGrouper
protocols::match::output::SameSequenceAndDSPositionGrouperClass 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
protocols::match::output::SameSequenceGrouperClass 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
protocols::jumping::SameStrandTiny 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,
protocols::match::upstream::SampleStrategyDataThis 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
protocols::docking::stateless::SaneDockingProtocol
protocols::simple_moves::SaneMinMover
protocols::simple_moves::SaneMinMoverCreator
core::pose::metrics::simple_calculators::SasaCalculator
core::scoring::packstat::SasaOptions
core::scoring::packstat::SasaResult
protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsSaves 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
protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator
protocols::rosetta_scripts::SavePoseMoverMover 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
protocols::rosetta_scripts::SavePoseMoverCreator
core::scoring::saxs::SAXSEnergy
core::scoring::saxs::SAXSEnergyCEN
core::scoring::saxs::SAXSEnergyCreator
core::scoring::saxs::SAXSEnergyCreatorCEN
core::scoring::saxs::SAXSEnergyCreatorFA
core::scoring::saxs::SAXSEnergyFA
protocols::simple_filters::SAXSScoreFilter
core::scoring::etable::SC_BB_EnergyInvoker< Derived >
core::scoring::etable::SC_SC_EnergyInvoker< Derived >
core::scoring::etable::SC_Whole_EnergyInvoker< Derived >
protocols::match::upstream::ScaffoldBuildPoint
core::scoring::constraints::ScalarWeightedFunc
protocols::optimize_weights::ScaleAnnealerTemperatureOperation
core::pack::task::SCANSCAN suggests to some packing routines that if there are multiple type choices for this residue, then each of them should be considered explicitly in one way or another
core::pack::scmin::SCMinMinimizerMap
core::pack::scmin::SCMinMultifunc
protocols::simple_filters::ScoreCutoffFilter
protocols::simple_filters::ScoreCutoffFilterCreator
protocols::frag_picker::scores::ScoreEValuatorComputes E-Value for a Profile object
protocols::simple_filters::ScoreEvaluatorThat rewrites the whole pss struct all previous entries will be lost... probably not what one wants..
core::io::raw_data::ScoreFileData
core::io::silent::ScoreFileSilentStruct
core::io::silent::ScoreFileSilentStructCreatorCreator for the ScoreFileSilentStruct class
core::scoring::ScoreFunctionThis object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated
core::scoring::ScoreFunctionFactoryCollection of functions making a single score_function
core::scoring::ScoreFunctionInfoInfo on the scorefunction settings
protocols::jd2::parser::ScoreFunctionLoaderA class for loading arbitrary data into the XML parser's DataMap
protocols::jd2::parser::ScoreFunctionLoaderCreator
core::import_pose::atom_tree_diffs::ScoreLessThanComparatorProvides a StrictWeakOrdering comparator for sorting elements of a ScoresMap by one particular score type
protocols::jd2::ScoreMap
protocols::simple_moves::ScoreMover
protocols::simple_moves::ScoreMoverCreator
protocols::jd2::ScoreOnlyJobOutputter
protocols::jd2::ScoreOnlyJobOutputterCreator
core::io::raw_data::ScoreStruct
protocols::features::ScoreTypeFeatures
protocols::features::ScoreTypeFeaturesCreatorCreator for the ScoreTypeFeatures class
protocols::protein_interface_design::ScoreTypeFilter
protocols::simple_filters::ScoreTypeFilter
protocols::simple_filters::ScoreTypeFilterCreator
core::scoring::ScoreTypeManager
protocols::qsar::scoring_grid::ScoringGridLoaderA class for loading ScoringGrids into the XML parser's DataMap
protocols::qsar::scoring_grid::ScoringGridLoaderCreator
core::scoring::ScoringManager
core::sequence::ScoringScheme
core::sequence::ScoringSchemeFactory
protocols::match::downstream::ScoringSecMatchRPE
core::chemical::sdf::SDFParser
protocols::match::downstream::SecMatchEvaluatorFactoryCollection of functions making a single score_function
protocols::match::downstream::SecMatchResiduePairEvaluatorBase for class used by secondary matcher to determine whether a given residue to be matched interacts satisfactorily with a target residue
protocols::frag_picker::scores::SecondaryIdentitySequenceIdentity score counts how many residues share the same secondary structure
protocols::match::downstream::SecondaryMatcherToDownstreamResidueA class for an algorithm. Given a conformation of the downstream partner, the algorithm is responsible for producing a set of hits
protocols::match::downstream::SecondaryMatcherToUpstreamResidueA class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits
protocols::enzdes::SecondaryMatchProtocol
protocols::match::downstream::SecondaryMatchUpstreamResProcessorA simple class to respond to the UpstreamBuilder's process_hit method and pass on the coordinates to its "owning" SecondaryMatcherToUpstreamResidue object
protocols::frag_picker::scores::SecondarySimilarityScores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms
If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster
core::fragment::SecondaryStructureTiny 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,
core::scoring::methods::SecondaryStructureEnergy
core::scoring::methods::SecondaryStructureEnergyCreator
protocols::fldsgn::filters::SecondaryStructureFilter
protocols::fldsgn::filters::SecondaryStructureFilterCreator
protocols::match::SecondaryStructureMPMRemoves positions at which the pose does not have the desired secondary structure
protocols::frag_picker::quota::SecondaryStructurePoolSingle pool used by quota selector
core::scoring::SecondaryStructurePotentialSecondary structure scoring cut from classic rosetta structure.h/structure.cc
core::scoring::SecondaryStructureWeightsHolds weights and flags for configuring a SecondaryStructureEnergy evaluation
core::fragment::picking_old::vall::gen::SecStructGenGenerator that requires fragments to have a specific secondary structure string
core::fragment::SecstructSRFD
protocols::seeded_abinitio::SeedFoldTree
protocols::seeded_abinitio::SeedFoldTreeCreator
protocols::seeded_abinitio::SeedSetupMover
protocols::seeded_abinitio::SeedSetupMoverCreator
protocols::forge::remodel::Segment
protocols::forge::build::SegmentInsertInsert an external segment flanked by new regions
protocols::forge::build::SegmentRebuildInstruction to rebuild a segment
protocols::forge::build::SegmentSwapInstruction to swap a segment with an external segment
core::scoring::SelectedResPredicate
protocols::simple_filters::SelectGdtEvaluator
protocols::simple_filters::SelectMaxsubEvaluator
core::chemical::Selector_AADoes the residue belong to ANY of these AAs?
core::chemical::Selector_CMDFLAGIs a certain string in the command-line option -chemical:allow_patch present ? this selector does actually not depend on the residuetype it is queried for
core::chemical::Selector_MATCH_VARIANTSDoes the residue have ALL of the variant types and no more
core::chemical::Selector_NAME1Does the residue belong to ANY of these AAs?
core::chemical::Selector_NAME3Does the residue have to ANY of these three-letter codes?
core::chemical::Selector_NO_VARIANTSDoes the residue have ANY of variant types?
core::chemical::Selector_PROPERTYDoes the residue have ANY of these properties?
core::chemical::Selector_VARIANT_TYPEDoes the residue have ANY of variant types?
protocols::simple_filters::SelectRDC_Evaluator
protocols::toolbox::SelectResiduesByLayer
protocols::simple_filters::SelectRmsdEvaluator
protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >This class is meant to represent the non-rotameric chi observed in several amino acids (asn, asp, gln, glu, his, phe, trp, tyr ) which are rotameric for the chi closest to the backbone and non rotameric for exactly one chi angle. This non-rotameric chi (abv. nrchi) is the last chi for each of these 8 amino acids except tyrosine, where this chi is the last heavy-atom chi. The last chi on tyrosine governs a hydroxyl. Unlike in the fully rotameric residues, the last heavyatom chi in semi-rotameric residues do not "communicate" to the rotameric chi. That is, in the rotameric chi, the mean chi1 value is sensitive to the chi3 value. If the third diherdal switches from trans to g+, then chi1 would shift in response. Changes to the non-rotameric chi do not effect the rotameric chi. The data structure here is good for this model but no other
protocols::dna::SeparateDnaFromNonDna
protocols::dna::SeparateDnaFromNonDnaCreator
protocols::toolbox::task_operations::SeqprofConsensusOperation
protocols::toolbox::task_operations::SeqprofConsensusOperationCreator
core::sequence::Sequence
core::sequence::SequenceAlignment
core::sequence::SequenceAlignmentHasher
protocols::topology_broker::SequenceClaim
protocols::topology_broker::SequenceClaimer
protocols::toolbox::pose_metric_calculators::SequenceComparison
core::sequence::SequenceCoupling
protocols::constraints_additional::SequenceCoupling1BDConstraint
protocols::constraints_additional::SequenceCoupling1BDConstraintCreatorMover creator for the SequenceCoupling1BDconstraint
protocols::constraints_additional::SequenceCouplingConstraint
protocols::constraints_additional::SequenceCouplingConstraintCreatorMover creator for the SequenceCouplingconstraint
core::sequence::SequenceCouplingCreator
core::sequence::SequenceCreatorAbstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class
core::scoring::methods::SequenceDependentRefEnergy
core::scoring::methods::SequenceDependentRefEnergyCreator
core::sequence::SequenceFactory
protocols::frag_picker::scores::SequenceIdentitySequenceIdentity score counts identical residues
core::id::SequenceMapping
protocols::moves::SequenceMoverA Mover that iterates through a vector of Movers, applying each one sequentially
core::sequence::SequenceProfile
core::scoring::constraints::SequenceProfileConstraint
core::scoring::constraints::SequenceProfileConstraintCreatorConstraint creator for the SequenceProfileConstraint constraint
core::sequence::SequenceProfileCreator
protocols::simple_moves::SequenceProfileMover
protocols::simple_moves::SequenceProfileMoverCreator
protocols::protein_interface_design::filters::SequenceRecoveryFilter
protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator
core::sequence::SequenceRegistrator< T >This templated class will register an instance of an SequenceCreator (class T) with the SequenceFactory. It will ensure that no SequenceCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
protocols::rbsegment_relax::SequenceShiftMover
protocols::simple_moves::symmetry::SequentialSymmetrySlider
protocols::loops::SerializedLoop
protocols::fldsgn::potentials::SetAACompositionPotential
protocols::fldsgn::potentials::SetAACompositionPotentialCreator
core::chemical::SetAtomicChargeSet an atom's charge
protocols::protein_interface_design::movers::SetAtomTreeMover that sets a user-defined atom tree
protocols::protein_interface_design::movers::SetAtomTreeCreator
core::chemical::SetAtomTypeSet atom's chemical type
core::chemical::SetBackboneHeavyatomSet an atom as backbone heavy atom
protocols::enzdes::SetCatalyticResPackBehaviorQueries the pose cst cache for the catalytic residues, and sets the behavior for them as specified in the cstfile
protocols::enzdes::SetCatalyticResPackBehaviorCreator
core::chemical::SetICoorSet an atom's AtomICoord
core::chemical::SetIO_StringSet atom's chemical type
core::chemical::SetMMAtomTypeSet atom's MM chemical type
core::chemical::SetPolymerConnectAtomSet an atom as polymer connection
protocols::simple_moves::SetReturningPackRotamersMover
core::pack::task::operation::SetRotamerCouplings
core::pack::task::operation::SetRotamerCouplingsCreator
core::pack::task::operation::SetRotamerLinks
core::pack::task::operation::SetRotamerLinksCreator
protocols::fldsgn::potentials::SetSecStructEnergies
protocols::fldsgn::potentials::SetSecStructEnergiesCreator
protocols::protein_interface_design::movers::SetTemperatureFactorSet 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
protocols::protein_interface_design::movers::SetTemperatureFactorCreator
protocols::simple_moves::SetTorsionA mover to change one torsion angle
protocols::simple_moves::SetTorsionCreator
protocols::electron_density::SetupForDensityScoringMover
protocols::electron_density::SetupForDensityScoringMoverCreator
protocols::fibril::SetupForFibrilMover
protocols::simple_moves::symmetry::SetupForSymmetryMover
protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator
protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator
protocols::simple_moves::symmetry::SetupNCSMover
protocols::simple_moves::symmetry::SetupNCSMoverCreator
protocols::toolbox::SF_Replica
core::scoring::disulfides::SG_Dist_Func
core::scoring::disulfides::SGSG_Dihedral_Func
protocols::simple_moves::ShakeStructureMover
core::scoring::sc::ShapeComplementarityCalculator
core::scoring::sc::ShapeComplementarityCalculatorException
protocols::simple_filters::ShapeComplementarityFilter
protocols::simple_filters::ShapeComplementarityFilterCreator
core::io::silent::SharedSilentData
protocols::simple_moves::ShearMoverA 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
protocols::simple_moves::ShearMoverCreator
protocols::fldsgn::topology::Sheet
protocols::jumping::SheetBuilderSelect jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++
protocols::fldsgn::SheetConstraintsRCG
protocols::simple_filters::SheetFilter
protocols::fldsgn::topology::SheetFoldTypeManager
protocols::fldsgn::topology::SheetSet
protocols::fldsgn::filters::SheetTopologyFilter
protocols::fldsgn::filters::SheetTopologyFilterCreator
protocols::nonlocal::SheetTranslate
core::kinematics::ShortestPathInFoldTree
protocols::loops::loop_closure::ccd::ShortLoopClosure
core::scoring::methods::ShortRangeTwoBodyEnergy
Show
protocols::abinitio::ShowViolation
protocols::jd2::ShuffleFileSystemJobDistributor
protocols::frag_picker::SidechainContactDistCutoffDefines sidechain contact distance cutoffs
protocols::simple_moves::sidechain_moves::SidechainMCMoverClass for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator
protocols::canonical_sampling::SidechainMetropolisHastingsMover
protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator
protocols::docking::SidechainMinMover
protocols::simple_moves::sidechain_moves::SidechainMoverClass for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
protocols::simple_moves::sidechain_moves::SidechainMoverBaseClass for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
protocols::simple_moves::sidechain_moves::SidechainMoverCreator
core::pack::scmin::SidechainStateAssignment
core::scoring::constraints::SigmoidFunc
core::scoring::SigmoidWeightedCenList< T >Keep track of the cenlist information stores both centroid counts (T = Real) as well as d_centroid_counts (T = Vector)
core::io::silent::SilentEnergyHelper class for silent-file classes to keep track of energy information
core::io::silent::SilentFileDataAbstract base class for classes that read and write different types of silent-files. Silent-files can contain SilentStruct objects which are expected, to be uniquely identified by some sort of string-based tag inside the file
protocols::jd2::SilentFileJobInputter
protocols::jd2::SilentFileJobInputterCreator
protocols::jd2::SilentFileJobOutputter
protocols::jd2::SilentFileJobOutputterCreator
core::import_pose::pose_stream::SilentFilePoseInputStream
protocols::viewer::SilentObserver
core::io::silent::SilentStruct
core::io::silent::SilentStructCreatorAbstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class
core::io::silent::SilentStructFactory
core::io::silent::SilentStructRegistrator< T >This templated class will register an instance of an SilentStructCreator (class T) with the SilentStructFactory. It will ensure that no SilentStructCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
protocols::wum::SilentStructStore
protocols::canonical_sampling::SilentTrajectoryRecorder
protocols::canonical_sampling::SilentTrajectoryRecorderCreator
protocols::swa::rna::SillyCountStruct
core::pack::annealer::SimAnnealerBase
SimpleAssociates fragment indices with Gunn scores
core::optimization::SimpleDerivCheckResult
core::pack::interaction_graph::SimpleEdge
core::pack::interaction_graph::SimpleInteractionGraphA simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver
core::pack::interaction_graph::SimpleNode
core::scoring::packstat::SimplePDB
core::scoring::packstat::SimplePDB_Atom
core::sequence::SimpleScoringScheme
core::sequence::SimpleSequenceCreator
core::io::silent::SimpleSequenceData
protocols::nonlocal::SimpleTreeBuilder
protocols::canonical_sampling::SimulatedTempering
protocols::canonical_sampling::SimulatedTemperingCreator
protocols::match::output::SingleDownstreamResidueWriterClass for writing conformations of the downstream partner in a kinemage description
protocols::jd2::SingleFileBuffer
protocols::nonlocal::SingleFragmentMover
protocols::nonlocal::SingleFragmentMoverCreator
core::pack::dunbrack::SingleLigandRotamerLibraryA fixed library of conformations for some residue type (doesn't have to be a ligand)
protocols::motifs::SingleMotif
core::pack::dunbrack::SingleResidueDunbrackLibrary
core::fragment::SingleResidueFragDataBase class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position
core::optimization::SingleResidueMultifuncA streamlined AtomTreeMultifunc designed specifically for RTMIN
core::pack::dunbrack::SingleResidueRotamerLibrary
protocols::frags::SingleResidueTorsionFragmentLibraryClass for collection of fragments for a single residue position
protocols::multistate_design::SingleState
protocols::multistate_design::SingleStateEntityData
protocols::multistate_design::SingleStateFitnessFunction
protocols::optimize_weights::SingleStructureData
protocols::evaluation::SingleValuePoseEvaluator< T >
core::scoring::saxs::SinXOverX
core::scoring::constraints::SiteConstraint
core::scoring::constraints::SiteConstraintCreatorMover creator for the SiteConstraint constraint
core::scoring::constraints::SkipViolFunc
core::scoring::packstat::Slice
protocols::swa::rna::SlicedPoseJobParameters
protocols::surface_docking::SlideIntoSurface
protocols::ligand_docking::SlideTogether
protocols::ligand_docking::SlideTogetherCreator
protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
core::scoring::SmallAtNb
protocols::topology_broker::weights::SmallFragWeight
protocols::simple_moves::SmallMoverA 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
protocols::simple_moves::SmallMoverCreator
core::scoring::methods::SmoothCenPairEnergy
core::scoring::methods::SmoothCenPairEnergyCreator
core::scoring::methods::SmoothEnvEnergy
core::scoring::methods::SmoothEnvEnergyCreator
core::scoring::SmoothEnvPairPotential
protocols::simple_moves::SmoothFragmentMover
protocols::topology_broker::weights::SmoothFragWeight
protocols::nonlocal::SmoothPolicy
core::scoring::SmoothScoreTermCoeffs
protocols::simple_moves::SmoothSymmetricFragmentMoverA SymmetricFragmentMover that applies uniform sampling of fragments
core::scoring::constraints::SoedingFuncDerived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation
core::scoring::constraints::SOGFuncDerived class of class Func representing a SOG distribution with a user-specified mean and standard deviation
core::scoring::constraints::SOGFunc_ImplDerived class of class Func representing a SOG distribution with a user-specified mean and standard deviation
protocols::frag_picker::scores::SolventAccessibilityScores a fragment by its predicted solvent accessibility
protocols::wum::sort_SilentStructOPs
protocols::jd2::archive::SortPredicate
protocols::coarse_rna::SourcePositions
core::pack::interaction_graph::SparseMatrixIndex
protocols::sparta::Sparta
protocols::scoring::methods::SpecialRotamerEnergy
protocols::scoring::methods::SpecialRotamerEnergyCreator
protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
core::pose::datacache::SpecialSegmentsObserverObserver that tracks the fate of a one or more segments (i.e. pose residues) of interest. note: the convention should be that a segment.second marks the end of the segment but is not part of it, i.e. the last position of a segment is segment.second - 1 reason: some peculiar stuff regarding the meaning of length events
protocols::jumping::SpecificGeometryLibrary
core::scoring::packstat::Sphere
protocols::pockets::spherical_coor_triplet
protocols::noesy_assign::CrossPeak::SpinSingle dimension of a multidimensional peak, stores putative assignments as indices into Resonance table
protocols::protein_interface_design::movers::SpinMover
protocols::protein_interface_design::movers::SpinMoverCreator
core::scoring::constraints::SplineFunc
core::scoring::constraints::SquareWellFunc
protocols::relax::SRelaxPose
protocols::fldsgn::topology::SS_Base
core::scoring::SS_Info
protocols::fldsgn::topology::SS_Info2
core::scoring::SS_Killhairpins_Info
protocols::comparative_modeling::features::SSFeature
protocols::fldsgn::potentials::sspot::SSPairPotentialSecondary structure scoring cut from classic rosetta structure.h/structure.cc
protocols::abinitio::Stage1Sampler
protocols::jumping::StandardDisulfPairingLibrary
protocols::jumping::StandardPairingLibrary
protocols::star::StarAbinitio
protocols::ligand_docking::StartFrom
protocols::ligand_docking::StartFromCreator
protocols::nonlocal::StarTreeBuilder
protocols::topology_broker::StartStructClaimer
protocols::match::output::StateAccumulatingMatchFilter
protocols::comparative_modeling::StealLigandMover
protocols::comparative_modeling::StealSideChainsMover
protocols::swa::protein::StepWiseBetaAntiParallelJumpSampleGenerator
protocols::swa::StepWiseClusterer
protocols::swa::StepWiseCombineSampleGenerator
protocols::swa::StepWiseDoNothingSampleGenerator
protocols::swa::StepWiseFilterer
protocols::swa::StepWiseIdentitySampleGenerator
protocols::swa::StepWiseJobParameters
protocols::swa::StepWisePoseCombineSampleGenerator
protocols::swa::StepWisePoseSampleGenerator
protocols::swa::StepWisePoseSetup
protocols::swa::protein::StepWiseProteinCCD_Closer
protocols::swa::protein::StepWiseProteinFilterer
protocols::swa::protein::StepWiseProteinFragmentSampleGenerator
protocols::swa::protein::StepWiseProteinJumpSampleGenerator
protocols::swa::protein::StepWiseProteinLoopBridger
protocols::swa::protein::StepWiseProteinMainChainSampleGenerator
protocols::swa::protein::StepWiseProteinPacker
protocols::swa::protein::StepWiseProteinPoseMinimizer
protocols::swa::protein::StepWiseProteinPoseSetup
protocols::swa::protein::StepWiseProteinResidueSampler
protocols::swa::protein::StepWiseProteinScreener
protocols::swa::StepWiseResidueSampler
protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
protocols::swa::rna::StepWiseRNA_Clusterer
protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
protocols::swa::rna::StepWiseRNA_JobParameters
protocols::swa::rna::StepWiseRNA_JobParameters_Setup
protocols::swa::rna::StepWiseRNA_Minimizer
protocols::swa::rna::StepWiseRNA_PoseSetup
protocols::swa::rna::StepWiseRNA_ResidueSampler
protocols::swa::rna::StepWiseRNA_RotamerGenerator
protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
protocols::swa::StepWiseScreener
protocols::filters::StochasticFilter
protocols::filters::StochasticFilterCreator
protocols::fldsgn::topology::Strand
protocols::abinitio::StrandConstraints
protocols::fldsgn::topology::StrandPairing
core::scoring::dssp::StrandPairing
core::scoring::dssp::StrandPairingSet
protocols::fldsgn::topology::StrandPairingSet
core::scoring::Strands
protocols::rbsegment_relax::StrandTwistingMover
core::optimization::StrongWolfeLineMinimization
protocols::simple_filters::StructuralSimilarityEvaluator
core::pose::metrics::StructureDependentCalculator
protocols::noesy_assign::StructureDependentPeakCalibrator
protocols::features::StructureFeatures
protocols::features::StructureFeaturesCreatorCreator for the StructureFeatures class
protocols::pack_daemon::StructureFileNames
protocols::noesy_assign::StructureIndependentPeakCalibrator
protocols::moves::StructureRestrictor
protocols::features::StructureScoresFeatures
protocols::features::StructureScoresFeaturesCreatorCreator for the StructureScoresFeatures class
protocols::simple_filters::StructureSimilarityEvaluatorCreatorCreator for the StructureSimilarityEvaluatorCreator class
protocols::abinitio::StructureStore
core::kinematics::StubStub class -- an object of orthogonal coordinate frame
core::id::StubID
protocols::protein_interface_design::filters::StubScoreFilter
protocols::protein_interface_design::filters::StubScoreFilterCreator
protocols::protein_interface_design::movers::SubroutineMover
protocols::protein_interface_design::movers::SubroutineMoverCreator
core::scoring::methods::SuckerEnergy
core::scoring::methods::SuckerEnergyCreator
protocols::topology_broker::SuggestValueMessage
core::scoring::constraints::SumFunc
protocols::simple_moves::SuperimposeMover
core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode)
core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it
protocols::toolbox::pose_metric_calculators::SurfaceCalculator
protocols::surface_docking::SurfaceDockingProtocol
core::pack::interaction_graph::SurfaceEdge< V, E, G >Defines a Surface edge which will be used in determining surface energy
core::scoring::solid_surface::SurfaceEnergies
core::pack::interaction_graph::SurfaceEnergyDefines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms
core::pack::interaction_graph::SurfaceEnergyCreator
core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >Defines the interaction graph that will keep track of changes to the surface score
core::pack::interaction_graph::SurfaceNode< V, E, G >Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph
protocols::surface_docking::SurfaceOrientMover
protocols::surface_docking::SurfaceParameters
core::pack::interaction_graph::SurfacePotential
core::scoring::packing::SurfEnergy
core::scoring::packing::SurfEnergyCreator
core::scoring::packing::SurfVol
core::scoring::packing::SurfVolDeriv
core::scoring::packing::SurfVolEnergy
core::scoring::packing::SurfVolEnergyCreator
protocols::pack_daemon::SurrogateVariableExpressionStores 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)
core::sequence::SWAligner
protocols::seeded_abinitio::SwapSegment
protocols::seeded_abinitio::SwapSegmentCreator
protocols::simple_moves::SwitchResidueTypeSetMoverA mover that switches a pose between residue type sets (e.g. centroid and fullatom)
protocols::simple_moves::SwitchResidueTypeSetMoverCreator
core::optimization::symmetry::SymAtomTreeMinimizerHigh-level atom tree minimizer class
core::optimization::symmetry::SymAtomTreeMultifuncAtom tree multifunction class
protocols::symmetric_docking::SymDockBaseProtocol
protocols::symmetric_docking::SymDockingHiRes
protocols::simple_moves::symmetry::SymDockingInitialPerturbation
protocols::symmetric_docking::SymDockingLowRes
protocols::simple_moves::symmetry::SymDockingSlideIntoContactContrary to the name, slides things apart first, then together
protocols::symmetric_docking::SymDockProtocol
core::conformation::symmetry::SymDof
core::scoring::sym_e::symECreator
core::scoring::sym_e::symEnergy
protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover
protocols::symmetric_docking::SymFoldandDockRbTrialMover
protocols::symmetric_docking::SymFoldandDockSlideTrialMover
protocols::symmetric_docking::SymInterfaceSidechainMinMover
core::conformation::symmetry::SymmData
core::conformation::symmetry::SymmDataFactory
core::conformation::symmetry::SymmetricConformationA symmetric conformation: has an additional data member "SymmetryInfo" class
core::scoring::symmetry::SymmetricEnergies
protocols::simple_moves::SymmetricFragmentMoverA SymmetricFragmentMover that applies uniform sampling of fragments
core::scoring::methods::SymmetricLigandEnergy
core::scoring::methods::SymmetricLigandEnergyCreator
protocols::simple_filters::SymmetricRmsdEvaluator
protocols::simple_moves::symmetry::SymmetricRMSMover
core::pack::rotamer_set::symmetry::SymmetricRotamerSet_Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" -- the rotamer present on the input pose before packing began. symmetrical version of RotamerSet_
core::pack::rotamer_set::symmetry::SymmetricRotamerSetFactory
core::pack::rotamer_set::symmetry::SymmetricRotamerSets
core::scoring::symmetry::SymmetricScoreFunction
core::conformation::symmetry::SymmetryInfo
protocols::simple_moves::symmetry::SymmetrySlider
core::optimization::symmetry::SymMinimizerMapAtom tree multifunction class
protocols::simple_moves::symmetry::SymMinMover
protocols::simple_moves::symmetry::SymMinMoverCreator
protocols::simple_moves::symmetry::SymPackRotamersMover
protocols::simple_moves::symmetry::SymPackRotamersMoverCreator
protocols::symmetric_docking::SymRestrictTaskForDocking
protocols::simple_moves::symmetry::SymRotamerTrialsMover
protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator
protocols::simple_moves::symmetry::SymShakeStructureMover
protocols::symmetric_docking::SymSidechainMinMover
core::conformation::symmetry::SymSlideInfo
protocols::simple_moves::TailsScoreMover
protocols::frag_picker::scores::TalosSSSimilarityScores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms
If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster
core::pack::task::TARGETTARGET flags the position as "targeted", and can optionally specify a "targeted" type
protocols::match::downstream::TargetRotamerCoords
protocols::protein_interface_design::movers::TaskAwareCstsApplies csts (currently only coordinate csts) to every designable position in pose according to taskoperations
protocols::protein_interface_design::movers::TaskAwareCstsCreator
protocols::simple_moves::TaskAwareMinMover
protocols::simple_moves::TaskAwareMinMoverCreator
core::pack::task::TaskFactoryFactory class for the creation and initialization of PackerTask objects
core::pack::task::operation::TaskOperation
core::pack::task::operation::TaskOperationCreatorThe TaskOperationCreator class's responsibilities are to create on demand a new TaskOperation class. The TaskOperationCreator must register itself with the TaskOperationFactory at load time (before main() begins) so that the TaskOperationFactory is ready to start creating TaskOperations by the time any protocol requests one
core::pack::task::operation::TaskOperationFactory
protocols::jd2::parser::TaskOperationLoaderA class for loading arbitrary data into the XML parser's DataMap
protocols::jd2::parser::TaskOperationLoaderCreator
protocols::match::TaskOperationMPMMpm 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
core::pack::task::operation::TaskOperationRegistrator< T >This templated class will register an instance of an TaskOperationCreator (class T) with the TaskOperationFactory. It will ensure that no TaskOperation creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place
protocols::canonical_sampling::TemperatureController
protocols::docking::TemperedDockingAllows docking using simulated or parallel tempering
protocols::docking::TemperedDockingCreator
protocols::canonical_sampling::TemperingBase
protocols::abinitio::Template
protocols::topology_broker::TemplateFragmentClaimerHacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates
protocols::comparative_modeling::hybridize::TemplateHistory
protocols::topology_broker::TemplateJumpClaimerHacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates
protocols::abinitio::TemplateJumpSetup
protocols::abinitio::Templates
core::scoring::TenANeighborEdge
core::scoring::TenANeighborGraph
core::scoring::TenANeighborNode
protocols::scoring::methods::pcs::TensorsOptimizer
protocols::scoring::methods::pcs2::TensorsOptimizer
protocols::scoring::methods::pcs2::TensorsOptimizerFix
protocols::scoring::methods::pcs2::TensorsOptimizerSvd
protocols::simple_filters::TerminusDistanceFilter
protocols::protein_interface_design::TerminusDistanceFilter
protocols::simple_filters::TerminusDistanceFilterCreator
protocols::ligand_docking::TetherLigand
protocols::canonical_sampling::ThermodynamicMover
protocols::canonical_sampling::ThermodynamicObserver
protocols::comparative_modeling::ThreadingJob
protocols::comparative_modeling::ThreadingJobInputter
protocols::comparative_modeling::ThreadingJobInputterCreator
protocols::comparative_modeling::ThreadingMover
protocols::toolbox::task_operations::ThreadSequenceOperation
protocols::toolbox::task_operations::ThreadSequenceOperationCreator
protocols::evaluation::TimeEvaluator
protocols::filters::TimeFilter
protocols::filters::TimeFilterCreator
protocols::checkpoint::Timer: singleton checkpoint timer class
protocols::features::TopCountOfAllInputs
protocols::features::TopCountOfEachInput
protocols::topology_broker::TopologyBroker
protocols::topology_broker::TopologyClaimer
protocols::topology_broker::TopologyClaimerFactoryA 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
core::scoring::constraints::TopOutFunc
protocols::features::TopPercentOfAllInputs
protocols::features::TopPercentOfEachInput
protocols::protein_interface_design::filters::Torsion
protocols::swa::rna::Torsion_Info
protocols::frag_picker::TorsionBinIO
protocols::frag_picker::quota::TorsionBinPoolSingle pool used by quota selector
protocols::frag_picker::scores::TorsionBinSimilarityScores a fragment by torsion bin similarity
protocols::protein_interface_design::filters::TorsionCreator
core::scoring::methods::TorsionDatabase
protocols::simple_moves::TorsionDOFMoverTODO: De-duplicate shared code from RotateJumpAxisMover (angle picking code)
protocols::comparative_modeling::features::TorsionFeature
protocols::frags::TorsionFragmentClass for single piece of torsion fragment
protocols::frags::TorsionFragmentLibraryClass for classic Rosetta fragment library
core::id::TorsionID
core::id::TorsionID_RangeKinematics DOF identifier (with range) class
core::fragment::TorsionInfoSet
protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturberTorsion sampling kinematic perturber
protocols::rna::TorsionSet
protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturberWARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber
core::scoring::packstat::trace
protocols::canonical_sampling::TrajectoryRecorder
protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
protocols::ligand_docking::Transform
protocols::ligand_docking::Transform_info
protocols::protein_interface_design::Transformation
Transformation
protocols::ligand_docking::TransformCreator
protocols::ligand_docking::Translate
protocols::ligand_docking::Translate_info
protocols::ligand_docking::TranslateCreator
core::coarse::Translator
core::coarse::TranslatorSet
protocols::nonlocal::TreeBuilder
protocols::nonlocal::TreeBuilderFactory
Trial
protocols::moves::TrialCounter
protocols::canonical_sampling::TrialCounterObserver
protocols::canonical_sampling::TrialCounterObserverCreator
protocols::moves::TrialMoverA TrialMover applies a Mover and then accepts or rejects the move according to a MonteCarlo object
protocols::viewer::triangle
protocols::viewer::triangleIterator
core::scoring::trie::TrieCollection
core::scoring::etable::etrie::TrieCountPair1BC3
core::scoring::etable::etrie::TrieCountPair1BC4
core::scoring::etable::etrie::TrieCountPairAll
core::scoring::trie::TrieCountPairBase
core::scoring::etable::etrie::TrieCountPairGeneric
core::scoring::etable::etrie::TrieCountPairNone
core::scoring::trie::TrieNode< AT, CPDATA >
protocols::filters::TrueFilter
protocols::filters::TrueFilterCreator
protocols::simple_filters::TruncatedScoreEvaluator
protocols::protein_interface_design::movers::TryRotamers
protocols::protein_interface_design::movers::TryRotamersCreator
core::scoring::TwelveANeighborEdge
core::scoring::TwelveANeighborGraph
core::scoring::TwelveANeighborNode
core::scoring::methods::TwoBodyEnergy
protocols::ub_e2c::ubi_e2c_modeler
protocols::moves::UDPSocketClientPyMolMover helper class. Handle low level UDP transactions stuff. This is a port of original Python version of UDP socket client written writen for PyRosetta
core::graph::UEEdge< V, E >
core::graph::UEVertex< V, E >
unary_function
UnaryExpression
core::pack::rotamer_set::UnboundRotamersOperationAdds in rotamers from the "unbound" or native structure(s), pulled from one or more PDBs supplied on the command line
protocols::ligand_docking::UnconstrainedTorsionsMoverJuggles torsional constraints with packing or rotamer trials
core::scoring::methods::UnfoldedStateEnergy
protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor
protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
core::scoring::methods::UnfoldedStateEnergyCreator
core::scoring::UnfoldedStatePotential
protocols::nonlocal::UniformPolicy
protocols::rigid::UniformSphereTransMoverRigid-body move that evenly samples the space within a sphere
boost::unordered_object_pool< T, UserAllocator >
core::pose::UnrecognizedAtomRecordInfo about an atom in a unrecognized res (not in pose, but we want to remember it)
core::fragment::UpJumpSRFD
core::graph::UpperEdgeGraph< V, E >
protocols::match::upstream_hit
protocols::match::upstream::UpstreamBuilder
protocols::match::output::UpstreamCollisionFilterThis 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
protocols::match::output::UpstreamDownstreamCollisionFilterThis class is used to detect collisions between upstream residues and downstream poses
protocols::match::output::UpstreamHitCacher
protocols::match::upstream::UpstreamResidueProcessor
protocols::match::upstream::UpstreamResTypeGeometryA 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
protocols::match::downstream::us_secmatch_hit_compareA 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
core::pack::task::USE_INPUT_SCUSE_INPUT_SC turns on inclusion of the current rotamer for the packer
protocols::simple_moves::UserDefinedGroupDiscriminator
V
core::chemical::sdf::V2Parser
core::chemical::sdf::V3Parser
protocols::frag_picker::VallChunkChunk of residues extracted from a vall
protocols::frag_picker::VallChunkFilterBase class for a chunk filtering mechanism
protocols::frags::VallData
core::fragment::picking_old::vall::eval::VallFragmentEvalBase class for Vall ExtentEvaluator
core::fragment::picking_old::vall::gen::VallFragmentGenBase class Vall ExtentGenerator
core::fragment::picking_old::vall::scores::VallFragmentScoreBase Vall FragmentScore struct
core::fragment::picking_old::vall::VallLibrarianLibrarian that picks fragments from the Vall
core::fragment::picking_old::vall::VallLibraryVall fragment library
protocols::frag_picker::VallProviderVector of vall chunks
core::fragment::picking_old::vall::VallResidueClass for managing a line of the Vall fragment library
protocols::frag_picker::VallResidueClass for managing a line of the Vall fragment library
core::fragment::picking_old::vall::VallResiduesWrapper for a collection of VallResidue
core::fragment::picking_old::vall::VallSectionClass implementing the Book concept for a continuous section of lines in the Vall library
core::fragment::picking_old::vall::VallSectionsWrapper for a collection of VallSection
protocols::enzdes::ValueEvaluatorTiny helper struct for EnzdesScoreFileFilter
VariableExpression
protocols::pack_daemon::VariableVectorExpression
protocols::forge::components::VarLengthBuildComponent that performs a protocol for user-specified variable length remodeling of protein backbone segments
core::scoring::methods::VDW_Energy
core::scoring::methods::VDW_EnergyCreator
protocols::swa::rna::VDW_RepScreeninfo
protocols::qsar::scoring_grid::VdwGrid
protocols::qsar::scoring_grid::VdwGridCreator
protocols::genetic_algorithm::Vec1Hash
utility::vector0
utility::vector1
core::fragment::VectorCacheUnit< T >
protocols::pack_daemon::VectorExpression
protocols::pack_daemon::VectorExpressionCreator
protocols::pack_daemon::VectorFunction
protocols::pack_daemon::VectorFunction2
utility::vectorL
protocols::vip::VIP_Mover
protocols::vip::VIP_Report
core::conformation::symmetry::VirtualCoordinate
core::conformation::symmetry::VirtualCoordinates
protocols::protein_interface_design::movers::VLBUser interface for YAB's Variable Length Build
protocols::protein_interface_design::movers::VLBCreator
protocols::pack_daemon::VMax
protocols::pack_daemon::VMaxByTake 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
protocols::pack_daemon::VMin
protocols::pack_daemon::VMinByTake 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
protocols::match::VoxelSetIteratorHelper class for the OccupiedSpaceHasher which manages the logic for how to iterate across the 64 voxels that each 6-D point covers
core::scoring::methods::WaterAdductHBondEnergy
core::scoring::methods::WaterAdductHBondEnergyCreator
core::scoring::WaterAdductHBondPotential
core::scoring::methods::WaterAdductIntraEnergy
core::scoring::methods::WaterAdductIntraEnergyCreator
core::pack::rotamer_set::WaterAnchorInfo
core::scoring::methods::WaterBuilder
core::pack::rotamer_set::WaterPackingInfo
core::scoring::geometric_solvation::WaterWeightGridSet
core::conformation::WatsonCrickResidueMatcher
protocols::dna::WatsonCrickRotamerCouplings
protocols::dna::WatsonCrickRotamerCouplingsCreator
core::scoring::hackelec::weight_triple
protocols::comparative_modeling::hybridize::WeightedFragmentTrialMover
protocols::optimize_weights::WeightRangeConstraint
protocols::moves::WhileMover
protocols::rigid::WholeBodyRotationMoverRotate the whole pose
protocols::rigid::WholeBodyTranslationMoverTranslate the whole pose
core::scoring::methods::WholeStructureEnergyBase class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation
core::scoring::etable::WholeWholeEnergyInvoker< Derived >
WidgetFactory
WidgetRegistrator
protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
protocols::simple_moves::WobbleMoverA protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: ----lfff bbb---- f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: ---bbb fffl--- the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment()
protocols::forge::remodel::WorkingRemodelSet
protocols::relax::WorkUnit_BatchRelax
protocols::relax::WorkUnit_BatchRelax_and_PostRescore
protocols::loophash::WorkUnit_LoopHash
protocols::wum::WorkUnit_MoverWrapperThis 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
protocols::wum::WorkUnit_SilentStructStoreThis WorkUnit type has structures in it. Most Workunits should derive from this one rather THe the Base class
protocols::wum::WorkUnit_Wait
protocols::wum::WorkUnitBaseThe base class for all work units
protocols::wum::WorkUnitListWOrkUnitList 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
protocols::wum::WorkUnitManager
protocols::wum::WorkUnitQueue
protocols::wum::WorkUnitQueue_Swapped
protocols::optimize_weights::WrappedOptEExpressionCreator
protocols::optimize_weights::WrapperOptEMultifuncOptE mode multifunction class
protocols::jd2::WriteFileSFB
protocols::match::output::WriteKinemageOutputter
protocols::jd2::WriteOut_MpiFileBuffer
protocols::match::output::WriteUpstreamCoordinateKinemage
protocols::match::output::WriteUpstreamHitKinemage
protocols::wum::WorkUnitBase::WU_HeaderThis structure can contain any non-dynamicly allocated data. Any simple data types can be used here, ints, real, floats, char, etc.
core::scoring::constraints::XYZ_FuncJust a simple class that takes an AtomID and returns a Vector (position)
core::conformation::signals::XYZEventSignals a change in XYZ coordinates in a Conformation
numeric::xyzMatrix
numeric::xyzVector
core::scoring::methods::YHHPlanarityEnergy
core::scoring::methods::YHHPlanarityEnergyCreator
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