- m -

m1_b1_Ktheta() : protocols::branch_angle::BranchParam1
m1_b1_theta0() : protocols::branch_angle::BranchParam1
m1_b2_Ktheta() : protocols::branch_angle::BranchParam2
m1_b2_theta0() : protocols::branch_angle::BranchParam2
m1_m2_Ktheta() : protocols::branch_angle::BranchParam1
m1_m2_theta0() : protocols::branch_angle::BranchParam1
m2_b1_Ktheta() : protocols::branch_angle::BranchParam1
m2_b1_theta0() : protocols::branch_angle::BranchParam1
m2_b2_Ktheta() : protocols::branch_angle::BranchParam2
m2_b2_theta0() : protocols::branch_angle::BranchParam2
magnitude() : protocols::abinitio::abscript::StructPerturberCM
magnitude_rotation() : protocols::rigid::RigidBodyMotionMover
magnitude_translation() : protocols::rigid::RigidBodyMotionMover
main_atom() : protocols::noesy_assign::CrossPeakInfo
main_chain_torsion_set() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
main_chain_torsion_set_lists() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
main_chain_torsion_set_lists_real() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
main_chain_torsion_set_save() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
main_chain_torsion_sets() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
MainChainTorsionSet() : protocols::stepwise::modeler::protein::MainChainTorsionSet
make() : protocols::frag_picker::scores::MakeABEGO_SS_Score , protocols::frag_picker::scores::MakeAmbigCSScore , protocols::frag_picker::scores::MakeAtomPairConstraintsScore , protocols::frag_picker::scores::MakeBFactor , protocols::frag_picker::scores::MakeConstScore , protocols::frag_picker::scores::MakeCSScore , protocols::frag_picker::scores::MakeDihedralConstraintsScore , protocols::frag_picker::scores::MakeDisulfideDistance , protocols::frag_picker::scores::MakeDisulfideIdentity , protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd , protocols::frag_picker::scores::MakeFragmentChunkCrms , protocols::frag_picker::scores::MakeFragmentCrmsd , protocols::frag_picker::scores::MakeFragmentCrmsdResDepth , protocols::frag_picker::scores::MakeFragmentDME , protocols::frag_picker::scores::MakeFragmentScoringMethod , protocols::frag_picker::scores::MakeGunnCostScore , protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity , protocols::frag_picker::scores::MakeHydrophobicitySimilarity , protocols::frag_picker::scores::MakeInterbondAngleScore , protocols::frag_picker::scores::MakeJCoupling , protocols::frag_picker::scores::MakeLAMBEGO_Similarity , protocols::frag_picker::scores::MakeMidPhiOut , protocols::frag_picker::scores::MakeMidPsiOut , protocols::frag_picker::scores::MakePartialSecondarySimilarity , protocols::frag_picker::scores::MakePCS_FragDistance , protocols::frag_picker::scores::MakePhi , protocols::frag_picker::scores::MakePhiPsiRmsd , protocols::frag_picker::scores::MakePhiPsiSquareWell , 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::MakeProlinePhiScore , protocols::frag_picker::scores::MakePsi , protocols::frag_picker::scores::MakeRamaScore , protocols::frag_picker::scores::MakeRDCScore , protocols::frag_picker::scores::MakeScoreEValuator , protocols::frag_picker::scores::MakeSecondaryIdentity , protocols::frag_picker::scores::MakeSecondarySimilarity , protocols::frag_picker::scores::MakeSequenceIdentity , protocols::frag_picker::scores::MakeSolventAccessibility , protocols::frag_picker::scores::MakeTalosSSSimilarity , protocols::frag_picker::scores::MakeTorsionBinSimilarity
make_calculator() : protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
make_chi_move() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
make_claim() : protocols::environment::claims::EnvClaim
make_compatible_with_ROCS_custom_ForceField() : protocols::pockets::GenPharmacophore
make_complete_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
make_constraint_covalent() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
make_constraint_covalent_helper() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
make_disjointed_foldtree() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
make_disulfide() : protocols::forge::remodel::RemodelDesignMover
make_disulfide_fast() : protocols::forge::remodel::RemodelDesignMover
make_dna_sequence_combinations() : protocols::dna::DnaInterfacePacker
make_dockmcm_mover() : protocols::ligand_docking::LigandDockProtocol , protocols::symmetric_docking::SymDockProtocol
make_extended_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
make_fibril() : protocols::topology_broker::FibrilModelingClaimer
make_fragment_moves() : protocols::farna::RNA_Relaxer
make_full_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
make_Hessian_ANM() : protocols::normalmode::NormalMode
make_Hessian_TNM() : protocols::normalmode::NormalMode
make_inner_cycle_from_string_name() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
make_interface_combos() : protocols::features::InterfaceFeatures
make_interface_set() : protocols::analysis::InterfaceAnalyzerMover
make_local_bb_change() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
make_local_bb_change_close_gaps() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
make_local_bb_change_include_cut() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
make_motif_filename() : protocols::motifs::IRCollection
make_move() : protocols::simple_moves::BackboneMover , protocols::simple_moves::BBConRotMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
make_movemap() : protocols::ligand_docking::LigandBaseProtocol
make_movie() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
make_multichain_interface_set() : protocols::analysis::InterfaceAnalyzerMover
make_mutant_structure() : protocols::pmut_scan::PointMutScanDriver
make_mutants() : protocols::pmut_scan::PointMutScanDriver
make_name() : protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
make_new_grid() : protocols::qsar::scoring_grid::GridManager
make_packer_task() : protocols::ligand_docking::HighResDocker , protocols::ligand_docking::LigandBaseProtocol
make_packer_task_from_vector() : protocols::ligand_docking::HighResDocker
make_packer_task_ligand_only() : protocols::ligand_docking::LigandBaseProtocol
make_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
make_pymol_script() : protocols::flxbb::LayerDesignOperation
make_rasmol_format_file() : protocols::toolbox::SelectResiduesByLayer
make_rotwell_jump() : protocols::simple_moves::sidechain_moves::SidechainMover
make_sec() : protocols::hybridization::TMalign
make_separated_pose() : protocols::analysis::InterfaceAnalyzerMover
make_sequence_claim() : protocols::topology_broker::SequenceClaimer
make_sequence_shift() : protocols::loops::Loops
make_sequence_symmetric() : protocols::topology_broker::TopologyBroker
make_simple_ssd_from_pdb() : protocols::optimize_weights::IterativeOptEDriver
make_specific_mutant() : protocols::pmut_scan::PointMutScanDriver
make_strand_neighbor_two() : protocols::fldsgn::topology::StrandPairingSet
make_symmetric_task() : protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover
make_tail() : protocols::simple_moves::TailsScoreMover
make_three_fold_symmetry_90_210_330() : protocols::make_rot_lib::MakeRotLibMover
make_tweaked_scorefxn() : protocols::ligand_docking::LigandBaseProtocol
make_two_fold_symmetry_0_180() : protocols::make_rot_lib::MakeRotLibMover
make_two_fold_symmetry_135_315() : protocols::make_rot_lib::MakeRotLibMover
MakeABEGO_SS_Score() : protocols::frag_picker::scores::MakeABEGO_SS_Score
MakeAmbigCSScore() : protocols::frag_picker::scores::MakeAmbigCSScore
MakeAtomPairConstraintsScore() : protocols::frag_picker::scores::MakeAtomPairConstraintsScore
MakeBFactor() : protocols::frag_picker::scores::MakeBFactor
makebinary() : protocols::sic_dock::XfoxmScore
MakeBundle() : protocols::helical_bundle::MakeBundle
MakeBundleHelix() : protocols::helical_bundle::MakeBundleHelix
MakeConstScore() : protocols::frag_picker::scores::MakeConstScore
MakeCSScore() : protocols::frag_picker::scores::MakeCSScore
MakeDihedralConstraintsScore() : protocols::frag_picker::scores::MakeDihedralConstraintsScore
MakeDisulfideDistance() : protocols::frag_picker::scores::MakeDisulfideDistance
MakeDisulfideIdentity() : protocols::frag_picker::scores::MakeDisulfideIdentity
MakeFragmentAllAtomCrmsd() : protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd
MakeFragmentChunkCrms() : protocols::frag_picker::scores::MakeFragmentChunkCrms
MakeFragmentCrmsd() : protocols::frag_picker::scores::MakeFragmentCrmsd
MakeFragmentCrmsdResDepth() : protocols::frag_picker::scores::MakeFragmentCrmsdResDepth
MakeFragmentDME() : protocols::frag_picker::scores::MakeFragmentDME
MakeFragmentScoringMethod() : protocols::frag_picker::scores::MakeFragmentScoringMethod
MakeGunnCostScore() : protocols::frag_picker::scores::MakeGunnCostScore
MakeHydrophobicityProfileSimilarity() : protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity
MakeHydrophobicitySimilarity() : protocols::frag_picker::scores::MakeHydrophobicitySimilarity
MakeInterbondAngleScore() : protocols::frag_picker::scores::MakeInterbondAngleScore
MakeJCoupling() : protocols::frag_picker::scores::MakeJCoupling
MakeLAMBEGO_Similarity() : protocols::frag_picker::scores::MakeLAMBEGO_Similarity
MakeMidPhiOut() : protocols::frag_picker::scores::MakeMidPhiOut
MakeMidPsiOut() : protocols::frag_picker::scores::MakeMidPsiOut
MakePartialSecondarySimilarity() : protocols::frag_picker::scores::MakePartialSecondarySimilarity
MakePCS_FragDistance() : protocols::frag_picker::scores::MakePCS_FragDistance
MakePhi() : protocols::frag_picker::scores::MakePhi
MakePhiPsiRmsd() : protocols::frag_picker::scores::MakePhiPsiRmsd
MakePhiPsiSquareWell() : protocols::frag_picker::scores::MakePhiPsiSquareWell
MakePolyXMover() : protocols::simple_moves::MakePolyXMover
MakeProfileScore() : protocols::frag_picker::scores::MakeProfileScore
MakeProfileScoreBlosum62() : protocols::frag_picker::scores::MakeProfileScoreBlosum62
MakeProfileScoreDistWeight() : protocols::frag_picker::scores::MakeProfileScoreDistWeight
MakeProfileScoreL1() : protocols::frag_picker::scores::MakeProfileScoreL1
MakeProfileScoreStructL1() : protocols::frag_picker::scores::MakeProfileScoreStructL1
MakeProfileScoreSubMatrix() : protocols::frag_picker::scores::MakeProfileScoreSubMatrix
MakeProlinePhiScore() : protocols::frag_picker::scores::MakeProlinePhiScore
MakePsi() : protocols::frag_picker::scores::MakePsi
MakeRamaScore() : protocols::frag_picker::scores::MakeRamaScore
MakeRDCScore() : protocols::frag_picker::scores::MakeRDCScore
MakeRotLibJob() : protocols::make_rot_lib::MakeRotLibJob
MakeRotLibJobInputter() : protocols::make_rot_lib::MakeRotLibJobInputter
MakeRotLibMover() : protocols::make_rot_lib::MakeRotLibMover
MakeRotLibOptionsData() : protocols::make_rot_lib::MakeRotLibOptionsData
MakeScoreEValuator() : protocols::frag_picker::scores::MakeScoreEValuator
MakeSecondaryIdentity() : protocols::frag_picker::scores::MakeSecondaryIdentity
MakeSecondarySimilarity() : protocols::frag_picker::scores::MakeSecondarySimilarity
MakeSequenceIdentity() : protocols::frag_picker::scores::MakeSequenceIdentity
MakeSolventAccessibility() : protocols::frag_picker::scores::MakeSolventAccessibility
MakeStarTopologyMover() : protocols::rbsegment_relax::MakeStarTopologyMover
MakeTalosSSSimilarity() : protocols::frag_picker::scores::MakeTalosSSSimilarity
MakeTorsionBinSimilarity() : protocols::frag_picker::scores::MakeTorsionBinSimilarity
manager() : protocols::forge::components::VarLengthBuild , protocols::jd2::archive::AbstractArchiveBase
manager_ptr() : protocols::jd2::archive::AbstractArchiveBase
manager_type() : protocols::jd2::JD2ResourceManagerCreator
manipulate_cut_bias() : protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
manual_call() : protocols::loophash::LoopHashRelaxProtocol
manualPackerTaskGen() : protocols::forge::remodel::RemodelWorkingSet
map2keyvector() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
map2target() : protocols::abinitio::Template
map2template() : protocols::abinitio::Template
map_pairing() : protocols::abinitio::Template
map_pairings2target() : protocols::abinitio::Template
map_pairings2template() : protocols::abinitio::Template
map_pdb_info_number() : protocols::hybridization::FoldTreeHybridize
map_ss_segments() : protocols::fldsgn::MatchResidues
mapfile_activated() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
MapHotspot() : protocols::protein_interface_design::movers::MapHotspot
mark() : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
mark_as_cancelled() : protocols::jd2::archive::Batch
mark_as_default() : protocols::kinematic_closure::perturbers::PerturberSet , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::LoopMoverGroup
mark_as_finished() : protocols::jd2::archive::Batch
mark_as_invalid() : protocols::jd2::archive::Batch
mark_as_test_run() : protocols::loop_modeling::LoopProtocol
mark_atom_espGrid_points() : protocols::pockets::ElectrostaticpotentialGrid
mark_buried_solvent_points() : protocols::pockets::ElectrostaticpotentialGrid
mark_current_job_id_for_repetition() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::MSDJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor
mark_designable() : protocols::toolbox::task_operations::DatabaseThread
mark_entity_as_unimportant() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
mark_job_as_bad() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor
mark_job_as_completed() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor
mark_last_entity_as_important() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
mark_leave_as_is() : protocols::toolbox::task_operations::DatabaseThread
mark_loop_moveable() : protocols::forge::remodel::RemodelLoopMover
mark_loops_moveable() : protocols::forge::remodel::RemodelLoopMover
mark_protein_espGrid_points() : protocols::pockets::ElectrostaticpotentialGrid
mark_structure_as_sampled() : protocols::features::StructureFeatures
mark_tags() : protocols::toolbox::KClusterData
markDepth() : protocols::pockets::PocketGrid
markEdgeDepth() : protocols::pockets::PocketGrid
markNativeInterface() : protocols::flexpep_docking::FlexPepDockingProtocol
markOneEdgeDepth() : protocols::pockets::PocketGrid
markPocketDepth() : protocols::pockets::PocketGrid
mask() : protocols::electron_density::SetupForDensityScoringMover
mask_from_offsets() : protocols::match::Bool3DGrid
master() : protocols::match::output::ResidueKinemageWriter , protocols::wum2::WorkUnit
master_add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
master_gather_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
master_get_new_job_id() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
master_go() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
master_job_succeeded() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
master_mark_current_job_id_for_repetition() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
master_rank() : protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
master_remove_bad_inputs_from_job_list() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
master_set_energy_terms() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
master_to_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
master_weight() : protocols::toolbox::pose_metric_calculators::EnergiesData
master_weight_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
Mat3VecMult() : protocols::sparta::PDB
match() : protocols::noesy_assign::Resonance
match2D() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance , protocols::noesy_assign::Resonance
match_dspos1() : protocols::match::match_dspos1
match_groups_dshits() : protocols::match::output::CloudPDBWriter
match_groups_ushits() : protocols::match::output::CloudPDBWriter
match_has_been_output() : protocols::match::MatchOutputTracker
match_possible_for_hit_geometry() : protocols::match::OccupiedSpaceHash
match_processing_successful() : protocols::match::output::MatchProcessor
match_variants() : protocols::environment::ProtectedConformation
MatchCollisionFilter() : protocols::match::output::MatchCollisionFilter
MatchConsolidator() : protocols::match::output::MatchConsolidator
MatchConstraintFileInfo() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
MatchConstraintFileInfoList() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
MatchCounter() : protocols::match::MatchCounter
Matcher() : protocols::match::Matcher
MatcherMover() : protocols::match::MatcherMover
MatcherOutputStats() : protocols::match::MatcherOutputStats
MatcherTask() : protocols::match::MatcherTask
matches() : protocols::topology_broker::ClaimerMessage
MatchFilter() : protocols::match::output::MatchFilter
MatchGrafter() : protocols::metal_interface::MatchGrafter
MatchGrouper() : protocols::match::output::MatchGrouper
MatchOutputter() : protocols::match::output::MatchOutputter
MatchOutputTracker() : protocols::match::MatchOutputTracker
MatchPositionModifier() : protocols::match::MatchPositionModifier
MatchProcessor() : protocols::match::output::MatchProcessor
MatchResidues() : protocols::fldsgn::MatchResidues
MatchResiduesMover() : protocols::fldsgn::MatchResiduesMover
MatchScoreWriter() : protocols::match::output::MatchScoreWriter
MatDesGreedyOptMutationMover() : protocols::matdes::MatDesGreedyOptMutationMover
MatDesPointMutationCalculator() : protocols::matdes::MatDesPointMutationCalculator
matrix() : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
matrix3f_to_xyzMatrix() : protocols::forge::remodel::RemodelGlobalFrame , protocols::simple_filters::RepeatParameterFilter
max_angle() : protocols::simple_filters::AngleToVector
max_angle_disp() : protocols::backrub::BackrubSegment
max_angle_disp_4() : protocols::backrub::BackrubMover
max_angle_disp_7() : protocols::backrub::BackrubMover
max_angle_disp_slope() : protocols::backrub::BackrubMover
max_atoms() : protocols::backrub::BackrubMover
max_bbrms() : protocols::loophash::LoopHashMoverWrapper
max_cache_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
max_cb_cb_dist() : protocols::protein_interface_design::movers::PlacementAuctionMover
max_cycles() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
max_degree() : protocols::sasa_scores::PPoly
max_dist_squared() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
max_distance() : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
max_frag_len() : protocols::frag_picker::FragmentPicker
max_generations() : protocols::genetic_algorithm::GeneticAlgorithmBase
max_inner_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
max_inter_ss_bbrms() : protocols::loophash::LoopHashDiversifier
max_intra_ss_bbrms() : protocols::loophash::LoopHashDiversifier
max_iter() : protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover
max_length() : protocols::antibody::CDRSetOptions , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
max_level_index() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
max_lib_size() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
max_linear_chainbreak() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
max_loop_length() : protocols::features::LoopAnchorFeatures
max_missing_weight() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
max_noe_distance() : protocols::noesy_assign::CrossPeakInfo
max_nstruct() : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashMoverWrapper
max_ntries() : protocols::stepwise::StepWiseSampleAndScreen
max_outgoing_wu_mem() : protocols::wum2::EndPoint
max_path_length() : protocols::simple_filters::AveragePathLengthFilter
max_per_move_torsion_delta_per_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
max_pools() : protocols::frag_picker::QuotaDebug
max_population_size() : protocols::genetic_algorithm::GeneticAlgorithmBase
max_rama_score_increase() : protocols::loops::loop_closure::ccd::RamaCheckBase
max_ref_lib_size() : protocols::mpi_refinement::MPI_Refinement
max_residue_count() : protocols::simple_filters::ResidueCountFilter
max_rms() : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
max_sample_iterations() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
max_samples() : protocols::helical_bundle::BundleGridSampler
max_separation_dist_to_target_atom() : protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
max_seq_sep() : protocols::constraints_additional::MaxSeqSepConstraintSet
max_seq_sep_fudge() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
max_struct() : protocols::simple_moves::CombinePoseMover
max_struct_try() : protocols::simple_moves::CombinePoseMover
max_total_torsion_delta_per_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
max_tries() : protocols::moves::FilterMover
max_tries_multiplier_for_ccd() : protocols::stepwise::options::StepWiseBasicOptions
max_value() : protocols::simple_moves::PSSM2BfactorMover
max_volume_contribution() : protocols::noesy_assign::CrossPeak
maxcycles() : protocols::moves::IteratedConvergenceMover
MaxSeqSepConstraintSet() : protocols::constraints_additional::MaxSeqSepConstraintSet
maxtrials() : protocols::simple_moves::GenericMonteCarloMover
mc() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle
MC() : protocols::moves::DualMonteCarlo
mc() : protocols::moves::TrialMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
mc_accepted() : protocols::moves::MonteCarlo
mc_accepted_string() : protocols::moves::MonteCarlo
mc_accpeted() : protocols::simple_moves::GenericMonteCarloMover
MC_Comb() : protocols::stepwise::sampler::MC_Comb
MC_OneTorsion() : protocols::stepwise::sampler::MC_OneTorsion
mc_ptr() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
MC_StepWiseSampler() : protocols::stepwise::sampler::MC_StepWiseSampler
mcfi() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
mcfi_list() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
mcfi_lists_size() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
mcfis_for_upstream_restype() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
MCShowMover() : protocols::moves::MCShowMover
MDBase() : protocols::md::MDBase
measure_bp_specificities() : protocols::dna::DnaInterfacePacker
measure_rotamer_recovery() : protocols::optimize_weights::IterativeOptEDriver , protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRProtocol
measure_sequence_recovery() : protocols::optimize_weights::IterativeOptEDriver , protocols::toolbox::pose_metric_calculators::SequenceComparison
measure_specificities() : protocols::dna::DnaInterfacePacker
measure_specificity() : protocols::dna::DnaInterfacePacker
MedalExchangeMover() : protocols::medal::MedalExchangeMover
MedalMover() : protocols::medal::MedalMover
median() : protocols::filters::ReplicateFilter
mem_foot_print() : protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMap , protocols::wum::WorkUnitManager , protocols::wum::WorkUnitQueue
mem_footprint() : protocols::relax::SRelaxPose , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
mem_stats() : protocols::wum::WorkUnitQueue
MembraneAbinitio() : protocols::abinitio::MembraneAbinitio
MembraneCenterPerturbationMover() : protocols::rigid::MembraneCenterPerturbationMover
MembraneEmbed_from_pose() : protocols::abinitio::MembraneAbinitio
MembraneJump() : protocols::jumping::MembraneJump
MembraneNormalPerturbationMover() : protocols::rigid::MembraneNormalPerturbationMover
MembranePositionFromTopologyMover() : protocols::membrane::MembranePositionFromTopologyMover
MembraneTopology() : protocols::simple_moves::MembraneTopology
MembraneTopology_from_pose() : protocols::abinitio::MembraneAbinitio
MembraneTopologyClaimer() : protocols::topology_broker::MembraneTopologyClaimer
Memento() : protocols::kinematic_closure::ClosureProblem::Memento
memory_use() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
merge() : protocols::comparative_modeling::AlignmentCluster , protocols::loophash::LoopHashLibrary , protocols::wum::WorkUnitList
merge_bbdb() : protocols::loophash::LoopHashLibrary
merge_protein_surface_poses() : protocols::surface_docking::SurfaceDockingProtocol
MetalloClaimer() : protocols::topology_broker::MetalloClaimer
MetalSiteResidue() : protocols::metal_interface::MetalSiteResidue
MetaPoseEvaluator() : protocols::evaluation::MetaPoseEvaluator
methodname() : protocols::mpi_refinement::Scheduler
methods_picked() : protocols::mpi_refinement::Scheduler
MethylNameLibrary() : protocols::noesy_assign::MethylNameLibrary
MethylNames() : protocols::noesy_assign::MethylNames
metric_value() : protocols::multistate_design::SingleStateEntityData
metric_value_getters() : protocols::multistate_design::MultiStateFitnessFunction
metric_value_map() : protocols::multistate_design::SingleStateEntityData
metric_value_template() : protocols::toolbox::pose_metric_calculators::MetricValueGetter
MetricCalculatorFitnessFunction() : protocols::multistate_design::MetricCalculatorFitnessFunction
MetricRecorder() : protocols::canonical_sampling::MetricRecorder
MetricValueGetter() : protocols::toolbox::pose_metric_calculators::MetricValueGetter
metropolis_hastings_mover() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
MetropolisHastingsMover() : protocols::canonical_sampling::MetropolisHastingsMover
mid_pos() : protocols::fldsgn::topology::SS_Base
middle_res() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
MidPhiOut() : protocols::frag_picker::scores::MidPhiOut
midpoint() : protocols::loops::Loop
MidPsiOut() : protocols::frag_picker::scores::MidPsiOut
min_angle() : protocols::simple_filters::AngleToVector
min_atoms() : protocols::backrub::BackrubMover
min_bb() : protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::DesignRepackMover
min_bb_set() : protocols::simple_moves::DesignRepackMover
min_bbrms() : protocols::loophash::LoopHashMoverWrapper
min_client_rank() : protocols::jd2::MPIFileBufJobDistributor
min_dist() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
min_heap() : protocols::cluster::Exemplar
min_inter_ss_bbrms() : protocols::loophash::LoopHashDiversifier
min_intra_ss_bbrms() : protocols::loophash::LoopHashDiversifier
min_len_helix() : protocols::frags::TorsionFragmentMover
min_len_strand() : protocols::frags::TorsionFragmentMover
min_length() : protocols::antibody::CDRSetOptions , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
min_loop_length() : protocols::features::LoopAnchorFeatures
min_loop_size() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
min_map() : protocols::normalmode::NormalModeMultifunc
min_move() : protocols::abinitio::FoldConstraints
min_neighbor_sc() : protocols::antibody::design::CDRGraftDesignOptions
min_options() : protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
min_rb() : protocols::antibody::design::CDRGraftDesignOptions , protocols::simple_moves::DesignRepackMover
min_rb_set() : protocols::simple_moves::DesignRepackMover
min_residue_count() : protocols::simple_filters::ResidueCountFilter
min_rms() : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
min_sc() : protocols::antibody::design::CDRGraftDesignOptions , protocols::simple_moves::DesignRepackMover
min_sc_set() : protocols::simple_moves::DesignRepackMover
min_seq_sep() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
min_seq_separation_residue_assignment() : protocols::noesy_assign::CrossPeak
min_tolerance() : protocols::stepwise::options::StepWiseBasicOptions
min_trial() : protocols::abinitio::FoldConstraints
min_type() : protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover , protocols::stepwise::options::StepWiseBasicOptions
min_value() : protocols::simple_moves::PSSM2BfactorMover
min_VC_to_write() : protocols::noesy_assign::PeakFileFormat_Base
mini_pose() : protocols::farna::ChunkSet
mini_pose_list() : protocols::farna::BasePairStepLibrary
MinimalistFlexbbEdge() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
MinimalistFlexbbInteractionGraph() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
MinimalistFlexbbNode() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
MinimalRotamer() : protocols::simple_moves::MinimalRotamer
minimization_score_function() : protocols::ddg::ddGMover
MinimizationRefiner() : protocols::loop_modeling::refiners::MinimizationRefiner
minimize() : protocols::analysis::PeptideDeriverFilter , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
minimize_() : protocols::simple_moves::PeptideStapleMover
minimize_after_delete() : protocols::stepwise::monte_carlo::mover::DeleteMover
minimize_all() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
minimize_all_rotamers() : protocols::make_rot_lib::MakeRotLibMover
minimize_and_score_native_pose() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
minimize_and_score_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
minimize_append_res() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
minimize_backbone() : protocols::ligand_docking::MoveMapBuilder
minimize_base_step() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
minimize_bond_angles() : protocols::relax::RelaxProtocolBase
minimize_bond_lengths() : protocols::relax::RelaxProtocolBase
minimize_bondangle_subset() : protocols::relax::RelaxProtocolBase
minimize_bondlength_subset() : protocols::relax::RelaxProtocolBase
minimize_cdrs() : protocols::antibody::design::AntibodyDesignModeler
minimize_conformation() : protocols::vip::VIP_Mover
minimize_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
minimize_in_stages() : protocols::enzdes::EnzRepackMinimize
minimize_interface() : protocols::antibody::design::AntibodyDesignModeler
minimize_no_bb() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
minimize_only() : protocols::flexpep_docking::FlexPepDockingProtocol
minimize_prepend_res() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
minimize_rebuild() : protocols::simple_moves::CyclizationMover
minimize_region() : protocols::enzdes::EnzdesFlexibleRegion
minimize_rotamer() : protocols::make_rot_lib::MakeRotLibMover
minimize_single_res() : protocols::stepwise::monte_carlo::mover::ResampleMover
minimize_single_res_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
minimize_sugar() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
minimize_sugar_sets_legacy() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
minimize_tensors_fix_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy
minimize_tensors_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
minimize_tensors_from_PCS_data_with_svd() : protocols::scoring::methods::pcs2::PcsEnergy
minimize_toward_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
minimize_with_constraints() : protocols::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
MinimizeBackbone() : protocols::ligand_docking::MinimizeBackbone
minimized_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
MinimizeHotspots() : protocols::protein_interface_design::movers::MapHotspot
MinimizeLigand() : protocols::ligand_docking::MinimizeLigand
minimizer() : protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial
minimizer_options() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
minimizer_rename_tag() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
MinimizeStoredRBConfs() : protocols::enzdes::MinimizeStoredRBConfs
minimum_peak_intensity() : protocols::noesy_assign::PeakFileFormat_Base
MiniRelax() : protocols::relax::MiniRelax
MinMover() : protocols::simple_moves::MinMover
MinPackMover() : protocols::simple_moves::MinPackMover
mintype() : protocols::antibody::design::CDRGraftDesignOptions , protocols::grafting::AnchoredGraftMover
missing_in_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
MissingDensityToJumpMover() : protocols::simple_moves::MissingDensityToJumpMover
mkdir_pred() : protocols::sparta::Sparta::SpartaLib
mm() : protocols::protein_interface_design::movers::PrepackMover
mode() : protocols::matdes::SymUnsatHbondFilter , protocols::normalmode::NormalMode , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::StoreCompoundTaskMover
mode1_1_packertask() : protocols::forge::remodel::RemodelDesignMover
mode1_packertask() : protocols::forge::remodel::RemodelDesignMover
mode2_packertask() : protocols::forge::remodel::RemodelDesignMover
mode3_packertask() : protocols::forge::remodel::RemodelDesignMover
mode4_packertask() : protocols::forge::remodel::RemodelDesignMover
mode5_packertask() : protocols::forge::remodel::RemodelDesignMover
mode6_packertask() : protocols::forge::remodel::RemodelDesignMover
model_count() : protocols::canonical_sampling::TrajectoryRecorder
model_h3() : protocols::antibody_legacy::CDRH3Modeler
model_loop() : protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::IndependentLoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves
model_post_design() : protocols::antibody::design::AntibodyDesignMover
model_post_graft() : protocols::antibody::design::AntibodyDesignMover
model_tag() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
ModelCDRH3() : protocols::antibody::ModelCDRH3
modeler_sugar() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
modeler_sugar_at_chain_break() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
models() : protocols::abinitio::PairingStatEntry
modifiable() : protocols::moves::ResId
modified2original_interval_endpoints() : protocols::forge::build::BuildManager
modified2original_intervals() : protocols::forge::build::BuildManager
modified_i2p_defined() : protocols::forge::build::BuildManager
modified_i2p_new() : protocols::forge::build::BuildManager
modified_i2p_preexisting() : protocols::forge::build::BuildManager
modified_i2p_undefined() : protocols::forge::build::BuildManager
modified_interval2movemap() : protocols::forge::build::BuildManager
modified_match_positions() : protocols::match::AddAllPositionsMPM , protocols::match::BfactorMPM , protocols::match::MatchPositionModifier , protocols::match::NumNeighborsMPM , protocols::match::RemoveNorCTermMPM , protocols::match::SecondaryStructureMPM , protocols::match::TaskOperationMPM
modified_task() : protocols::enzdes::EnzdesFlexBBProtocol
modify() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
modify_after_jump() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
modify_before_jump() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
modify_impl() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
modify_pose_build_resids_from_endes_input() : protocols::match::MatcherTask
modify_relative_filters_pdb_names() : protocols::simple_filters::Operator
modify_unselected_residues() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
modify_was_successful() : protocols::forge::build::BuildInstruction
ModifyAnnealer() : protocols::toolbox::task_operations::ModifyAnnealer
ModifyStoredRBConfs() : protocols::enzdes::ModifyStoredRBConfs
ModifyVariantTypeMover() : protocols::simple_moves::ModifyVariantTypeMover
MolarMassFilter() : protocols::ligand_docking::MolarMassFilter
MolecularDynamics() : protocols::cartesian::MolecularDynamics
MolecularMassFilter() : protocols::ligand_docking::MolecularMassFilter
MolecularWeightNormalization() : protocols::qsar::scoring_grid::MolecularWeightNormalization
moltenres_2_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
moltenres_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
moltenres_part_of_flexsegment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
moltenres_rotid_2_rotid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
monoub_apply() : protocols::ub_e2c::ubi_e2c_modeler
monoub_assign_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
monoub_calc_interaction_energy() : protocols::ub_e2c::ubi_e2c_modeler
monoub_calc_Lrmsd() : protocols::ub_e2c::ubi_e2c_modeler
monoub_centroid_filter() : protocols::ub_e2c::ubi_e2c_modeler
monoub_centroid_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
monoub_CSP_fraction() : protocols::ub_e2c::ubi_e2c_modeler
monoub_first_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
monoub_fold_tree() : protocols::ub_e2c::ubi_e2c_modeler
monoub_fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
monoub_fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
monoub_initial_cter_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
monoub_initial_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
monoub_setup_key_residues() : protocols::ub_e2c::ubi_e2c_modeler
monoub_setup_move_maps() : protocols::ub_e2c::ubi_e2c_modeler
monte_carlo() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController
MonteCarlo() : protocols::moves::MonteCarlo
MonteCarloLoader() : protocols::jd2::parser::MonteCarloLoader
MonteCarloRecover() : protocols::simple_moves::MonteCarloRecover
MonteCarloReset() : protocols::simple_moves::MonteCarloReset
MonteCarloTest() : protocols::simple_moves::MonteCarloTest
MonteCarloUtil() : protocols::moves::MonteCarloUtil
most_probable_bin() : protocols::frag_picker::quota::ABEGO_SS_Config
Motif() : protocols::motifs::Motif
motif_hash() : protocols::sic_dock::scores::MotifHashRigidScore
motif_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
motifcop() : protocols::motifs::MotifHit
MotifDnaPacker() : protocols::motifs::MotifDnaPacker
MotifGraftMover() : protocols::motif_grafting::movers::MotifGraftMover
MotifHashRigidScore() : protocols::sic_dock::scores::MotifHashRigidScore
MotifHit() : protocols::motifs::MotifHit
MotifLibrary() : protocols::motifs::MotifLibrary
MotifMatch() : protocols::motif_grafting::movers::MotifMatch
MotifScoreFilter() : protocols::simple_filters::MotifScoreFilter
MotifSearch() : protocols::motifs::MotifSearch
movable_jumps() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::toolbox::task_operations::InterfaceTaskOperation
move_all_inserted() : protocols::abinitio::MembraneAbinitio
move_atoms_to_collcheck_begin() : protocols::toolbox::match_enzdes_util::LigandConformer
move_element() : protocols::stepwise::monte_carlo::SWA_Move
move_forward_to_next_model() : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
move_jump_points_away() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
move_jumps_between_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
move_ligand_and_update_rhos_() : protocols::pockets::PlaidFingerprint
move_ligand_to_desired_centroid() : protocols::ligand_docking::LigandBaseProtocol
move_map() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::SaneMinMover
move_pose_to_standard_orie() : protocols::pockets::PocketGrid
move_side_chain() : protocols::stepwise::modeler::StepWiseMinimizer
move_spans() : protocols::topology_broker::TMHTopologySamplerClaimer
move_type() : protocols::stepwise::monte_carlo::SWA_Move
MoveBeforeFilter() : protocols::filters::MoveBeforeFilter
moveFromStubFrame() : protocols::hotspot_hashing::StubGenerator
moveIntoStubFrame() : protocols::hotspot_hashing::StubGenerator
movemap() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::grafting::AnchoredGraftMover , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::md::CartesianMD , protocols::md::MDBase , protocols::moves::MoveMapMover , protocols::moves::NullMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::MinMover , protocols::simple_moves::RingConformationMover
movemap_as_OP() : protocols::forge::build::BuildManager
movemap_cen() : protocols::anchored_design::AnchorMoversData
movemap_cen_all() : protocols::anchored_design::AnchorMoversData
movemap_cen_omegafixed() : protocols::anchored_design::AnchorMoversData
movemap_fa() : protocols::anchored_design::AnchorMoversData
movemap_fa_all() : protocols::anchored_design::AnchorMoversData
movemap_fa_omegafixed() : protocols::anchored_design::AnchorMoversData
movemap_from_blueprint() : protocols::flxbb::FlxbbDesign
movemap_ptr() : protocols::abinitio::KinematicControl
MoveMapBuilder() : protocols::ligand_docking::MoveMapBuilder
MoveMapBuilderLoader() : protocols::ligand_docking::MoveMapBuilderLoader
MoveMapMover() : protocols::moves::MoveMapMover
MovePoseToMembraneCenterMover() : protocols::rigid::MovePoseToMembraneCenterMover
mover() : protocols::abinitio::abscript::FragmentCM , protocols::abinitio::FragmentSampler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::flxbb::DesignTask
Mover() : protocols::moves::Mover
mover() : protocols::moves::MoverApplyingMover , protocols::moves::TrialMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::TopologyBroker
mover_by_index() : protocols::canonical_sampling::MetropolisHastingsMover
Mover_LoopHashRefine() : protocols::loophash::Mover_LoopHashRefine
mover_name() : protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::contact_map::ContactMapCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::design_opt::ParetoOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::DensityMorphingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::features::ReportToDBCreator , protocols::features::TrajectoryReportToDBCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetCstGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::forge::constraints::ConstraintFileCstGeneratorCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCCstGeneratorCreator , protocols::forge::constraints::RemoveCstsCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianHybridizeCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::FoldTreeHybridizeCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::hybridization::HybridizeSetupMoverCreator , protocols::idealize::IdealizeMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCMCreator , protocols::match::MatcherMoverCreator , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMoverCreator , protocols::md::CartesianMDCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::PyMolMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::BoltzmannRotamerMoverCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::ddGCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FindConsensusSequenceCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::MinMoverCreator , protocols::simple_moves::MinPackMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::simple_moves::MonteCarloResetCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::simple_moves::MSDMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::PackRotamersMoverLazyCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ResetBaselineMoverCreator , protocols::simple_moves::ResidueTypeConstraintMoverCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::simple_moves::symmetry::TaskAwareSymMinMoverCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::toolbox::task_operations::StoreCompoundTaskMoverCreator , protocols::toolbox::task_operations::StoreTaskMoverCreator
mover_stopping_condition() : protocols::simple_moves::GenericMonteCarloMover
mover_tag() : protocols::topology_broker::FragmentClaimer
mover_weight() : protocols::topology_broker::TopologyClaimer
MoverApplyingMover() : protocols::moves::MoverApplyingMover
MoverContainer() : protocols::moves::MoverContainer
MoverCreator() : protocols::moves::MoverCreator
MoverFactory() : protocols::moves::MoverFactory
MoverFilterPair() : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
MoverForPoseList() : protocols::moves::MoverForPoseList
moverkey() : protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData
MoverList() : protocols::wum::MoverList
MoverRegistrator() : protocols::moves::MoverRegistrator< T >
movers() : protocols::moves::MoverContainer
MoverStatistics() : protocols::moves::MoverStatistics
moving_partition_res() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::monte_carlo::SWA_Move , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
moving_res_contact_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
moving_residue_at_origin() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
MPDockingMover() : protocols::docking::membrane::MPDockingMover
MPDockingSetupMover() : protocols::docking::membrane::MPDockingSetupMover
MPFastRelaxMover() : protocols::relax::membrane::MPFastRelaxMover
mpi_broadcast_eval_dfunc() : protocols::optimize_weights::OptEMultifunc
mpi_broadcast_eval_func() : protocols::optimize_weights::OptEMultifunc
mpi_broadcast_receive_vars() : protocols::optimize_weights::OptEMultifunc
mpi_broadcast_send_vars() : protocols::optimize_weights::OptEMultifunc
mpi_feedback() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
mpi_finalize() : protocols::jd2::JobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
MPI_LoopHashRefine() : protocols::loophash::MPI_LoopHashRefine
MPI_LoopHashRefine_Emperor() : protocols::loophash::MPI_LoopHashRefine_Emperor
MPI_LoopHashRefine_Master() : protocols::loophash::MPI_LoopHashRefine_Master
mpi_receive_dfunc() : protocols::optimize_weights::OptEMultifunc
mpi_receive_func() : protocols::optimize_weights::OptEMultifunc
MPI_Refine_Emperor() : protocols::mpi_refinement::MPI_Refine_Emperor
MPI_Refine_Master() : protocols::mpi_refinement::MPI_Refine_Master
MPI_Refinement() : protocols::mpi_refinement::MPI_Refinement
mpi_resume() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
MPI_WorkUnitManager() : protocols::wum::MPI_WorkUnitManager
MPI_WorkUnitManager_Slave() : protocols::wum::MPI_WorkUnitManager_Slave
MPIArchiveJobDistributor() : protocols::jd2::archive::MPIArchiveJobDistributor
MPIBPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
MpiFileBuffer() : protocols::jd2::MpiFileBuffer
MPIFileBufJobDistributor() : protocols::jd2::MPIFileBufJobDistributor
MPIHPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
MPIMultiCommJobDistributor() : protocols::jd2::MPIMultiCommJobDistributor
MPIMultistateFitnessFunction() : protocols::pack_daemon::MPIMultistateFitnessFunction
MPIPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
MPIWorkPartitionJobDistributor() : protocols::jd2::MPIWorkPartitionJobDistributor
MPIWorkPoolJobDistributor() : protocols::jd2::MPIWorkPoolJobDistributor
MPSymDockMover() : protocols::symmetric_docking::membrane::MPSymDockMover
MRMover() : protocols::hybridization::MRMover
MSDMover() : protocols::simple_moves::MSDMover
multi_fast_relax() : protocols::abinitio::AbrelaxApplication
multi_origin_list() : protocols::pockets::FingerprintBase
multi_relative() : protocols::simple_filters::Operator
multi_threading_inner_job() : protocols::jd2::MultiThreadingJob
multi_use() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
multicomp() : protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter
MultiObjective() : protocols::mpi_refinement::MultiObjective
MultiPhosphateSampler() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
MultipleDomainMover() : protocols::farna::MultipleDomainMover
MultipleOutputWrapper() : protocols::rosetta_scripts::MultipleOutputWrapper
MultiplePoseMover() : protocols::rosetta_scripts::MultiplePoseMover
MultipleSigmoids() : protocols::simple_filters::MultipleSigmoids
MultiStateAggregateFunction() : protocols::multistate_design::MultiStateAggregateFunction
MultistateAggregateFunction() : protocols::pack_daemon::MultistateAggregateFunction
MultiStateEntity() : protocols::multistate_design::MultiStateEntity< T >
MultiStateFitnessFunction() : protocols::multistate_design::MultiStateFitnessFunction
MultistateFitnessFunction() : protocols::pack_daemon::MultistateFitnessFunction
MultiStatePacker() : protocols::multistate_design::MultiStatePacker
MultiTemperatureTrialCounter() : protocols::canonical_sampling::MultiTemperatureTrialCounter
MultiThreadingJob() : protocols::jd2::MultiThreadingJob
MultiThreadingMover() : protocols::comparative_modeling::MultiThreadingMover
multivec2poseBfacts() : protocols::electron_density::BfactorMultifunc
must_switch_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::PerturbByBins
mut_residue() : protocols::pmut_scan::MutationData
mut_to_gly() : protocols::analysis::InterfaceAnalyzerMover
Mutant() : protocols::pmut_scan::Mutant
mutant_score_components() : protocols::ddg::ddGMover
mutants_begin() : protocols::pmut_scan::PointMutScanDriver
mutants_end() : protocols::pmut_scan::PointMutScanDriver
mutate() : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::Mutate1Randomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
mutate_and_relax() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
MutateResidue() : protocols::simple_moves::MutateResidue
mutation_label() : protocols::ddg::ddGMover
mutation_rate() : protocols::genetic_algorithm::EntityRandomizer
mutation_string() : protocols::pmut_scan::MutationData
mutation_string_PDB_numbering() : protocols::pmut_scan::MutationData
mutation_threshold() : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
MutationData() : protocols::pmut_scan::MutationData
mutations() : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
mutations_begin() : protocols::pmut_scan::Mutant
mutations_end() : protocols::pmut_scan::Mutant
MutationsFilter() : protocols::simple_filters::MutationsFilter
my_emperor() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
MyAtom() : protocols::fldsgn::MyAtom