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Rosetta
2020.50
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Namespaces | |
abscript | |
Classes | |
class | _HashEntry |
class | _MergableEntries |
class | AbrelaxApplication |
application level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT. More... | |
class | AbrelaxMover |
class | AllResiduesChanged |
(helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values More... | |
class | AlternativePairings |
class | ClassicAbinitio |
class | ComputeTotalDistCst |
class | ConstraintFragmentSampler |
class | CoordinateConstraintKC |
class | DomainAssembly |
insert fragments in a linker region. Very similar to what's in looprelax_main More... | |
class | DomainAssemblyCreator |
class | DoubleLayerKinematicAbinitio |
class | FixTemplateJumpSetup |
class | FoldConstraints |
extension 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() More... | |
class | FragmentSampler |
class | hConvergenceCheck |
class | HedgeArchive |
class | IterativeAbrelax |
class | IterativeBase |
class | IterativeCentroid |
class | IterativeFullatom |
class | JumpingFoldConstraintsWrapper |
class | KinematicAbinitio |
class | KinematicControl |
class | KinematicTaskControl |
class | LoopJumpFoldCst |
class | MembraneAbinitio |
class | OrderSortPredicate |
class | PairingStatEntry |
class | PairingStatistics |
class | PcaEvaluator |
class | Protocol |
class | ResolutionSwitcher |
class | ShowViolation |
class | Stage1Sampler |
class | StrandConstraints |
class | StructureStore |
class | Template |
class | TemplateJumpSetup |
class | Templates |
Typedefs | |
typedef std::pair < core::pose::Pose, core::Real > | PoseWithScore |
typedef utility::pointer::shared_ptr < AbrelaxMover > | AbrelaxMoverOP |
typedef utility::pointer::shared_ptr < AbrelaxMover const > | AbrelaxMoverCOP |
using | hConvergenceCheckOP = utility::pointer::shared_ptr< hConvergenceCheck > |
typedef utility::pointer::shared_ptr < ClassicAbinitio > | ClassicAbinitioOP |
typedef utility::pointer::shared_ptr < ClassicAbinitio const > | ClassicAbinitioCOP |
typedef utility::pointer::shared_ptr < ConstraintFragmentSampler > | ConstraintFragmentSamplerOP |
typedef utility::pointer::shared_ptr < DoubleLayerKinematicAbinitio > | DoubleLayerKinematicAbinitioOP |
typedef utility::pointer::shared_ptr < DoubleLayerKinematicAbinitio const > | DoubleLayerKinematicAbinitioCOP |
typedef utility::pointer::shared_ptr < FoldConstraints > | FoldConstraintsOP |
typedef utility::pointer::shared_ptr < FoldConstraints const > | FoldConstraintsCOP |
typedef utility::pointer::shared_ptr < FragmentSampler > | FragmentSamplerOP |
typedef utility::pointer::shared_ptr < FragmentSampler const > | FragmentSamplerCOP |
typedef utility::pointer::shared_ptr < HedgeArchive > | HedgeArchiveOP |
typedef utility::pointer::shared_ptr < HedgeArchive const > | HedgeArchiveCOP |
typedef utility::pointer::shared_ptr < KinematicAbinitio > | KinematicAbinitioOP |
typedef utility::pointer::shared_ptr < KinematicAbinitio const > | KinematicAbinitioCOP |
typedef utility::pointer::shared_ptr < JumpingFoldConstraintsWrapper > | JumpingFoldConstraintsWrapperOP |
typedef utility::pointer::shared_ptr < JumpingFoldConstraintsWrapper const > | JumpingFoldConstraintsWrapperCOP |
typedef utility::pointer::shared_ptr < KinematicControl > | KinematicControlOP |
typedef utility::pointer::shared_ptr < KinematicControl const > | KinematicControlCOP |
typedef utility::pointer::shared_ptr < KinematicTaskControl > | KinematicTaskControlOP |
typedef utility::pointer::shared_ptr < KinematicTaskControl const > | KinematicTaskControlCOP |
typedef utility::pointer::shared_ptr < LoopJumpFoldCst > | LoopJumpFoldCstOP |
typedef utility::pointer::shared_ptr < LoopJumpFoldCst const > | LoopJumpFoldCstCOP |
typedef utility::pointer::shared_ptr < MembraneAbinitio > | MembraneAbinitioOP |
typedef utility::pointer::shared_ptr < MembraneAbinitio const > | MembraneAbinitioCOP |
typedef utility::pointer::shared_ptr < PairingStatistics > | PairingStatisticsOP |
typedef utility::pointer::shared_ptr < PairingStatistics const > | PairingStatisticsCOP |
typedef utility::vector1 < PairingStatEntry > | StatEntryList |
typedef boost::unordered_map < core::scoring::dssp::StrandPairing, PairingStatEntry, _HashEntry, _MergableEntries > | StatEntries |
typedef utility::pointer::shared_ptr < Protocol > | ProtocolOP |
typedef utility::pointer::shared_ptr < Protocol const > | ProtocolCOP |
typedef utility::pointer::shared_ptr < ResolutionSwitcher > | ResolutionSwitcherOP |
typedef utility::pointer::shared_ptr < ResolutionSwitcher const > | ResolutionSwitcherCOP |
using | SizeList = utility::vector1< core::Size > |
typedef utility::pointer::shared_ptr < Template > | TemplateOP |
typedef utility::pointer::shared_ptr < Template const > | TemplateCOP |
typedef utility::pointer::shared_ptr < TemplateJumpSetup > | TemplateJumpSetupOP |
typedef utility::pointer::shared_ptr < TemplateJumpSetup const > | TemplateJumpSetupCOP |
typedef utility::pointer::weak_ptr < Templates > | TemplatesAP |
typedef utility::pointer::weak_ptr < Templates const > | TemplatesCAP |
typedef utility::pointer::shared_ptr < Templates > | TemplatesOP |
typedef utility::pointer::shared_ptr < Templates const > | TemplatesCOP |
Enumerations | |
enum | StageID { ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3, STAGE_3a, STAGE_3b, STAGE_4, END_ABINITIO, LOOP_CLOSURE, SWITCH_TO_FULLATOM, RELAX, LAST_STAGE } |
Functions | |
bool | sort_PoseWithScore (const PoseWithScore &left, const PoseWithScore &right) |
void | register_options_broker () |
Registers options that are relevant to the application. This function must be called prior to Broker_main() or Loopbuild_Threading_main(). More... | |
void | common_setup () |
void | Broker_main () |
Initiates AbrelaxMover using the job distribution (jd2) More... | |
bool | contains_stageid (utility::vector1< ClassicAbinitio::StageID > vec, ClassicAbinitio::StageID query) |
static basic::Tracer | TR ("protocols.protein_interface_design.movers.DomainAssembly") |
Size | noe_stage (core::Size total_res, Real factor) |
bool | contains_stageid (utility::vector1< abinitio::StageID > vec, abinitio::StageID query) |
std::string | filename (core::Size batch_id) |
void | fix_chainbreak_patch (scoring::ScoreFunctionOP scorefxn, std::string const &patch_name) |
bool | decide_on_beta_jumping_from_frags () |
void | get_core (toolbox::DecoySetEvaluation &eval, core::Real cutoff, loops::Loops &rigid) |
void | find_sampling_cuts (kinematics::FoldTree const &sampling, kinematics::FoldTree const &final, utility::vector1< core::Size > &sample_cuts) |
std::ostream & | operator<< (std::ostream &out, PairingStatistics const &ps) |
std::istream & | operator>> (std::istream &is, PairingStatEntry &ps) |
std::ostream & | operator<< (std::ostream &out, StatEntries const &ps) |
std::istream & | operator>> (std::istream &is, StatEntries &pslist) |
std::istream & | operator>> (std::istream &is, PairingStatistics &ps) |
std::ostream & | operator<< (std::ostream &out, PairingStatEntry const &ps) |
std::size_t | hash_value (PairingStatEntry const &val) |
std::size_t | hash_value (core::scoring::dssp::StrandPairing const &val) |
std::istream & | operator<< (std::istream &, StatEntries &) |
bool | copy_side_chains (core::pose::Pose &pose, utility::vector1< bool > &needToRepack, core::pose::Pose const &fa_input_pose) |
Size | register_cutoff (5) |
Size | residue_cutoff (5) |
std::ostream & | operator<< (std::ostream &out, AlternativePairings const &alt_pairs) |
std::ostream & | operator<< (std::ostream &out, StrandConstraints const &st) |
void | dump_movemap (kinematics::MoveMap const &mm, core::Size nres, std::ostream &out) |
void | register_common_options () |
int | run_boinc_debug () |
typedef utility::pointer::shared_ptr<AbrelaxMover const> protocols::abinitio::AbrelaxMoverCOP |
typedef utility::pointer::shared_ptr<AbrelaxMover> protocols::abinitio::AbrelaxMoverOP |
typedef utility::pointer::shared_ptr< ClassicAbinitio const > protocols::abinitio::ClassicAbinitioCOP |
typedef utility::pointer::shared_ptr< ClassicAbinitio > protocols::abinitio::ClassicAbinitioOP |
typedef utility::pointer::shared_ptr< ConstraintFragmentSampler > protocols::abinitio::ConstraintFragmentSamplerOP |
typedef utility::pointer::shared_ptr< DoubleLayerKinematicAbinitio const > protocols::abinitio::DoubleLayerKinematicAbinitioCOP |
typedef utility::pointer::shared_ptr< DoubleLayerKinematicAbinitio > protocols::abinitio::DoubleLayerKinematicAbinitioOP |
typedef utility::pointer::shared_ptr< FoldConstraints const > protocols::abinitio::FoldConstraintsCOP |
typedef utility::pointer::shared_ptr< FoldConstraints > protocols::abinitio::FoldConstraintsOP |
typedef utility::pointer::shared_ptr< FragmentSampler const > protocols::abinitio::FragmentSamplerCOP |
typedef utility::pointer::shared_ptr< FragmentSampler > protocols::abinitio::FragmentSamplerOP |
using protocols::abinitio::hConvergenceCheckOP = typedef utility::pointer::shared_ptr<hConvergenceCheck> |
typedef utility::pointer::shared_ptr<HedgeArchive const> protocols::abinitio::HedgeArchiveCOP |
typedef utility::pointer::shared_ptr<HedgeArchive> protocols::abinitio::HedgeArchiveOP |
typedef utility::pointer::shared_ptr< JumpingFoldConstraintsWrapper const > protocols::abinitio::JumpingFoldConstraintsWrapperCOP |
typedef utility::pointer::shared_ptr< JumpingFoldConstraintsWrapper > protocols::abinitio::JumpingFoldConstraintsWrapperOP |
typedef utility::pointer::shared_ptr< KinematicAbinitio const > protocols::abinitio::KinematicAbinitioCOP |
typedef utility::pointer::shared_ptr< KinematicAbinitio > protocols::abinitio::KinematicAbinitioOP |
typedef utility::pointer::shared_ptr< KinematicControl const > protocols::abinitio::KinematicControlCOP |
typedef utility::pointer::shared_ptr< KinematicControl > protocols::abinitio::KinematicControlOP |
typedef utility::pointer::shared_ptr< KinematicTaskControl const > protocols::abinitio::KinematicTaskControlCOP |
typedef utility::pointer::shared_ptr< KinematicTaskControl > protocols::abinitio::KinematicTaskControlOP |
typedef utility::pointer::shared_ptr< LoopJumpFoldCst const > protocols::abinitio::LoopJumpFoldCstCOP |
typedef utility::pointer::shared_ptr< LoopJumpFoldCst > protocols::abinitio::LoopJumpFoldCstOP |
typedef utility::pointer::shared_ptr< MembraneAbinitio const > protocols::abinitio::MembraneAbinitioCOP |
typedef utility::pointer::shared_ptr< MembraneAbinitio > protocols::abinitio::MembraneAbinitioOP |
typedef utility::pointer::shared_ptr< PairingStatistics const > protocols::abinitio::PairingStatisticsCOP |
typedef utility::pointer::shared_ptr< PairingStatistics > protocols::abinitio::PairingStatisticsOP |
typedef std::pair< core::pose::Pose, core::Real > protocols::abinitio::PoseWithScore |
typedef utility::pointer::shared_ptr< Protocol const > protocols::abinitio::ProtocolCOP |
typedef utility::pointer::shared_ptr< Protocol > protocols::abinitio::ProtocolOP |
typedef utility::pointer::shared_ptr< ResolutionSwitcher const > protocols::abinitio::ResolutionSwitcherCOP |
typedef utility::pointer::shared_ptr< ResolutionSwitcher > protocols::abinitio::ResolutionSwitcherOP |
using protocols::abinitio::SizeList = typedef utility::vector1<core::Size> |
typedef boost::unordered_map< core::scoring::dssp::StrandPairing, PairingStatEntry, _HashEntry, _MergableEntries > protocols::abinitio::StatEntries |
typedef utility::vector1< PairingStatEntry > protocols::abinitio::StatEntryList |
typedef utility::pointer::shared_ptr< Template const > protocols::abinitio::TemplateCOP |
typedef utility::pointer::shared_ptr< TemplateJumpSetup const > protocols::abinitio::TemplateJumpSetupCOP |
typedef utility::pointer::shared_ptr< TemplateJumpSetup > protocols::abinitio::TemplateJumpSetupOP |
typedef utility::pointer::shared_ptr< Template > protocols::abinitio::TemplateOP |
typedef utility::pointer::weak_ptr< Templates > protocols::abinitio::TemplatesAP |
typedef utility::pointer::weak_ptr< Templates const > protocols::abinitio::TemplatesCAP |
typedef utility::pointer::shared_ptr< Templates const > protocols::abinitio::TemplatesCOP |
typedef utility::pointer::shared_ptr< Templates > protocols::abinitio::TemplatesOP |
void protocols::abinitio::Broker_main | ( | ) |
Initiates AbrelaxMover using the job distribution (jd2)
References common_setup(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::go(), and protocols::jd2::archive::MPIArchiveJobDistributor::set_archive().
void protocols::abinitio::common_setup | ( | ) |
References core::scoring::func::FuncFactory::add_type(), core::scoring::constraints::ConstraintIO::get_func_factory(), and tr().
Referenced by Broker_main().
bool protocols::abinitio::contains_stageid | ( | utility::vector1< abinitio::StageID > | vec, |
abinitio::StageID | query | ||
) |
bool protocols::abinitio::contains_stageid | ( | utility::vector1< ClassicAbinitio::StageID > | vec, |
ClassicAbinitio::StageID | query | ||
) |
bool protocols::abinitio::copy_side_chains | ( | core::pose::Pose & | pose, |
utility::vector1< bool > & | needToRepack, | ||
core::pose::Pose const & | fa_input_pose | ||
) |
References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::conformation::Residue::natoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), tr(), and core::conformation::Atom::xyz().
Referenced by protocols::abinitio::ResolutionSwitcher::apply().
bool protocols::abinitio::decide_on_beta_jumping_from_frags | ( | ) |
void protocols::abinitio::dump_movemap | ( | kinematics::MoveMap const & | mm, |
core::Size | nres, | ||
std::ostream & | out | ||
) |
References core::kinematics::MoveMap::get_bb().
std::string protocols::abinitio::filename | ( | core::Size | batch_id | ) |
Referenced by core::chemical::add_atom_type_set_parameters_from_command_line(), core::chemical::add_atom_types_from_command_line(), protocols::topology_broker::add_cmdline_claims(), core::import_pose::pose_stream::PDBPoseInputStream::add_list_filenames(), core::chemical::add_mm_atom_type_set_parameters_from_command_line(), core::chemical::ResidueTypeSet::add_patches(), protocols::nmr::ParaNMRScoreMover::add_pcs_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_pre_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map(), protocols::moves::PDBDumpMover::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::parser::FragmentReader::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::jd2::SingleFileBuffer::block(), core::io::pdb::build_pose_from_pdb_as_is(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::dna::checkpoint_cleanup(), core::scoring::ChemicalShiftAnisotropy::ChemicalShiftAnisotropy(), protocols::jd2::MpiFileBuffer::close_file(), core::chemical::carbohydrates::CarbohydrateInfoManager::codes_to_root_map_file(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect(), core::chemical::ChemicalManager::create_element_set(), core::chemical::ChemicalManager::create_ideal_bond_length_set(), core::scoring::ScoringManager::create_mhc_csv_contents(), core::scoring::ScoringManager::create_mhc_map_from_db(), core::chemical::ChemicalManager::create_mm_atom_type_set(), protocols::abinitio::abscript::ConstraintPreparer::cst_file(), protocols::ddG_main(), protocols::ddG::ddGData::ddGData(), core::scoring::DipolarCoupling::DipolarCoupling(), protocols::cartesian::MolecularDynamics::doMD(), protocols::cartesian::MolecularDynamics::doMinimising(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), core::io::pdb::dump_pdb(), protocols::mpi_refinement::Serial_Refine::dump_structures(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::mpi_refinement::MPI_Refinement::dump_structures(), protocols::pockets::PocketGrid::dumpExemplarToFile(), protocols::pockets::PocketGrid::dumpGridToFile(), protocols::genetic_algorithm::GeneticAlgorithmBase::entities_checkpoint_filename(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline(), core::import_pose::pose_stream::filenames_from_list_file(), protocols::backrub::BackrubSidechainMover::finalize_simulation(), core::io::NomenclatureManager::find_alternate_codes_file(), protocols::jd3::full_model_inputters::PDBFullModelInputter::full_model_from_input_source(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source(), core::chemical::ChemicalManager::gasteiger_atom_type_set(), protocols::jd2::WriteOut_MpiFileBuffer::generate_new_channel(), protocols::jd2::DebugOut_MpiFileBuffer::generate_new_channel(), protocols::comparative_modeling::AlignmentClustering::generateRankedAlignments(), protocols::genetic_algorithm::GeneticAlgorithmBase::generations_checkpoint_filename(), protocols::antibody::design::get_cdr_set_options(), core::chemical::rings::RingConformerManager::get_conformers_for_ring_size_and_type(), protocols::antibody::design::get_graft_design_options(), protocols::antibody::design::get_seq_design_options(), protocols::motifs::get_targetconformers_user(), core::scoring::electron_density::getDensityMap_legacy(), protocols::cluster::calibur::PreloadedPDB::getSimPDB(), core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline(), core::chemical::GlobalResidueTypeSet::init_restypes_from_database(), protocols::simple_moves::WaterRotsDB::initialize(), protocols::cluster::calibur::Clustering::initialize(), protocols::match::MatcherTask::initialize_active_site_definition_from_command_line(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::initialize_from_command_line(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::initialize_from_directory(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file(), core::scoring::netcharge_energy::NetChargeEnergySetup::initialize_from_file(), core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file(), protocols::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), core::pack::palette::PackerPaletteFactory::initialize_packer_palette_from_global_defaults(), core::scoring::facts::FACTSRsdTypeInfo::initialize_parameters(), protocols::relax::RelaxScriptManager::initialize_relax_scripts_in_database(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_base_backbone_xy(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_aa_rna_backbone(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_base_pair(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_pair(), core::scoring::rna::RNP_LowResPairDistPotential::initialize_rnp_pair_dist(), core::scoring::rna::RNP_LowResStackData::initialize_rnp_stack_xy(), core::scoring::rna::RNA_AtomVDW::initialize_rnp_vdw_parameters(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::initialize_sfd_from_options_and_tag(), protocols::jd3::pose_inputters::SilentFilePoseInputter::initialize_sfd_from_options_and_tag(), protocols::jd2::input_pdb_files_from_command_line(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_beta_nov16_library(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_canonical_talaris_library(), protocols::jobdist::PlainPdbJobDistributor::is_finished(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::is_old_canonical_dun02_library(), protocols::jd3::pose_outputters::PDBPoseOutputter::job_has_already_completed(), core::chemical::carbohydrates::CarbohydrateInfoManager::linkage_conformers_map(), core::scoring::bin_transitions::BinTransitionCalculator::load_bin_params(), protocols::dna::load_checkpoint(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_csv(), core::scoring::Ramachandran::load_custom_rama_table(), protocols::antibody::design::MutateFrameworkForCluster::load_data(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_database(), protocols::dna::load_dna_design_defs_from_file(), protocols::qsar::scoring_grid::ShapeGrid::load_kbp_data(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::load_lib(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), protocols::rpc::JSON_RPC::load_new_set_of_virtual_files(), core::energy_methods::AARepeatEnergy::load_penalty_table_from_file(), protocols::stepwise::setup::load_s_and_l(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), core::pack::dunbrack::load_unboundrot(), protocols::cluster::calibur::PreloadedPDB::loadPDBFromList(), protocols::cluster::calibur::PreloadedPDB::loadSilentFile(), protocols::ncbb::SecStructFinder::make_filename(), core::chemical::MergeBehaviorManager::MergeBehaviorManager(), protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop(), core::scoring::methods::EnergyMethodOptions::nmer_svm(), core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix(), core::scoring::methods::EnergyMethodOptions::nmer_svm_list(), core::scoring::methods::EnergyMethodOptions::nmer_svm_rank(), core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list(), core::io::NomenclatureManager::NomenclatureManager(), protocols::noesy_assign::open_stream(), protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(), protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::minimization_packing::SetReturningPackRotamersMover::output_repacked_poses(), core::pack::pack_rotamers_setup(), protocols::loops::JSONFormattedLoopsFileReader::parse_json_residue_info(), protocols::loops::loops_definers::LoopsFileDefiner::parse_my_tag(), protocols::pose_creation::ExtendedPoseMover::parse_my_tag(), protocols::nmr::pre::PREMover::parse_my_tag(), protocols::nmr::pcs::PCSLigandTransformMover::parse_my_tag(), protocols::legacy_sewing::LegacyReadNativeRotamersFile::parse_tag(), protocols::scoring::methods::pcs::PCS_data::PCS_data(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::PCS_data_Ts1(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::PCS_data_Ts2(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::PCS_data_Ts3(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::PCS_data_Ts4(), protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter(), protocols::denovo_design::movers::pdb_filename(), core::chemical::rotamers::PDBRotamerLibrarySpecification::pdb_rotamers_file(), core::scoring::cryst::PhenixInterface::PhenixInterface(), core::import_pose::pose_from_file(), core::import_pose::pose_from_pdbstring(), core::import_pose::poseOPs_from_files(), core::import_pose::poses_from_files(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::mean_field::GenMeanFieldMover::read_aa_matrix(), core::import_pose::read_all_poses(), protocols::parser::BluePrint::read_blueprint_stream(), core::scoring::ChemicalShiftAnisotropy::read_CSA_file(), core::fragment::FragmentIO::read_data(), core::scoring::DipolarCoupling::read_DC_file(), protocols::genetic_algorithm::GeneticAlgorithmBase::read_entities_checkpoint(), core::chemical::ResidueTypeSet::read_files_for_base_residue_types(), core::chemical::ResidueTypeSet::read_files_for_unpatchable_residue_types(), protocols::jumping::DisulfPairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file_no_filters(), protocols::genetic_algorithm::GeneticAlgorithmBase::read_generations_checkpoint(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::mean_field::GenMeanFieldMover::read_input_pdbs(), core::pose::read_psipred_ss2_file(), core::chemical::mainchain_potential::read_rama_map_file_shapovalov(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag(), protocols::topology_broker::PcsEnergyController::read_tag(), protocols::topology_broker::StartStructClaimer::read_tag(), core::chemical::read_topology_file(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::jd2::MpiFileBuffer::release_file(), protocols::abinitio::HedgeArchive::remove_pending_decoys(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), protocols::forge::components::BDR::resfile(), core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling(), protocols::abinitio::IterativeCentroid::restore_from_file(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::abinitio::HedgeArchive::restore_status(), core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map_file(), core::scoring::SecondaryStructurePotential::rsigma_dot_initializer(), protocols::jd2::MpiFileBuffer::run(), protocols::motifs::MotifDnaPacker::run_motifs(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::archive::ArchiveBase::save_decoys(), protocols::abinitio::HedgeArchive::save_pending_decoys(), protocols::fldsgn::BluePrintBDR::set_blueprint(), protocols::denovo_design::constraints::FileConstraintGenerator::set_cstfile(), protocols::anchored_design::Anchor::set_filename(), protocols::noesy_assign::CrossPeakInfo::set_filename(), protocols::match::output::WriteUpstreamCoordinateKinemage::set_kinemage_file_name(), core::io::nmr::SpinlabelDatabaseEntry::set_path_to_distance_potential_histogram(), core::scoring::nmr::NMRSpinlabel::set_path_to_distance_potential_histogram_file(), core::io::nmr::SpinlabelDatabaseEntry::set_path_to_ensemble_conformers(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::md::MDBase::set_write_dynamic_rsr(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::energy_methods::CustomAtomPairEnergy::setup_for_scoring(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::setup_predictor(), core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map(), core::energy_methods::DumpTrajectoryEnergy::start_new_activity(), core::chemical::carbohydrates::CarbohydrateInfoManager::sugar_modifications_table_file(), protocols::motifs::IRCollection::try_for_more(), protocols::jobdist::universal_main(), protocols::docking::DockingEnsemble::update_pdblist_file(), protocols::genetic_algorithm::GeneticAlgorithmBase::write_entities_checkpoint(), protocols::genetic_algorithm::GeneticAlgorithmBase::write_generations_checkpoint(), protocols::noesy_assign::PeakFileFormat::write_header(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), protocols::noesy_assign::CrossPeakList::write_peak_files(), protocols::loop_grower::LoopGrower::write_to_disk(), and protocols::loop_grower::LoopPartialSolutionStore::writelpsstore().
void protocols::abinitio::find_sampling_cuts | ( | kinematics::FoldTree const & | sampling, |
kinematics::FoldTree const & | final, | ||
utility::vector1< core::Size > & | sample_cuts | ||
) |
void protocols::abinitio::fix_chainbreak_patch | ( | scoring::ScoreFunctionOP | scorefxn, |
std::string const & | patch_name | ||
) |
References core::scoring::chainbreak, core::scoring::linear_chainbreak, core::scoring::overlap_chainbreak, and tr().
Referenced by protocols::abinitio::IterativeBase::initialize().
void protocols::abinitio::get_core | ( | toolbox::DecoySetEvaluation & | eval, |
core::Real | cutoff, | ||
loops::Loops & | rigid | ||
) |
References protocols::loops::Loops::add_loop(), protocols::loops::Loops::clear(), protocols::toolbox::DecoySetEvaluation::n_atoms(), protocols::toolbox::DecoySetEvaluation::rmsf(), protocols::toolbox::DecoySetEvaluation::superimpose(), tr(), protocols::jd2::archive::EvaluatedArchive::weights(), and protocols::toolbox::DecoySetEvaluation::wRMSD().
Referenced by protocols::abinitio::IterativeBase::compute_cores().
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inline |
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inline |
References core::scoring::dssp::StrandPairing::hash_value().
Size protocols::abinitio::noe_stage | ( | core::Size | total_res, |
Real | factor | ||
) |
References protocols::mean_field::min(), and protocols::abinitio::FoldConstraints::total_res().
Referenced by protocols::abinitio::FoldConstraints::do_stage1_cycles(), protocols::abinitio::FoldConstraints::do_stage2_cycles(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage3(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage4(), and protocols::abinitio::FoldConstraints::prepare_stage2().
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inline |
std::ostream & protocols::abinitio::operator<< | ( | std::ostream & | out, |
AlternativePairings const & | alt_pairs | ||
) |
std::istream& protocols::abinitio::operator<< | ( | std::istream & | , |
StatEntries & | |||
) |
std::ostream & protocols::abinitio::operator<< | ( | std::ostream & | out, |
StrandConstraints const & | st | ||
) |
std::ostream & protocols::abinitio::operator<< | ( | std::ostream & | out, |
PairingStatistics const & | ps | ||
) |
References core::scoring::dssp::StrandPairingSet::begin(), core::scoring::dssp::StrandPairingSet::end(), core::chemical::element::F, protocols::abinitio::PairingStatistics::is_native_pairing(), protocols::abinitio::PairingStatistics::model_weight_, core::conformation::membrane::out, core::scoring::dssp::StrandPairingSet::size(), protocols::abinitio::PairingStatistics::strand_weight(), protocols::abinitio::PairingStatistics::topology(), and tr().
std::ostream & protocols::abinitio::operator<< | ( | std::ostream & | out, |
StatEntries const & | ps | ||
) |
References core::conformation::membrane::out.
std::istream& protocols::abinitio::operator>> | ( | std::istream & | is, |
PairingStatEntry & | ps | ||
) |
std::istream& protocols::abinitio::operator>> | ( | std::istream & | is, |
StatEntries & | pslist | ||
) |
References protocols::abinitio::PairingStatEntry::pairing().
std::istream& protocols::abinitio::operator>> | ( | std::istream & | is, |
PairingStatistics & | ps | ||
) |
References protocols::abinitio::PairingStatistics::entries_, protocols::abinitio::PairingStatistics::model_weight_, protocols::abinitio::PairingStatEntry::models(), core::scoring::dssp::StrandPairingSet::push_back(), protocols::abinitio::PairingStatEntry::set_weight(), protocols::abinitio::PairingStatistics::topols_, and tr().
void protocols::abinitio::register_common_options | ( | ) |
References core::pack::interaction_graph::debug, and protocols::antibody::design::relax.
Referenced by protocols::abinitio::AbrelaxApplication::register_options(), and register_options_broker().
Size protocols::abinitio::register_cutoff | ( | 5 | ) |
Referenced by protocols::abinitio::AlternativePairings::compatible().
void protocols::abinitio::register_options_broker | ( | ) |
Registers options that are relevant to the application. This function must be called prior to Broker_main() or Loopbuild_Threading_main().
References register_common_options().
Referenced by protocols::protein_interface_design::movers::TopologyBrokerMover::apply().
Size protocols::abinitio::residue_cutoff | ( | 5 | ) |
Referenced by protocols::abinitio::AlternativePairings::compatible().
int protocols::abinitio::run_boinc_debug | ( | ) |
References core::chemical::CENTROID, core::pack::interaction_graph::debug, core::chemical::element::F, core::scoring::get_score_function(), core::pose::make_pose_from_sequence(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::sequence::read_fasta_file(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), and core::io::silent::SilentFileData::write_silent_struct().
bool protocols::abinitio::sort_PoseWithScore | ( | const PoseWithScore & | left, |
const PoseWithScore & | right | ||
) |
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static |
Referenced by protocols::abinitio::DomainAssembly::apply().