protocols::abinitio Namespace Reference

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 Documentation

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

Enumeration Type Documentation

enum protocols::abinitio::StageID

Enumerator
ALL_STAGES
STAGE_1
STAGE_2
STAGE_3
STAGE_3a
STAGE_3b
STAGE_4
END_ABINITIO
LOOP_CLOSURE
SWITCH_TO_FULLATOM
RELAX
LAST_STAGE

Function Documentation

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
	)

Referenced by protocols::abinitio::FragmentSampler::apply(), protocols::abinitio::FragmentSampler::recover_low(), and protocols::abinitio::ClassicAbinitio::recover_low().

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

(

)

References core::fragment::SecondaryStructure::helix_fraction(), mem_tr, core::fragment::FragmentIO::read_data(), core::fragment::SecondaryStructure::strand_fraction(), core::fragment::SecondaryStructure::total_residue(), and tr().

Referenced by protocols::abinitio::IterativeBase::initialize().

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::motifs::MotifDnaPacker::apply(), protocols::moves::PDBDumpMover::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(), protocols::denovo_design::components::create_debug_filename(), 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_Ts3::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::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::glycopeptide_docking::GlycopeptideDockingFlags::set_constraints_file(), 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
	)

References core::kinematics::FoldTree::cutpoint(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by protocols::abinitio::KinematicControl::add_chainbreak_variants().

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().

std::size_t protocols::abinitio::hash_value ( PairingStatEntry const &  val )

inline

References core::scoring::dssp::StrandPairing::hash_value(), and protocols::abinitio::PairingStatEntry::pairing().

Referenced by protocols::abinitio::_HashEntry::operator()().

std::size_t protocols::abinitio::hash_value ( core::scoring::dssp::StrandPairing const &  val )

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().

std::ostream& protocols::abinitio::operator<< ( std::ostream &  out, PairingStatEntry const &  ps  )

inline

References core::conformation::membrane::out, and protocols::abinitio::PairingStatEntry::show().

std::ostream & protocols::abinitio::operator<<	(	std::ostream &	out,
		AlternativePairings const &	alt_pairs
	)

References core::conformation::membrane::out, and protocols::abinitio::AlternativePairings::show().

std::istream& protocols::abinitio::operator<<	(	std::istream &	,
		StatEntries &
	)

std::ostream & protocols::abinitio::operator<<	(	std::ostream &	out,
		StrandConstraints const &	st
	)

References core::conformation::membrane::out, and protocols::abinitio::StrandConstraints::show().

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
	)

References protocols::abinitio::PairingStatEntry::models_, protocols::abinitio::PairingStatEntry::strand_pairing_, tr(), and protocols::abinitio::PairingStatEntry::weight_.

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, protocols::moves::Mover::register_options(), 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
	)

static basic::Tracer protocols::abinitio::TR ( "protocols.protein_interface_design.movers.DomainAssembly"  )

static

Referenced by protocols::abinitio::DomainAssembly::apply().