protocols::abinitio Namespace Reference

Namespaces
	abscript

Classes
class	PcaEvaluator
class	ShowViolation
class	ComputeTotalDistCst
class	Stage1Sampler
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. @detail calls of operator ( pose ) compare the initial phi/psi values More...
class	hConvergenceCheck
class	ClassicAbinitio
class	ConstraintFragmentSampler
class	DomainAssembly
	insert fragments in a linker region. Very similar to what's in looprelax_main More...
class	DomainAssemblyCreator
class	DoubleLayerKinematicAbinitio
class	FoldConstraints
	extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints @detail 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	HedgeArchive
class	IterativeAbrelax
class	IterativeBase
class	OrderSortPredicate
class	IterativeCentroid
class	IterativeFullatom
class	KinematicAbinitio
class	JumpingFoldConstraintsWrapper
class	KinematicControl
class	CoordinateConstraintKC
class	KinematicTaskControl
class	LoopJumpFoldCst
class	MembraneAbinitio
class	PairingStatEntry
class	_MergableEntries
class	_HashEntry
class	PairingStatistics
class	Protocol
class	ResolutionSwitcher
class	AlternativePairings
class	StrandConstraints
class	Template
class	TemplateJumpSetup
class	FixTemplateJumpSetup
class	StructureStore
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

AbrelaxMoverCOP

typedef utility::pointer::shared_ptr<AbrelaxMover const> protocols::abinitio::AbrelaxMoverCOP

AbrelaxMoverOP

typedef utility::pointer::shared_ptr<AbrelaxMover> protocols::abinitio::AbrelaxMoverOP

ClassicAbinitioCOP

typedef utility::pointer::shared_ptr< ClassicAbinitio const > protocols::abinitio::ClassicAbinitioCOP

ClassicAbinitioOP

typedef utility::pointer::shared_ptr< ClassicAbinitio > protocols::abinitio::ClassicAbinitioOP

ConstraintFragmentSamplerOP

typedef utility::pointer::shared_ptr< ConstraintFragmentSampler > protocols::abinitio::ConstraintFragmentSamplerOP

DoubleLayerKinematicAbinitioCOP

typedef utility::pointer::shared_ptr< DoubleLayerKinematicAbinitio const > protocols::abinitio::DoubleLayerKinematicAbinitioCOP

DoubleLayerKinematicAbinitioOP

typedef utility::pointer::shared_ptr< DoubleLayerKinematicAbinitio > protocols::abinitio::DoubleLayerKinematicAbinitioOP

FoldConstraintsCOP

typedef utility::pointer::shared_ptr< FoldConstraints const > protocols::abinitio::FoldConstraintsCOP

FoldConstraintsOP

typedef utility::pointer::shared_ptr< FoldConstraints > protocols::abinitio::FoldConstraintsOP

FragmentSamplerCOP

typedef utility::pointer::shared_ptr< FragmentSampler const > protocols::abinitio::FragmentSamplerCOP

FragmentSamplerOP

typedef utility::pointer::shared_ptr< FragmentSampler > protocols::abinitio::FragmentSamplerOP

hConvergenceCheckOP

using protocols::abinitio::hConvergenceCheckOP = typedef utility::pointer::shared_ptr<hConvergenceCheck>

HedgeArchiveCOP

typedef utility::pointer::shared_ptr<HedgeArchive const> protocols::abinitio::HedgeArchiveCOP

HedgeArchiveOP

typedef utility::pointer::shared_ptr<HedgeArchive> protocols::abinitio::HedgeArchiveOP

JumpingFoldConstraintsWrapperCOP

typedef utility::pointer::shared_ptr< JumpingFoldConstraintsWrapper const > protocols::abinitio::JumpingFoldConstraintsWrapperCOP

JumpingFoldConstraintsWrapperOP

typedef utility::pointer::shared_ptr< JumpingFoldConstraintsWrapper > protocols::abinitio::JumpingFoldConstraintsWrapperOP

KinematicAbinitioCOP

typedef utility::pointer::shared_ptr< KinematicAbinitio const > protocols::abinitio::KinematicAbinitioCOP

KinematicAbinitioOP

typedef utility::pointer::shared_ptr< KinematicAbinitio > protocols::abinitio::KinematicAbinitioOP

KinematicControlCOP

typedef utility::pointer::shared_ptr< KinematicControl const > protocols::abinitio::KinematicControlCOP

KinematicControlOP

typedef utility::pointer::shared_ptr< KinematicControl > protocols::abinitio::KinematicControlOP

KinematicTaskControlCOP

typedef utility::pointer::shared_ptr< KinematicTaskControl const > protocols::abinitio::KinematicTaskControlCOP

KinematicTaskControlOP

typedef utility::pointer::shared_ptr< KinematicTaskControl > protocols::abinitio::KinematicTaskControlOP

LoopJumpFoldCstCOP

typedef utility::pointer::shared_ptr< LoopJumpFoldCst const > protocols::abinitio::LoopJumpFoldCstCOP

LoopJumpFoldCstOP

typedef utility::pointer::shared_ptr< LoopJumpFoldCst > protocols::abinitio::LoopJumpFoldCstOP

MembraneAbinitioCOP

typedef utility::pointer::shared_ptr< MembraneAbinitio const > protocols::abinitio::MembraneAbinitioCOP

MembraneAbinitioOP

typedef utility::pointer::shared_ptr< MembraneAbinitio > protocols::abinitio::MembraneAbinitioOP

PairingStatisticsCOP

typedef utility::pointer::shared_ptr< PairingStatistics const > protocols::abinitio::PairingStatisticsCOP

PairingStatisticsOP

typedef utility::pointer::shared_ptr< PairingStatistics > protocols::abinitio::PairingStatisticsOP

PoseWithScore

typedef std::pair< core::pose::Pose, core::Real > protocols::abinitio::PoseWithScore

ProtocolCOP

typedef utility::pointer::shared_ptr< Protocol const > protocols::abinitio::ProtocolCOP

ProtocolOP

typedef utility::pointer::shared_ptr< Protocol > protocols::abinitio::ProtocolOP

ResolutionSwitcherCOP

typedef utility::pointer::shared_ptr< ResolutionSwitcher const > protocols::abinitio::ResolutionSwitcherCOP

ResolutionSwitcherOP

typedef utility::pointer::shared_ptr< ResolutionSwitcher > protocols::abinitio::ResolutionSwitcherOP

SizeList

using protocols::abinitio::SizeList = typedef utility::vector1<core::Size>

StatEntries

typedef boost::unordered_map< core::scoring::dssp::StrandPairing, PairingStatEntry, _HashEntry, _MergableEntries > protocols::abinitio::StatEntries

StatEntryList

typedef utility::vector1< PairingStatEntry > protocols::abinitio::StatEntryList

TemplateCOP

typedef utility::pointer::shared_ptr< Template const > protocols::abinitio::TemplateCOP

TemplateJumpSetupCOP

typedef utility::pointer::shared_ptr< TemplateJumpSetup const > protocols::abinitio::TemplateJumpSetupCOP

TemplateJumpSetupOP

typedef utility::pointer::shared_ptr< TemplateJumpSetup > protocols::abinitio::TemplateJumpSetupOP

TemplateOP

typedef utility::pointer::shared_ptr< Template > protocols::abinitio::TemplateOP

TemplatesAP

typedef utility::pointer::weak_ptr< Templates > protocols::abinitio::TemplatesAP

TemplatesCAP

typedef utility::pointer::weak_ptr< Templates const > protocols::abinitio::TemplatesCAP

TemplatesCOP

typedef utility::pointer::shared_ptr< Templates const > protocols::abinitio::TemplatesCOP

TemplatesOP

typedef utility::pointer::shared_ptr< Templates > protocols::abinitio::TemplatesOP

Enumeration Type Documentation

StageID

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

Broker_main()

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().

common_setup()

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().

contains_stageid() [1/2]

bool protocols::abinitio::contains_stageid	(	utility::vector1< abinitio::StageID >	vec,
		abinitio::StageID	query
	)

contains_stageid() [2/2]

bool protocols::abinitio::contains_stageid	(	utility::vector1< ClassicAbinitio::StageID >	vec,
		ClassicAbinitio::StageID	query
	)

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

copy_side_chains()

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::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), tr(), and core::conformation::Atom::xyz().

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

decide_on_beta_jumping_from_frags()

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().

dump_movemap()

void protocols::abinitio::dump_movemap	(	kinematics::MoveMap const &	mm,
		core::Size	nres,
		std::ostream &	out
	)

References core::kinematics::MoveMap::get_bb(), and core::conformation::membrane::out.

filename()

std::string protocols::abinitio::filename

(

core::Size

batch_id

)

Referenced by core::scoring::ScoreFunction::_add_weights_from_file(), core::scoring::ScoreFunction::_add_weights_from_stream(), protocols::legacy_sewing::SewGraph::add_all_model_edges_from_binary(), core::chemical::add_atom_type_set_parameters_from_command_line(), core::chemical::add_atom_types_from_command_line(), core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::PoseResidueTypeSet::add_base_residue_type(), protocols::topology_broker::add_cmdline_claims(), protocols::legacy_sewing::SewGraph::add_edges_from_binary(), core::import_pose::pose_stream::PDBPoseInputStream::add_list_filenames(), core::chemical::add_mm_atom_type_set_parameters_from_command_line(), protocols::task_operations::JointSequenceOperation::add_native_pdb(), core::chemical::AtomTypeSet::add_parameters_from_file(), core::chemical::ResidueTypeSet::add_patches(), protocols::nmr::ParaNMRScoreMover::add_pcs_scores_to_scorefile(), protocols::task_operations::JointSequenceOperation::add_pdb(), protocols::nmr::ParaNMRScoreMover::add_pre_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), protocols::hybridization::HybridizeProtocol::add_template(), core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type(), core::scoring::ScoreFunction::add_weights_from_file(), 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::anchored_design::Anchor::Anchor(), protocols::motifs::MotifDnaPacker::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::moves::PDBDumpMover::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::parser::FragmentReader::apply(), protocols::flxbb::InterlockAroma::apply(), core::import_pose::atom_tree_diffs::AtomTreeDiff::AtomTreeDiff(), protocols::jd2::SingleFileBuffer::block(), protocols::jd2::MpiFileBuffer::block_file(), protocols::parser::BluePrint::BluePrint(), protocols::fldsgn::BluePrintBDR::BluePrintBDR(), core::io::pdb::build_pose_from_pdb_as_is(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), core::import_pose::centroid_pose_from_pdb(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size(), core::chemical::mainchain_potential::MainchainScoreTable::check_linestream(), protocols::dna::checkpoint_cleanup(), core::scoring::ChemicalShiftAnisotropy::ChemicalShiftAnisotropy(), core::scoring::func::CircularGeneral1D_Func::CircularGeneral1D_Func(), protocols::jd2::MpiFileBuffer::close_file(), core::chemical::carbohydrates::CarbohydrateInfoManager::codes_to_root_map_file(), protocols::abinitio::abscript::ConstraintPreparer::combine_exclude_file(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect(), core::fragment::ConstantLengthFragSet::ConstantLengthFragSet(), core::chemical::sdf::convert_to_ResidueTypes(), core::scoring::ScoringManager::create_aa_composition_energy_setup_instance(), core::scoring::nmr::NMRDataFactory::create_attach_nmr_data_to_pose(), protocols::helical_bundle_predict::HBPHelixParameters::create_calculator_from_file(), protocols::aa_composition::AddCompositionConstraintMover::create_constraint_from_file(), protocols::aa_composition::AddMHCEpitopeConstraintMover::create_constraint_from_file(), protocols::aa_composition::AddNetChargeConstraintMover::create_constraint_from_file(), protocols::denovo_design::components::create_debug_filename(), core::chemical::ChemicalManager::create_element_set(), protocols::relax::RelaxScriptManager::create_energy_map_instance(), core::io::external::PsiPredInterface::create_fasta_file(), core::scoring::ScoringManager::create_file_contents_instance(), protocols::rosetta_scripts::XmlObjects::create_from_file(), core::chemical::ChemicalManager::create_ideal_bond_length_set(), core::scoring::ScoringManager::create_mhc_csv_contents(), core::scoring::ScoringManager::create_mhc_epitope_energy_setup_instance(), core::scoring::ScoringManager::create_mhc_map_from_db(), core::scoring::ScoringManager::create_mhc_matrix_contents(), core::chemical::ChemicalManager::create_mm_atom_type_set(), core::scoring::ScoringManager::create_netcharge_energy_setup_instance(), core::scoring::ScoringManager::create_nmer_pssm(), core::scoring::ScoringManager::create_nmer_svm_aa_matrix(), core::scoring::ScoringManager::create_nmer_svm_rank(), protocols::relax::RelaxScriptManager::create_relax_script_instance(), core::scoring::ScoringManager::create_svm_rosetta(), protocols::abinitio::abscript::ConstraintPreparer::cst_file(), protocols::ddG_main(), protocols::ddG::ddGData::ddGData(), core::scoring::interface_::DDPlookup::DDPlookup(), protocols::loop_grower::DensSkeleton::DensSkeleton(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::determine_rotamer_well_order(), core::scoring::DipolarCoupling::DipolarCoupling(), core::scoring::dna::DNA_DihedralPotential::DNA_DihedralPotential(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::do_all_checks_and_corrections(), protocols::cartesian::MolecularDynamics::doMD(), protocols::cartesian::MolecularDynamics::doMinimising(), protocols::toolbox::dump_as_pdb(), protocols::simple_moves::PeriodicBoxMover::dump_ASU(), core::fragment::dump_frames_as_pdb(), core::io::carbohydrates::dump_gws(), core::io::carbohydrates::dump_gws_chain(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), protocols::abinitio::KinematicAbinitio::dump_jump_log(), core::pack::rotamers::dump_library(), core::io::pdb::dump_pdb(), core::pack::rotamer_set::RotamerSets::dump_pdb(), protocols::helix_capper::HelixNCapperMover::dump_pdb_to_file(), protocols::vip::VIP_Mover::dump_pdb_to_file(), protocols::viewer::dump_pose_kinemage(), protocols::design_opt::GreedyOptMutationMover::dump_scoring_table(), protocols::matdes::MatDesGreedyOptMutationMover::dump_scoring_table(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::mpi_refinement::MPI_Refinement::dump_structures(), protocols::mpi_refinement::Serial_Refine::dump_structures(), protocols::mean_field::AAMatrix::dump_transfac(), protocols::pockets::PocketGrid::dumpExemplarToFile(), protocols::pockets::PocketGrid::dumpGridToFile(), protocols::nonlocal::emit_intermediate(), 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::scoring::ScoreFunction::extract_weights_from_file(), core::scoring::ScoreFunction::extract_weights_from_stream(), core::import_pose::atom_tree_diffs::file_is_atom_tree_diff(), core::import_pose::pose_stream::filenames_from_list_file(), protocols::cluster::calibur::filetype(), core::fragment::fill_template_frames_from_pdb(), protocols::backrub::BackrubSidechainMover::finalize_simulation(), core::io::NomenclatureManager::find_alternate_codes_file(), core::chemical::carbohydrates::find_glycan_sequence_file(), core::chemical::carbohydrates::CarbohydrateInfoManager::find_linkage_conformer_data_file(), protocols::noesy_assign::FragsToAtomDist::FragsToAtomDist(), protocols::jd3::full_model_inputters::PDBFullModelInputter::full_model_from_input_source(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source(), core::fragment::rna::FullAtomRNA_Fragments::FullAtomRNA_Fragments(), core::chemical::ChemicalManager::gasteiger_atom_type_set(), protocols::noesy_assign::FragsToAtomDist::generate_from_frag_file(), 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::constraint_movers::CstInfoMover::get_constraints_from_file(), protocols::pack_daemon::DynamicAggregateFunction::get_file_contents(), protocols::antibody::design::get_graft_design_options(), core::scoring::ScoringManager::get_mhc_csv_contents(), core::scoring::ScoringManager::get_mhc_map_from_db(), core::scoring::ScoringManager::get_mhc_matrix_contents(), core::scoring::ScoringManager::get_nmer_pssm(), core::scoring::ScoringManager::get_nmer_svm(), core::scoring::ScoringManager::get_nmer_svm_aa_matrix(), core::scoring::ScoringManager::get_nmer_svm_list_file_contents(), core::scoring::ScoringManager::get_nmer_svm_rank(), core::scoring::ScoringManager::get_nmer_svm_rank_list_file_contents(), core::scoring::nmr::NMRDataFactory::get_nmr_data(), protocols::relax::RelaxScriptManager::get_relax_script(), protocols::antibody::design::get_seq_design_options(), protocols::motifs::get_targetconformers_user(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::getDensityMap_legacy(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), protocols::cluster::calibur::PreloadedPDB::getSimPDB(), core::pose::carbohydrates::glycosylate_pose_by_file(), core::kinematics::MoveMap::init_from_file(), protocols::helical_bundle::BundleParametrizationCalculator::init_from_file(), core::pack::rotamers::SingleLigandRotamerLibrary::init_from_file(), core::scoring::nmr::pre::PRESingleSet::init_from_filedata(), core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata(), core::scoring::nmr::rdc::RDCSingleSet::init_from_rdc_filedata(), core::scoring::nmr::pcs::PCSData::init_pcs_data_from_file(), protocols::qsar::scoring_grid::PCSSingleGrid::init_pcs_values_from_file(), core::scoring::nmr::pre::PREData::init_pre_data_from_file(), core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file(), 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(), protocols::canonical_sampling::HamiltonianExchange::initialize_exchange_schedule_from_file(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::initialize_from_command_line(), protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::initialize_from_directory(), core::scoring::aa_composition_energy::AACompositionConstraint::initialize_from_file(), core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file(), core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::initialize_from_file(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file(), core::scoring::netcharge_energy::NetChargeConstraint::initialize_from_file(), core::scoring::netcharge_energy::NetChargeEnergySetup::initialize_from_file(), core::scoring::ScoreFunction::initialize_from_file(), protocols::canonical_sampling::TemperingBase::initialize_from_file(), protocols::chromophore::ChromophoreDataReader::initialize_from_file(), protocols::canonical_sampling::HamiltonianExchange::initialize_from_file(), protocols::canonical_sampling::SimulatedTempering::initialize_from_file(), core::pack::palette::CustomBaseTypePackerPalette::initialize_from_file_contents(), 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::qsar::scoring_grid::PCSMultiGrid::initialize_pcs_data_from_input_file(), core::scoring::rna::RNA_TorsionPotential::initialize_potential_from_file(), 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::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file(), 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::jd2::MpiFileBuffer::is_open_channel(), 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::cluster::APCluster::load_binary(), protocols::motifs::load_build_position_data(), 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::jd2::archive::ArchiveBase::load_decoys(), protocols::loop_grower::DensSkeleton::load_density(), protocols::dna::load_dna_design_defs_from_file(), core::chemical::GlobalResidueTypeSet::load_exclude_pdb_component_ids(), protocols::qsar::scoring_grid::ShapeGrid::load_kbp_data(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_neighbor_atoms(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_parameters(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_reference_shifts(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_weights(), 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::optimize_weights::IterativeOptEDriver::load_pose(), protocols::stepwise::setup::load_s_and_l(), core::chemical::rdkit::load_sdf(), 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(), protocols::make_rot_lib::MakeRotLibOptionsData::MakeRotLibOptionsData(), core::scoring::mm::MMBondAngleLibrary::MMBondAngleLibrary(), core::scoring::mm::MMBondLengthLibrary::MMBondLengthLibrary(), core::scoring::mm::MMTorsionLibrary::MMTorsionLibrary(), 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::cluster::calibur::num_lines_in_file(), core::scoring::nv::NVlookup::NVlookup(), core::scoring::OneDDistPotential::OneDDistPotential(), protocols::noesy_assign::open_stream(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::output_atom_bin(), protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(), protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::pose_length_moves::PossibleLoop::output_fragment_debug(), protocols::minimization_packing::SetReturningPackRotamersMover::output_repacked_poses(), core::pack::pack_rotamers_setup(), core::chemical::mmCIF::mmCIFParser::parse(), protocols::antibody::CDRSetOptionsParser::parse_default_and_user_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_default_and_user_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_default_and_user_options(), core::chemical::sdf::MolFileIOReader::parse_file(), protocols::loops::JSONFormattedLoopsFileReader::parse_json_formatted_data(), protocols::loops::JSONFormattedLoopsFileReader::parse_json_residue_info(), protocols::pose_creation::ExtendedPoseMover::parse_my_tag(), protocols::nmr::pcs::PCSLigandTransformMover::parse_my_tag(), protocols::nmr::pre::PREMover::parse_my_tag(), protocols::loops::loops_definers::LoopsFileDefiner::parse_my_tag(), protocols::antibody::CDRSetOptionsParser::parse_options(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::chemical::mainchain_potential::MainchainScoreTable::parse_rama_map_file_shapovalov(), core::pack::task::parse_resfile(), protocols::ligand_docking::StartFrom::parse_startfrom_file(), 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(), core::scoring::nmr::pcs::PCSData::PCSData(), protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter(), protocols::qsar::scoring_grid::PCSMultiGrid::PCSMultiGrid(), protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid(), core::scoring::nmr::pcs::PCSSingleSet::PCSSingleSet(), protocols::denovo_design::movers::pdb_filename(), core::chemical::rotamers::PDBRotamerLibrarySpecification::pdb_rotamers_file(), core::scoring::cryst::PhenixInterface::PhenixInterface(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::pose_from_file(), core::import_pose::pose_from_pdb_stream(), core::import_pose::pose_from_pdbstring(), core::import_pose::poseOPs_from_files(), core::import_pose::poses_from_files(), core::scoring::nmr::pre::PREData::PREData(), core::scoring::nmr::pre::PRESingleSet::PRESingleSet(), protocols::dna::DnaInterfacePacker::protein_scan(), core::io::rna::RDAT::RDAT(), core::scoring::nmr::rdc::RDCData::RDCData(), core::scoring::nmr::rdc::RDCSingleSet::RDCSingleSet(), core::grid::CartGrid< T >::read(), protocols::mean_field::GenMeanFieldMover::read_aa_matrix(), core::sequence::read_alignment_file(), core::import_pose::read_all_poses(), core::sequence::read_aln(), core::io::read_alternative_3_letter_codes_from_database_file(), protocols::anchored_design::Anchor::read_anchorfile(), core::energy_methods::IdealParametersDatabase::read_bbdep_table(), protocols::parser::BluePrint::read_blueprint(), protocols::parser::BluePrint::read_blueprint_stream(), core::chemical::gasteiger::GasteigerAtomTypeSet::read_bond_file(), core::chemical::carbohydrates::read_codes_and_roots_from_database_file(), protocols::branch_angle::BranchAngleOptimizer::read_coef1(), protocols::branch_angle::BranchAngleOptimizer::read_coef2(), core::chemical::rings::read_conformers_from_database_file_for_ring_size(), protocols::chromophore::ReadResidueCoordinatesFromPDB::read_coordinates_from_file(), core::scoring::elec::read_cp_tables_from_db(), core::scoring::ChemicalShiftAnisotropy::read_CSA_file(), core::fragment::FragmentIO::read_data(), protocols::hotspot_hashing::HotspotStubSet::read_data(), core::io::rna::RNA_DataReader::read_data_from_file(), core::io::rna::RNA_DataReader::read_data_from_rdat(), core::fragment::FragmentIO::read_data_from_stream(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::read_database(), core::scoring::GenericBondedPotential::read_database(), core::scoring::HydroxylTorsionPotential::read_database(), core::scoring::UnfoldedStatePotential::read_database_file(), core::scoring::SplitUnfoldedTwoBodyPotential::read_database_file(), protocols::loophash::BackboneDB::read_db(), protocols::loophash::LoopHashMap::read_db(), core::scoring::DipolarCoupling::read_DC_file(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::scoring::dna::DNA_DihedralPotential::read_dna_geometry_log_file(), protocols::genetic_algorithm::GeneticAlgorithmBase::read_entities_checkpoint(), core::enzymes::read_enzyme_data_from_file(), core::sequence::read_fasta_file(), core::sequence::read_fasta_file_and_concatenate(), core::sequence::read_fasta_file_return_str(), core::sequence::read_fasta_file_section(), core::sequence::read_fasta_file_str(), core::chemical::AtomTypeSet::read_file(), core::chemical::ElementSet::read_file(), core::chemical::gasteiger::GasteigerAtomTypeSet::read_file(), core::chemical::IdealBondLengthSet::read_file(), core::chemical::Metapatch::read_file(), core::chemical::MMAtomTypeSet::read_file(), core::chemical::orbitals::OrbitalTypeSet::read_file(), core::chemical::Patch::read_file(), protocols::frags::RMSVallData::read_file(), protocols::frags::VallData::read_file(), protocols::frags::TorsionFragmentLibrary::read_file(), core::import_pose::atom_tree_diffs::AtomTreeDiff::read_file(), protocols::cyclic_peptide_predict::read_file_into_string(), core::chemical::ResidueTypeSet::read_files_for_base_residue_types(), core::chemical::ResidueTypeSet::read_files_for_unpatchable_residue_types(), core::fragment::MinimalFragSet::read_fragment_file(), core::fragment::ConstantLengthFragSet::read_fragment_file(), core::fragment::MinimalFragSet::read_fragment_stream(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), core::fragment::FragmentIO::read_frames_from_file(), protocols::optimize_weights::OptEData::read_from_binary_file(), protocols::legacy_sewing::Hasher::read_from_disk(), protocols::wum::SilentStructStore::read_from_file(), core::sequence::SequenceAlignment::read_from_file(), protocols::noesy_assign::FragsToAtomDist::read_from_file(), protocols::jumping::DisulfPairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file(), protocols::optimize_weights::OptEData::read_from_file(), protocols::jumping::PairingLibrary::read_from_file_no_filters(), core::scoring::carbohydrates::read_Gaussian_parameters_from_database_file(), core::sequence::read_general_aln_file(), protocols::genetic_algorithm::GeneticAlgorithmBase::read_generations_checkpoint(), protocols::jd2::EnsembleJobInputter::read_get_weights(), core::chemical::carbohydrates::read_glycan_sequence_file(), core::sequence::read_grishin_aln_file(), protocols::rosetta_scripts::RosettaScriptsParser::read_in_and_recursively_replace_includes(), core::io::nmr::read_in_database_file(), protocols::read_in_mutations(), protocols::mean_field::GenMeanFieldMover::read_input_pdbs(), protocols::loophash::BackboneDB::read_legacydb(), protocols::loophash::LoopHashMap::read_legacydb(), protocols::enzdes::EnzdesBaseProtocol::read_ligand_superposition_file(), core::chemical::carbohydrates::read_linkage_conformers_from_database_file(), protocols::loops::JSONFormattedLoopsFileReader::read_loop_file(), protocols::loops::LoopsFileIO::read_loop_file(), protocols::loops::LoopsFileIO::read_loop_file_stream(), protocols::toolbox::match_enzdes_util::EnzdesLoopsFile::read_loops_file(), core::chemical::io::read_merge_behaviors_from_database_file(), core::chemical::AtomTypeSet::read_meta_file(), protocols::helical_bundle::read_minor_helix_params(), protocols::legacy_sewing::read_model_file(), protocols::sewing::hashing::ModelFileReader::read_model_file(), protocols::legacy_sewing::read_native_residue_file(), core::chemical::carbohydrates::read_nomenclature_table_from_database_file(), protocols::quantum_annealing::ExternalPackerResultLoader::read_packer_problem_file(), protocols::abinitio::Templates::read_pairings(), core::import_pose::RNA_DeNovoParameters::read_parameters_from_file(), core::io::nmr::read_pcs_datafile(), protocols::cyclic_peptide_predict::read_peptide_design_file(), protocols::enzdes::enzutil::read_pose_from_file(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), core::io::nmr::read_pre_datafile(), core::fragment::SecondaryStructure::read_psipred_ss2(), core::pose::read_psipred_ss2_file(), core::scoring::methods::NMerSVMEnergy::read_pssm_features(), protocols::ligand_docking::ProtLigEnsemble::read_qsar_file(), core::chemical::mainchain_potential::read_rama_map_file_shapovalov(), protocols::rbsegment_relax::read_RBSegment_file(), core::io::rna::RDAT::read_rdat_file(), core::io::nmr::read_rdc_datafile(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), protocols::scoring::ResidualDipolarCouplingRigidSegments::read_RDC_segment_file(), core::io::pdb::read_record_definitions_from_file(), core::chemical::carbohydrates::read_ring_sizes_and_morphemes_from_database_file(), protocols::quantum_annealing::ExternalPackerResultLoader::read_rotamer_selection_file(), core::pose::rna::RNA_SecStruct::read_secstruct_from_file(), core::conformation::symmetry::SymmetryInfo::read_silent_struct(), core::chemical::io::read_split_behaviors_from_database_file(), core::conformation::symmetry::SymmData::read_symmetry_data_from_file(), protocols::topology_broker::PcsEnergyController::read_tag(), 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::StartStructClaimer::read_tag(), core::io::raw_data::RawFileData::read_tags_fast(), core::fragment::SecondaryStructure::read_talos_ss(), protocols::cluster::read_template_scores(), core::chemical::read_topology_file(), protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef1(), protocols::branch_angle::BranchAngleOptimizer::read_undefined_coef2(), core::fragment::rna::FullAtomRNA_Fragments::read_vall_torsions(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::jd2::MpiFileBuffer::release_file(), protocols::jd2::MpiFileBuffer::remote_close_file(), protocols::abinitio::HedgeArchive::remove_pending_decoys(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), protocols::legacy_sewing::SewGraph::report_binary_stats(), 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(), protocols::frags::RMSVallData::RMSVallData(), core::scoring::SecondaryStructurePotential::rsigma_dot_initializer(), protocols::jd2::MpiFileBuffer::run(), protocols::motifs::MotifDnaPacker::run_motifs(), core::io::external::runpsipred_name_mangle_check(), protocols::cluster::APCluster::save_binary(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::archive::ArchiveBase::save_decoys(), protocols::abinitio::HedgeArchive::save_pending_decoys(), protocols::rosetta_scripts::save_schema(), protocols::wum::SilentStructStore::serialize_to_file(), protocols::fldsgn::BluePrintBDR::set_blueprint(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_constraints_file(), protocols::helical_bundle::MakeBundle::set_crick_params_file_for_helix(), 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(), protocols::helical_bundle::MakeBundleHelix::set_minor_helix_params_from_file(), 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::glycopeptide_docking::GlycopeptideDockingProtocol::set_ref_pose_from_filename(), protocols::loops::set_secstruct_from_dssp(), protocols::loops::set_secstruct_from_psipred_ss2(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::md::MDBase::set_write_dynamic_rsr(), protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies(), 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::sequence::simple_mapping_from_file(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::SixDTransRotPotential(), core::scoring::SplitUnfoldedTwoBodyPotential::SplitUnfoldedTwoBodyPotential(), core::energy_methods::DumpTrajectoryEnergy::start_new_activity(), core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(), core::chemical::carbohydrates::CarbohydrateInfoManager::sugar_modifications_table_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::symmetrize_library(), protocols::motifs::IRCollection::try_for_more(), core::scoring::UnfoldedStatePotential::UnfoldedStatePotential(), protocols::jobdist::universal_main(), protocols::docking::DockingEnsemble::update_pdblist_file(), protocols::loops::validate_loop_start_stop(), protocols::hybridization::HybridizeProtocol::validate_template(), core::fragment::picking_old::vall::vall_library_from_file(), protocols::frag_picker::VallProvider::vallChunksFromLibrary(), protocols::frags::VallData::VallData(), protocols::frag_picker::VallProvider::vallNumLines(), core::grid::CartGrid< T >::write(), protocols::hotspot_hashing::HotspotStubSet::write_all(), core::io::raw_data::RawFileData::write_all(), core::scoring::constraints::ConstraintIO::write_constraints(), protocols::loophash::BackboneDB::write_db(), protocols::loophash::LoopHashMap::write_db(), protocols::denovo_design::components::PoseBuilder::write_debug_pdb(), protocols::genetic_algorithm::GeneticAlgorithmBase::write_entities_checkpoint(), protocols::genetic_algorithm::GeneticAlgorithmBase::write_generations_checkpoint(), protocols::legacy_sewing::write_hashing_scores_to_file(), protocols::noesy_assign::FragsToAtomDist::write_hist_to_file(), protocols::loops::Loops::write_loops_to_file(), protocols::helical_bundle::write_minor_helix_params(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), protocols::legacy_sewing::write_model_file(), protocols::motifs::write_motifs_to_disk(), protocols::legacy_sewing::write_native_residue_file(), protocols::noesy_assign::CrossPeakList::write_peak_files(), protocols::flxbb::LayerDesignOperation::write_pymol_script(), core::conformation::symmetry::SymmetryInfo::write_silent_struct(), protocols::optimize_weights::OptEData::write_to_binary_file(), core::grid::CartGrid< T >::write_to_BRIX(), protocols::loop_grower::LoopGrower::write_to_disk(), protocols::legacy_sewing::Hasher::write_to_disk(), protocols::noesy_assign::FragsToAtomDist::write_to_file(), protocols::simple_filters::write_to_file(), protocols::contact_map::ContactMap::write_to_file(), protocols::optimize_weights::OptEData::write_to_file(), core::chemical::write_topology_file(), protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef1(), protocols::branch_angle::BranchAngleOptimizer::write_undefined_coef2(), and protocols::loop_grower::LoopPartialSolutionStore::writelpsstore().

find_sampling_cuts()

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().

fix_chainbreak_patch()

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().

get_core()

void protocols::abinitio::get_core	(	toolbox::DecoySetEvaluation &	eval,
		core::Real	cutoff,
		loops::Loops &	rigid
	)

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::clear(), core::energy_methods::eval(), tr(), and protocols::jd2::archive::EvaluatedArchive::weights().

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

hash_value() [1/2]

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

inline

References protocols::hybridization::val.

hash_value() [2/2]

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

inline

References protocols::hybridization::val.

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

noe_stage()

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().

operator<<() [1/6]

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

operator<<() [2/6]

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

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

operator<<() [3/6]

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

inline

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

operator<<() [4/6]

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

operator<<() [5/6]

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

References core::conformation::membrane::out.

operator<<() [6/6]

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

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

operator>>() [1/3]

std::istream& protocols::abinitio::operator>>	(	std::istream &	is,
		PairingStatEntry &	ps
	)

operator>>() [2/3]

std::istream& protocols::abinitio::operator>>	(	std::istream &	is,
		PairingStatistics &	ps
	)

operator>>() [3/3]

std::istream& protocols::abinitio::operator>>	(	std::istream &	is,
		StatEntries &	pslist
	)

References protocols::abinitio::PairingStatEntry::pairing().

register_common_options()

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().

register_cutoff()

Size protocols::abinitio::register_cutoff

(

5

)

Referenced by protocols::abinitio::AlternativePairings::compatible().

register_options_broker()

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().

residue_cutoff()

Size protocols::abinitio::residue_cutoff

(

5

)

Referenced by protocols::abinitio::AlternativePairings::compatible().

run_boinc_debug()

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().

sort_PoseWithScore()

bool protocols::abinitio::sort_PoseWithScore	(	const PoseWithScore &	left,
		const PoseWithScore &	right
	)

References core::sequence::left.

TR()

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

static

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