protocols::abinitio Namespace Reference

Classes
class	PcaEvaluator
class	ShowViolation
class	ComputeTotalDistCst
class	Stage1Sampler
class	AbrelaxApplication
	application level code for Abrelax, Foldconstraints and JumpingFoldconstraints 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	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 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	IterativeCentroid
class	IterativeFullatom
class	JumpingFoldConstraints
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::owning_ptr < AbrelaxMover >	AbrelaxMoverOP
typedef utility::pointer::owning_ptr < AbrelaxMover const >	AbrelaxMoverCOP
typedef utility::pointer::owning_ptr < hConvergenceCheck >	hConvergenceCheckOP
typedef utility::pointer::owning_ptr < ClassicAbinitio >	ClassicAbinitioOP
typedef utility::pointer::owning_ptr < ClassicAbinitio const >	ClassicAbinitioCOP
typedef utility::pointer::owning_ptr < ConstraintFragmentSampler >	ConstraintFragmentSamplerOP
typedef utility::pointer::owning_ptr < DoubleLayerKinematicAbinitio >	DoubleLayerKinematicAbinitioOP
typedef utility::pointer::owning_ptr < DoubleLayerKinematicAbinitio const >	DoubleLayerKinematicAbinitioCOP
typedef utility::pointer::owning_ptr < FoldConstraints >	FoldConstraintsOP
typedef utility::pointer::owning_ptr < FoldConstraints const >	FoldConstraintsCOP
typedef utility::pointer::owning_ptr < FragmentSampler >	FragmentSamplerOP
typedef utility::pointer::owning_ptr < FragmentSampler const >	FragmentSamplerCOP
typedef utility::pointer::owning_ptr < HedgeArchive >	HedgeArchiveOP
typedef utility::pointer::owning_ptr < HedgeArchive const >	HedgeArchiveCOP
typedef utility::pointer::owning_ptr < KinematicAbinitio >	KinematicAbinitioOP
typedef utility::pointer::owning_ptr < KinematicAbinitio const >	KinematicAbinitioCOP
typedef utility::pointer::owning_ptr < JumpingFoldConstraintsWrapper >	JumpingFoldConstraintsWrapperOP
typedef utility::pointer::owning_ptr < JumpingFoldConstraintsWrapper const >	JumpingFoldConstraintsWrapperCOP
typedef utility::pointer::owning_ptr < KinematicControl >	KinematicControlOP
typedef utility::pointer::owning_ptr < KinematicControl const >	KinematicControlCOP
typedef utility::pointer::owning_ptr < KinematicTaskControl >	KinematicTaskControlOP
typedef utility::pointer::owning_ptr < KinematicTaskControl const >	KinematicTaskControlCOP
typedef utility::pointer::owning_ptr < LoopJumpFoldCst >	LoopJumpFoldCstOP
typedef utility::pointer::owning_ptr < LoopJumpFoldCst const >	LoopJumpFoldCstCOP
typedef utility::pointer::owning_ptr < MembraneAbinitio >	MembraneAbinitioOP
typedef utility::pointer::owning_ptr < MembraneAbinitio const >	MembraneAbinitioCOP
typedef utility::pointer::owning_ptr < PairingStatistics >	PairingStatisticsOP
typedef utility::pointer::owning_ptr < PairingStatistics const >	PairingStatisticsCOP
typedef utility::vector1 < PairingStatEntry >	StatEntryList
typedef boost::unordered_map < core::scoring::dssp::StrandPairing, PairingStatEntry, _HashEntry, _MergableEntries >	StatEntries
typedef utility::pointer::owning_ptr < Protocol >	ProtocolOP
typedef utility::pointer::owning_ptr < Protocol const >	ProtocolCOP
typedef utility::pointer::owning_ptr < ResolutionSwitcher >	ResolutionSwitcherOP
typedef utility::pointer::owning_ptr < ResolutionSwitcher const >	ResolutionSwitcherCOP
typedef utility::vector1< Size >	SizeList
typedef utility::pointer::owning_ptr < Template >	TemplateOP
typedef utility::pointer::owning_ptr < Template const >	TemplateCOP
typedef utility::pointer::owning_ptr < TemplateJumpSetup >	TemplateJumpSetupOP
typedef utility::pointer::owning_ptr < TemplateJumpSetup const >	TemplateJumpSetupCOP
typedef utility::pointer::owning_ptr < Templates >	TemplatesOP
typedef utility::pointer::owning_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 (Size total_res, Real factor)
bool	contains_stageid (utility::vector1< abinitio::StageID > vec, abinitio::StageID query)
std::string	filename (core::Size batch_id)
static numeric::random::RandomGenerator	RG (42089)
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< Size > &sample_cuts)
static numeric::random::RandomGenerator	RG (5651234)
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, Size nres, std::ostream &out)
static numeric::random::RandomGenerator	RG (1259812489)
static numeric::random::RandomGenerator	RG (12598234)
int	run_boinc_debug ()

Typedef Documentation

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

Definition at line 23 of file AbrelaxMover.fwd.hh.

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

Definition at line 21 of file AbrelaxMover.fwd.hh.

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

Definition at line 32 of file ClassicAbinitio.fwd.hh.

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

Definition at line 28 of file ClassicAbinitio.fwd.hh.

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

Definition at line 45 of file ConstraintFragmentSampler.hh.

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

Definition at line 32 of file DoubleLayerKinematicAbinitio.fwd.hh.

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

Definition at line 28 of file DoubleLayerKinematicAbinitio.fwd.hh.

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

Definition at line 32 of file FoldConstraints.fwd.hh.

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

Definition at line 28 of file FoldConstraints.fwd.hh.

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

Definition at line 32 of file FragmentSampler.fwd.hh.

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

Definition at line 28 of file FragmentSampler.fwd.hh.

typedef utility::pointer::owning_ptr< hConvergenceCheck > protocols::abinitio::hConvergenceCheckOP

Definition at line 788 of file ClassicAbinitio.cc.

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

Definition at line 23 of file HedgeArchive.fwd.hh.

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

Definition at line 21 of file HedgeArchive.fwd.hh.

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

Definition at line 37 of file KinematicAbinitio.fwd.hh.

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

Definition at line 34 of file KinematicAbinitio.fwd.hh.

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

Definition at line 32 of file KinematicAbinitio.fwd.hh.

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

Definition at line 28 of file KinematicAbinitio.fwd.hh.

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

Definition at line 31 of file KinematicControl.fwd.hh.

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

Definition at line 27 of file KinematicControl.fwd.hh.

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

Definition at line 32 of file KinematicTaskControl.fwd.hh.

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

Definition at line 28 of file KinematicTaskControl.fwd.hh.

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

Definition at line 39 of file KinematicTaskControl.fwd.hh.

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

Definition at line 35 of file KinematicTaskControl.fwd.hh.

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

Definition at line 32 of file MembraneAbinitio.fwd.hh.

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

Definition at line 28 of file MembraneAbinitio.fwd.hh.

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

Definition at line 27 of file PairingStatistics.fwd.hh.

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

Definition at line 25 of file PairingStatistics.fwd.hh.

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

Definition at line 2041 of file AbrelaxApplication.cc.

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

Definition at line 27 of file Protocol.fwd.hh.

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

Definition at line 25 of file Protocol.fwd.hh.

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

Definition at line 32 of file ResolutionSwitcher.fwd.hh.

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

Definition at line 28 of file ResolutionSwitcher.fwd.hh.

typedef utility::vector1< Size > protocols::abinitio::SizeList

Definition at line 98 of file StrandConstraints.cc.

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

Definition at line 148 of file PairingStatistics.hh.

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

Definition at line 142 of file PairingStatistics.hh.

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

Definition at line 27 of file Template.fwd.hh.

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

Definition at line 32 of file TemplateJumpSetup.fwd.hh.

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

Definition at line 28 of file TemplateJumpSetup.fwd.hh.

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

Definition at line 25 of file Template.fwd.hh.

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

Definition at line 27 of file Templates.fwd.hh.

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

Definition at line 25 of file Templates.fwd.hh.

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

Definition at line 34 of file FragmentSampler.fwd.hh.

Function Documentation

void protocols::abinitio::Broker_main

(

)

Initiates AbrelaxMover using the job distribution (jd2)

Definition at line 212 of file BrokerMain.cc.

References common_setup(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::go(), protocols::jd2::archive::MPIArchiveJobDistributor::is_archive_rank(), and protocols::jd2::archive::MPIArchiveJobDistributor::set_archive().

void protocols::abinitio::common_setup

(

)

Definition at line 191 of file BrokerMain.cc.

References core::scoring::constraints::FuncFactory::add_type(), core::scoring::constraints::ConstraintIO::get_func_factory(), core::scoring::constraints::ConstraintFactory::get_instance(), core::scoring::constraints::ConstraintFactory::replace_creator(), and tr().

Referenced by Broker_main().

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

Definition at line 91 of file FragmentSampler.cc.

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

Definition at line 130 of file ClassicAbinitio.cc.

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
	)

Definition at line 79 of file ResolutionSwitcher.cc.

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::total_residue(), and tr().

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

bool protocols::abinitio::decide_on_beta_jumping_from_frags

(

)

Definition at line 343 of file IterativeBase.cc.

References core::fragment::SecondaryStructure::helix_fraction(), 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,
		Size	nres,
		std::ostream &	out
	)

Definition at line 86 of file Template.cc.

References core::kinematics::MoveMap::get_bb().

std::string protocols::abinitio::filename

(

core::Size

batch_id)

Definition at line 84 of file HedgeArchive.cc.

Referenced by core::chemical::add_atom_type_set_parameters_from_command_line(), core::import_pose::pose_stream::PDBPoseInputStream::add_list_filenames(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::swa::rna::Analyze_base_bin_map(), protocols::motifs::MotifDnaPacker::apply(), protocols::moves::PDBDumpMover::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::jd2::SingleFileBuffer::block(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::dna::checkpoint_cleanup(), core::scoring::ChemicalShiftAnisotropy::ChemicalShiftAnisotropy(), protocols::jd2::MpiFileBuffer::close_file(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), 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(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::pockets::PocketGrid::dumpGridToFile(), core::chemical::ChemicalManager::element_set(), protocols::genetic_algorithm::GeneticAlgorithm::entities_checkpoint_filename(), core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::eval_dipolar(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_dipolar(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::motifs::MotifDnaPacker::expand_motifs(), core::import_pose::pose_stream::filenames_from_list_file(), protocols::backrub::BackrubSidechainMover::finalize_simulation(), protocols::comparative_modeling::AlignmentClustering::generateRankedAlignments(), protocols::genetic_algorithm::GeneticAlgorithm::generations_checkpoint_filename(), protocols::pack_daemon::DynamicAggregateFunction::get_file_contents(), protocols::motifs::get_filenames(), protocols::vip::VIP_Report::get_GOE_packstat_report(), protocols::mpi::ArchiveMasterBase::get_new_decoys(), protocols::motifs::get_targetconformers_user(), core::chemical::ChemicalManager::ideal_bond_length_set(), 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::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_basepair_xy(), protocols::jobdist::PlainPdbJobDistributor::is_finished(), protocols::dna::load_checkpoint(), protocols::dna::load_dna_design_defs_from_file(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::load_lib(), protocols::jobdist::load_s_and_l(), protocols::swa::load_s_and_l(), core::pack::dunbrack::load_unboundrot(), core::chemical::ChemicalManager::mm_atom_type_set(), protocols::motifs::MotifLibrary::MotifLibrary(), protocols::noesy_assign::open_stream(), protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::simple_moves::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::scoring::methods::pcs::PCS_data::PCS_data(), protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdbstring(), protocols::wum::MPI_Relax::process_inbound_wus_master(), protocols::dna::DnaInterfacePacker::protein_scan(), core::scoring::ChemicalShiftAnisotropy::read_CSA_file(), core::fragment::FragmentIO::read_data(), core::scoring::DipolarCoupling::read_DC_file(), protocols::genetic_algorithm::GeneticAlgorithm::read_entities_checkpoint(), protocols::jumping::PairingLibrary::read_from_file(), protocols::jumping::DisulfPairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file_no_filters(), protocols::genetic_algorithm::GeneticAlgorithm::read_generations_checkpoint(), protocols::rna::RNA_JumpLibrary::read_jumps_from_file(), core::pose::read_psipred_ss2_file(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), protocols::topology_broker::PseudocontactShiftEnergyController::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_decoys(), protocols::forge::components::BDR::resfile(), core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::ResidueTypeSet::ResidueTypeSet(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::abinitio::HedgeArchive::restore_status(), protocols::jd2::MpiFileBuffer::run(), protocols::motifs::MotifDnaPacker::run_motifs(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::abinitio::HedgeArchive::save_decoys(), protocols::jd2::archive::ArchiveBase::save_to_file(), protocols::forge::constraints::ConstraintFileRCG::set_cstfile(), protocols::anchored_design::Anchor::set_filename(), protocols::noesy_assign::CrossPeakInfo::set_filename(), protocols::match::output::WriteUpstreamCoordinateKinemage::set_kinemage_file_name(), core::chemical::ResidueType::set_RotamerLibraryName(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::pack::symmetric_pack_rotamers_setup(), protocols::motifs::IRCollection::try_for_more(), protocols::jobdist::universal_main(), protocols::outputter::FormatStringOutputter::write(), protocols::genetic_algorithm::GeneticAlgorithm::write_entities_checkpoint(), protocols::genetic_algorithm::GeneticAlgorithm::write_generations_checkpoint(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), protocols::noesy_assign::CrossPeakList::write_peak_files(), and core::chemical::write_topology_file().

void protocols::abinitio::find_sampling_cuts	(	kinematics::FoldTree const &	sampling,
		kinematics::FoldTree const &	final,
		utility::vector1< Size > &	sample_cuts
	)

Definition at line 82 of file KinematicControl.cc.

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
	)

Definition at line 326 of file IterativeBase.cc.

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
	)

Definition at line 1924 of file IterativeBase.cc.

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

Definition at line 121 of file PairingStatistics.hh.

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

Definition at line 124 of file PairingStatistics.hh.

References core::scoring::dssp::StrandPairing::hash_value().

Size protocols::abinitio::noe_stage	(	Size	total_res,
		Real	factor
	)

Definition at line 190 of file FoldConstraints.cc.

References 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

Definition at line 116 of file PairingStatistics.hh.

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

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

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

Definition at line 256 of file StrandConstraints.cc.

References protocols::abinitio::AlternativePairings::show().

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

Definition at line 305 of file PairingStatistics.cc.

References core::scoring::dssp::StrandPairingSet::begin(), core::scoring::dssp::StrandPairingSet::end(), protocols::abinitio::PairingStatistics::is_native_pairing(), protocols::abinitio::PairingStatistics::model_weight_, core::scoring::dssp::StrandPairingSet::size(), protocols::abinitio::PairingStatistics::strand_weight(), protocols::abinitio::PairingStatistics::topology(), and tr().

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

Definition at line 310 of file StrandConstraints.cc.

References protocols::abinitio::StrandConstraints::show().

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

Definition at line 369 of file PairingStatistics.cc.

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

Definition at line 352 of file PairingStatistics.cc.

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
	)

Definition at line 377 of file PairingStatistics.cc.

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

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

Definition at line 386 of file PairingStatistics.cc.

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().

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().

Definition at line 61 of file BrokerMain.cc.

References core::pack::interaction_graph::debug.

Size protocols::abinitio::residue_cutoff

(

5

)

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

static numeric::random::RandomGenerator protocols::abinitio::RG ( 1259812489  )

static

static numeric::random::RandomGenerator protocols::abinitio::RG ( 5651234  )

static

static numeric::random::RandomGenerator protocols::abinitio::RG ( 12598234  )

static

static numeric::random::RandomGenerator protocols::abinitio::RG ( 42089  )

static

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::HedgeArchive::collect(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::abinitio::TemplateJumpSetup::create_jump_sample(), protocols::abinitio::AbrelaxApplication::fold(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::abinitio::HedgeArchive::incorporate_batch(), protocols::abinitio::AbrelaxApplication::insert_template_frags(), protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops(), protocols::abinitio::LoopJumpFoldCst::select_loops(), and protocols::abinitio::PairingStatistics::suggest_topology().

int protocols::abinitio::run_boinc_debug

(

)

Definition at line 72 of file vs_test.cc.

References core::chemical::CENTROID, core::pack::interaction_graph::debug, core::chemical::ChemicalManager::get_instance(), core::scoring::getScoreFunction(), 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::total_residue(), and core::io::silent::SilentFileData::write_silent_struct().

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

Definition at line 2042 of file AbrelaxApplication.cc.

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

static

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