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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< 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< 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 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 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

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 ( )
void protocols::abinitio::common_setup ( )
bool protocols::abinitio::contains_stageid ( utility::vector1< abinitio::StageID >  vec,
abinitio::StageID  query 
)
bool protocols::abinitio::contains_stageid ( utility::vector1< ClassicAbinitio::StageID >  vec,
ClassicAbinitio::StageID  query 
)
bool protocols::abinitio::copy_side_chains ( core::pose::Pose pose,
utility::vector1< bool > &  needToRepack,
core::pose::Pose const &  fa_input_pose 
)
bool protocols::abinitio::decide_on_beta_jumping_from_frags ( )
void protocols::abinitio::dump_movemap ( kinematics::MoveMap const &  mm,
core::Size  nres,
std::ostream &  out 
)
std::string protocols::abinitio::filename ( core::Size  batch_id)

Referenced by core::chemical::add_atom_type_set_parameters_from_command_line(), core::chemical::add_atom_types_from_command_line(), protocols::topology_broker::add_cmdline_claims(), core::import_pose::pose_stream::PDBPoseInputStream::add_list_filenames(), core::chemical::add_mm_atom_type_set_parameters_from_command_line(), core::chemical::ResidueTypeSet::add_patches(), protocols::nmr::ParaNMRScoreMover::add_pcs_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_pre_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map(), protocols::moves::PDBDumpMover::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::parser::FragmentReader::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::jd2::SingleFileBuffer::block(), core::io::pdb::build_pose_from_pdb_as_is(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::dna::checkpoint_cleanup(), core::scoring::ChemicalShiftAnisotropy::ChemicalShiftAnisotropy(), protocols::jd2::MpiFileBuffer::close_file(), core::chemical::carbohydrates::CarbohydrateInfoManager::codes_to_root_map_file(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect(), core::chemical::ChemicalManager::create_element_set(), core::chemical::ChemicalManager::create_ideal_bond_length_set(), core::scoring::ScoringManager::create_mhc_csv_contents(), core::scoring::ScoringManager::create_mhc_map_from_db(), core::chemical::ChemicalManager::create_mm_atom_type_set(), protocols::abinitio::abscript::ConstraintPreparer::cst_file(), protocols::ddG_main(), protocols::ddG::ddGData::ddGData(), core::scoring::DipolarCoupling::DipolarCoupling(), protocols::cartesian::MolecularDynamics::doMD(), protocols::cartesian::MolecularDynamics::doMinimising(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), core::io::pdb::dump_pdb(), protocols::mpi_refinement::Serial_Refine::dump_structures(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::mpi_refinement::MPI_Refinement::dump_structures(), protocols::pockets::PocketGrid::dumpExemplarToFile(), protocols::pockets::PocketGrid::dumpGridToFile(), protocols::genetic_algorithm::GeneticAlgorithmBase::entities_checkpoint_filename(), core::scoring::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::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::scoring::aa_repeat_energy::AARepeatEnergy::load_penalty_table_from_file(), protocols::stepwise::setup::load_s_and_l(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), core::pack::dunbrack::load_unboundrot(), protocols::cluster::calibur::PreloadedPDB::loadPDBFromList(), protocols::cluster::calibur::PreloadedPDB::loadSilentFile(), protocols::ncbb::SecStructFinder::make_filename(), core::chemical::MergeBehaviorManager::MergeBehaviorManager(), protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop(), core::scoring::methods::EnergyMethodOptions::nmer_svm(), core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix(), core::scoring::methods::EnergyMethodOptions::nmer_svm_list(), core::scoring::methods::EnergyMethodOptions::nmer_svm_rank(), core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list(), core::io::NomenclatureManager::NomenclatureManager(), protocols::noesy_assign::open_stream(), protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(), protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::minimization_packing::SetReturningPackRotamersMover::output_repacked_poses(), core::pack::pack_rotamers_setup(), protocols::loops::JSONFormattedLoopsFileReader::parse_json_residue_info(), protocols::loops::loops_definers::LoopsFileDefiner::parse_my_tag(), protocols::pose_creation::ExtendedPoseMover::parse_my_tag(), protocols::nmr::pre::PREMover::parse_my_tag(), protocols::nmr::pcs::PCSLigandTransformMover::parse_my_tag(), protocols::legacy_sewing::LegacyReadNativeRotamersFile::parse_tag(), protocols::scoring::methods::pcs::PCS_data::PCS_data(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::PCS_data_Ts1(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::PCS_data_Ts2(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::PCS_data_Ts3(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::PCS_data_Ts4(), protocols::scoring::methods::pcs2::PcsDataCenter::PcsDataCenter(), protocols::denovo_design::movers::pdb_filename(), core::chemical::rotamers::PDBRotamerLibrarySpecification::pdb_rotamers_file(), core::scoring::cryst::PhenixInterface::PhenixInterface(), core::import_pose::pose_from_file(), core::import_pose::pose_from_pdbstring(), core::import_pose::poseOPs_from_files(), core::import_pose::poses_from_files(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::mean_field::GenMeanFieldMover::read_aa_matrix(), core::import_pose::read_all_poses(), protocols::parser::BluePrint::read_blueprint_stream(), core::scoring::ChemicalShiftAnisotropy::read_CSA_file(), core::fragment::FragmentIO::read_data(), core::scoring::DipolarCoupling::read_DC_file(), protocols::genetic_algorithm::GeneticAlgorithmBase::read_entities_checkpoint(), core::chemical::ResidueTypeSet::read_files_for_base_residue_types(), core::chemical::ResidueTypeSet::read_files_for_unpatchable_residue_types(), protocols::jumping::DisulfPairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file(), protocols::jumping::PairingLibrary::read_from_file_no_filters(), protocols::genetic_algorithm::GeneticAlgorithmBase::read_generations_checkpoint(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::mean_field::GenMeanFieldMover::read_input_pdbs(), core::pose::read_psipred_ss2_file(), core::chemical::mainchain_potential::read_rama_map_file_shapovalov(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag(), protocols::topology_broker::PcsEnergyController::read_tag(), protocols::topology_broker::StartStructClaimer::read_tag(), core::chemical::read_topology_file(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::jd2::MpiFileBuffer::release_file(), protocols::abinitio::HedgeArchive::remove_pending_decoys(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), protocols::forge::components::BDR::resfile(), core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling(), protocols::abinitio::IterativeCentroid::restore_from_file(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::abinitio::HedgeArchive::restore_status(), core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map_file(), core::scoring::SecondaryStructurePotential::rsigma_dot_initializer(), protocols::jd2::MpiFileBuffer::run(), protocols::motifs::MotifDnaPacker::run_motifs(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::archive::ArchiveBase::save_decoys(), protocols::abinitio::HedgeArchive::save_pending_decoys(), protocols::fldsgn::BluePrintBDR::set_blueprint(), protocols::denovo_design::constraints::FileConstraintGenerator::set_cstfile(), protocols::anchored_design::Anchor::set_filename(), protocols::noesy_assign::CrossPeakInfo::set_filename(), protocols::match::output::WriteUpstreamCoordinateKinemage::set_kinemage_file_name(), core::io::nmr::SpinlabelDatabaseEntry::set_path_to_distance_potential_histogram(), core::scoring::nmr::NMRSpinlabel::set_path_to_distance_potential_histogram_file(), core::io::nmr::SpinlabelDatabaseEntry::set_path_to_ensemble_conformers(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::md::MDBase::set_write_dynamic_rsr(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::setup_predictor(), core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map(), core::scoring::util_methods::DumpTrajectoryEnergy::start_new_activity(), core::chemical::carbohydrates::CarbohydrateInfoManager::sugar_modifications_table_file(), protocols::motifs::IRCollection::try_for_more(), protocols::jobdist::universal_main(), protocols::docking::DockingEnsemble::update_pdblist_file(), protocols::genetic_algorithm::GeneticAlgorithmBase::write_entities_checkpoint(), protocols::genetic_algorithm::GeneticAlgorithmBase::write_generations_checkpoint(), protocols::noesy_assign::PeakFileFormat::write_header(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), protocols::noesy_assign::CrossPeakList::write_peak_files(), protocols::loop_grower::LoopGrower::write_to_disk(), and protocols::loop_grower::LoopPartialSolutionStore::writelpsstore().

void protocols::abinitio::find_sampling_cuts ( kinematics::FoldTree const &  sampling,
kinematics::FoldTree const &  final,
utility::vector1< core::Size > &  sample_cuts 
)
void protocols::abinitio::fix_chainbreak_patch ( scoring::ScoreFunctionOP  scorefxn,
std::string const &  patch_name 
)
void protocols::abinitio::get_core ( toolbox::DecoySetEvaluation &  eval,
core::Real  cutoff,
loops::Loops &  rigid 
)
std::size_t protocols::abinitio::hash_value ( PairingStatEntry const &  val)
inline
std::size_t protocols::abinitio::hash_value ( core::scoring::dssp::StrandPairing const &  val)
inline
Size protocols::abinitio::noe_stage ( core::Size  total_res,
Real  factor 
)
std::ostream& protocols::abinitio::operator<< ( std::ostream &  out,
PairingStatEntry const &  ps 
)
inline
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
AlternativePairings const &  alt_pairs 
)
std::istream& protocols::abinitio::operator<< ( std::istream &  ,
StatEntries &   
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
StrandConstraints const &  st 
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
PairingStatistics const &  ps 
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
StatEntries const &  ps 
)
std::istream& protocols::abinitio::operator>> ( std::istream &  is,
PairingStatEntry &  ps 
)
std::istream& protocols::abinitio::operator>> ( std::istream &  is,
StatEntries &  pslist 
)
std::istream& protocols::abinitio::operator>> ( std::istream &  is,
PairingStatistics &  ps 
)
void protocols::abinitio::register_common_options ( )
Size protocols::abinitio::register_cutoff ( )
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 ( )
int protocols::abinitio::run_boinc_debug ( )
bool protocols::abinitio::sort_PoseWithScore ( const PoseWithScore &  left,
const PoseWithScore &  right 
)
static basic::Tracer protocols::abinitio::TR ( "protocols.protein_interface_design.movers.DomainAssembly"  )
static