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Rosetta
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Classes | |
| class | ANN |
| class | ChemicalShiftEvaluator |
| class | ChemicalShiftEvaluatorCreator |
| creator for the ChemicalShiftsEvaluatorCreator class More... | |
| class | GDB |
| struct | PDB_Entry |
| struct | RingData |
| class | PDB |
| class | Sparta |
Typedefs | |
| typedef float | Vec3[3] |
| typedef float | Mat3[3][3] |
| typedef boost::unordered_map< int, PDB_Entry > | Mol |
| typedef boost::unordered_map< int, Mol > | Mols |
| typedef utility::vector0< std::string > | StringList |
| typedef boost::unordered_map< float, boost::unordered_map< float, float > > | PHIPSI_ERR_SURF |
Functions | |
| static basic::Tracer | tr ("protocols.sparta") |
| std::ostream & | operator<< (std::ostream &os, PDB_Entry const &pe) |
| static basic::Tracer | tr ("protocols.sparta") |
| void | calc_per_residue_scores (Sparta::SpartaLib::AtomNameList &atom_names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab, utility::vector1< float > &per_residue_scores) |
| Real | compareRef_fxn (Sparta::SpartaLib::AtomNameList &names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab) |
| float | getDiff (float ang1, float ang2) |
| float | getAVG (utility::vector0< float > &v1) |
| float | getSTD (utility::vector0< float > &v1) |
| float | getRMS (utility::vector0< float > &v1, utility::vector0< float > &v2) |
| char * | itoa (int n, char *buff, platform::Size s, int) |
| char * | ftoa (float n, char *buff, platform::Size s, char f, int prec) |
| int | MKDIR (const char *dirName) |
| bool | isDirExists (const string &Dir) |
| std::string | simplifyWhiteSpace (const std::string &str) |
| int | contains (const std::string &str, const std::string &c) |
| int | contains (const string &str, const char &c) |
| bool | isDigit (const char &c) |
| bool | isSpace (const char &c) |
| StringList | split (const char sep, const string &str) |
| StringList | split (const string &sep, const string &str) |
| StringList | split_WhiteSpace (const string &str) |
| char * | section (const string &str, const char &sep, char *buff, platform::Size n, int start, int end) |
| typedef float protocols::sparta::Mat3[3][3] |
| typedef boost::unordered_map<int, PDB_Entry> protocols::sparta::Mol |
| typedef boost::unordered_map<int, Mol> protocols::sparta::Mols |
| typedef boost::unordered_map<float, boost::unordered_map<float, float> > protocols::sparta::PHIPSI_ERR_SURF |
| typedef utility::vector0< std::string > protocols::sparta::StringList |
| typedef float protocols::sparta::Vec3[3] |
| void protocols::sparta::calc_per_residue_scores | ( | Sparta::SpartaLib::AtomNameList & | atom_names, |
| GDB & | Pred_Sum, | ||
| GDB & | REF_CS_Tab, | ||
| GDB & | COMP_Tab, | ||
| utility::vector1< float > & | per_residue_scores | ||
| ) |
References protocols::sparta::GDB::DATA, protocols::sparta::GDB::Entries, protocols::sparta::GDB::FORMAT_str_parser(), getAVG(), protocols::sparta::GDB::getEntry(), getRMS(), protocols::sparta::GDB::isVarFloat(), protocols::sparta::GDB::REMARKS, protocols::hybridization::score, protocols::sparta::GDB::showGDB(), tr(), and protocols::sparta::GDB::VARS_str_parser().
Referenced by compareRef_fxn(), and protocols::sparta::Sparta::score_pose_per_residue().
| core::Real protocols::sparta::compareRef_fxn | ( | Sparta::SpartaLib::AtomNameList & | names, |
| GDB & | Pred_Sum, | ||
| GDB & | REF_CS_Tab, | ||
| GDB & | COMP_Tab | ||
| ) |
References calc_per_residue_scores(), core::sequence::end, and protocols::sparta::GDB::Entries.
Referenced by protocols::sparta::Sparta::run_A_ANN_Prediction().
| int protocols::sparta::contains | ( | const std::string & | str, |
| const std::string & | c | ||
| ) |
References protocols::kinmatch::str().
Referenced by protocols::sparta::GDB::addVAR(), core::chemical::annotate_backbone(), protocols::enzymatic_movers::EnzymaticMover::apply(), protocols::sparta::GDB::checkFormat(), core::pose::PDBInfo::clear_reslabel(), core::chemical::MutableResidueType::delete_atom(), core::chemical::MutableResidueType::delete_child_proton(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::GDB::isVarFloat(), protocols::sparta::GDB::isVarInt(), protocols::sparta::GDB::isVarString(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::match::BumpGrid::occupied(), core::scoring::dssp::StrandPairing::paired(), core::chemical::sdf::SDFParser::parse(), core::chemical::sdf::CtabV3000Parser::parse(), protocols::antibody::design::CDRGraftDesignOptionsParser::parse_options(), protocols::antibody::design::CDRSeqDesignOptionsParser::parse_options(), core::simple_metrics::composite_metrics::ProtocolSettingsMetric::parse_options(), protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(), protocols::simple_moves::BBDihedralSamplerMover::setup_samplers(), protocols::sparta::GDB::setVAR(), protocols::sparta::GDB::showGDB(), core::sequence::split_sequence_motif(), and protocols::features::BetaTurnDetection::validate_ramachandran_hash().
| int protocols::sparta::contains | ( | const string & | str, |
| const char & | c | ||
| ) |
References protocols::kinmatch::str().
Referenced by core::select::get_pymol_selection_for_atoms(), and core::pose::rna::virtualize_free_rna_moieties().
| char * protocols::sparta::ftoa | ( | float | n, |
| char * | buff, | ||
| platform::Size | s, | ||
| char | f, | ||
| int | prec | ||
| ) |
| float protocols::sparta::getAVG | ( | utility::vector0< float > & | v1 | ) |
References core::simple_metrics::metrics::sum.
Referenced by calc_per_residue_scores(), and getSTD().
| float protocols::sparta::getDiff | ( | float | ang1, |
| float | ang2 | ||
| ) |
References core::pose::motif::a().
| float protocols::sparta::getRMS | ( | utility::vector0< float > & | v1, |
| utility::vector0< float > & | v2 | ||
| ) |
References core::simple_metrics::metrics::sum.
Referenced by calc_per_residue_scores().
| float protocols::sparta::getSTD | ( | utility::vector0< float > & | v1 | ) |
References getAVG(), and core::simple_metrics::metrics::sum.
| bool protocols::sparta::isDigit | ( | const char & | c | ) |
Referenced by protocols::sparta::GDB::checkFormat().
| bool protocols::sparta::isDirExists | ( | const string & | Dir | ) |
Referenced by protocols::sparta::Sparta::SpartaLib::mkdir_pred().
| bool protocols::sparta::isSpace | ( | const char & | c | ) |
Referenced by simplifyWhiteSpace().
| char * protocols::sparta::itoa | ( | int | n, |
| char * | buff, | ||
| platform::Size | s, | ||
| int | |||
| ) |
| int protocols::sparta::MKDIR | ( | const char * | dirName | ) |
Referenced by protocols::sparta::Sparta::SpartaLib::mkdir_pred().
| std::ostream & protocols::sparta::operator<< | ( | std::ostream & | os, |
| PDB_Entry const & | pe | ||
| ) |
| char * protocols::sparta::section | ( | const string & | str, |
| const char & | sep, | ||
| char * | buff, | ||
| platform::Size | n, | ||
| int | start, | ||
| int | end | ||
| ) |
References core::sequence::end, split(), protocols::loops::start, and protocols::kinmatch::str().
Referenced by core::fragment::picking_old::vall::VallLibrary::add_section(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::hydrate::is_inside(), core::scoring::constraints::ConstraintIO::read_constraints(), core::sequence::read_fasta_file_section(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), and core::fragment::picking_old::vall::vall_library_from_file().
| std::string protocols::sparta::simplifyWhiteSpace | ( | const std::string & | str | ) |
References isSpace(), and protocols::kinmatch::str().
Referenced by protocols::sparta::GDB::checkFormat(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB_Entry(), main(), and protocols::sparta::GDB::showGDB().
| StringList protocols::sparta::split | ( | const char | sep, |
| const string & | str | ||
| ) |
References protocols::kinmatch::str().
Referenced by core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::add_segment_envelopes_from_string(), protocols::jd2::JobOutputter::affixed_numbered_name(), protocols::hybridization::CartesianSampler::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), core::scoring::ScoringManager::create_nmer_svm_rank(), protocols::surface_docking::SurfaceVectorLoader::create_surface_params(), protocols::loophash::extract_sample_weights(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file(), protocols::splice::RotLibdb::fill_rotamer_matrix_from_db_file(), protocols::splice::RBInMover::init(), core::kinematics::MoveMap::init_from_file(), protocols::enzdes::EnzdesScorefileFilter::initialize_value_evaluators_from_file(), protocols::antibody::clusters::CDRClusterMatcher::load_center_data(), protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight(), protocols::mpi_refinement::MPI_Refine_Master::load_sample_weight(), protocols::kinematic_closure::perturbers::LogFilePerturber::LogFilePerturber(), main(), protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input(), protocols::rbsegment_relax::ConfChangeMover::multi_rb(), protocols::jobdist::BasicJob::output_tag(), core::chemical::sdf::parse_bond_type_data(), protocols::hotspot_hashing::LSMSearchPattern::parse_lsm_spec(), protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement::parse_my_tag(), protocols::rbsegment_relax::ConfChangeMover::parse_my_tag(), protocols::md::MDBase::parse_schfile(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_segment_file(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_segment_file_and_get_random_vector_set(), core::import_pose::pose_from_file(), core::conformation::symmetry::SymDof::read(), protocols::parser::BluePrint::read_blueprint_stream(), protocols::mpi_refinement::Scheduler::read_cmd(), protocols::toolbox::match_enzdes_util::ResInteractions::read_data(), protocols::toolbox::match_enzdes_util::CstResInteractions::read_data(), core::scoring::epr_deer::EPRSpinLabel::read_db_file(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::energy_methods::SequenceDependentRefEnergy::read_energy_weight_table(), protocols::loophash::BackboneDB::read_homologs(), update_ResidueType_enum_files::read_lines_from_file(), protocols::loops::LoopsFileIO::read_loop_file_stream(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::read_loops_file_block(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), core::scoring::methods::NMerRefEnergy::read_nmer_table_list(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), section(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::set_apolar_res(), protocols::constraint_movers::ConstraintSetMover::set_cst_map_file_contents(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), protocols::relax::FastRelax::set_script_from_lines(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), protocols::moves::StructureRestrictor::setup_relevant_chains(), core::scoring::epr_deer::DEERIO::split_line(), protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner(), and protocols::sparta::GDB::VARS_str_parser().
| StringList protocols::sparta::split | ( | const string & | sep, |
| const string & | str | ||
| ) |
References protocols::kinmatch::str().
Referenced by protocols::features::deserialize_db_listener_data(), and protocols::mpi_refinement::read_ss2().
| StringList protocols::sparta::split_WhiteSpace | ( | const string & | str | ) |
References protocols::kinmatch::str().
Referenced by protocols::sparta::GDB::loadGDB().
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Referenced by protocols::sparta::GDB::addVAR(), protocols::sparta::ANN::applyANNTransformation(), calc_per_residue_scores(), protocols::sparta::Sparta::check_pose(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::sparta::Sparta::SpartaLib::getResInfo(), protocols::sparta::Sparta::SpartaLib::init(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB(), protocols::sparta::ANN::loadWeightBias3(), protocols::sparta::GDB::saveGDB(), protocols::sparta::GDB::setEntry(), protocols::sparta::Sparta::SpartaLib::setup_for_scoring(), and protocols::sparta::GDB::setVAR().
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1.9.1