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core::scoring::dssp::Dssp Class Reference

#include <Dssp.hh>

Public Member Functions

 Dssp (core::pose::Pose const &)
 
 ~Dssp ()
 
void dssp_reduced_IG_as_L_if_adjcent_H (ObjexxFCL::FArray1_char &secstruct)
 
void dssp_reduced_IG_as_L (ObjexxFCL::FArray1_char &secstruct)
 
void dssp_reduced (ObjexxFCL::FArray1_char &secstruct)
 
void dssp_reduced ()
 
void dssp_featurizer (ObjexxFCL::FArray1_char &secstruct)
 
void dssp (ObjexxFCL::FArray1_char &dssp_secstruct)
 
bool paired (core::Size res1, core::Size res2, bool antiparallel)
 
StrandPairingSet const & strand_pairing_set ()
 
void insert_ss_into_pose (core::pose::Pose &pose, bool recompute=true)
 
void insert_dssp_ss_into_pose (core::pose::Pose &pose, bool recompute=true)
 
void insert_edge_ss_into_pose (core::pose::Pose &pose, bool recompute=true)
 
void insert_ss_into_pose_no_IG_helix (core::pose::Pose &pose, bool recompute=true)
 
char get_dssp_secstruct (core::Size resid)
 
std::string get_dssp_secstruct ()
 
std::string get_dssp_unreduced_secstruct ()
 
std::string get_dssp_plus_abego_L_def (core::pose::Pose const &pose)
 
std::string get_dssp_reduced_IG_as_L_secstruct ()
 
float bb_pair_score (Size res1, Size res2)
 
Size num_pairings (Size resi) const
 
bool in_paired_strands (Size res1, Size res2) const
 

Private Member Functions

void compute (core::pose::Pose const &)
 Runs dssp, calculating per-residue secondary structure. More...
 

Private Attributes

ObjexxFCL::FArray1D_char dssp_secstruct_
 
StrandPairingSetOP pair_set_
 
ObjexxFCL::FArray2D_float hbond_bb_pair_score_
 

Detailed Description

Non-protein residues get a DSSP value of ' '

Constructor & Destructor Documentation

core::scoring::dssp::Dssp::Dssp ( core::pose::Pose const &  pose)
core::scoring::dssp::Dssp::~Dssp ( )
default

Member Function Documentation

float core::scoring::dssp::Dssp::bb_pair_score ( Size  res1,
Size  res2 
)
void core::scoring::dssp::Dssp::compute ( core::pose::Pose const &  pose)
private

Runs dssp, calculating per-residue secondary structure.

dssp is a standard algorithm for per-residue secondary structure analysis. It has the following alphabet: H: 4-turn helix B: beta bridge E: extended beta strand G: 3-turn helix I: 5-turn helix T: helix-like loop (some nearby hbonds) S: loop with high curvature : loop Most of these determinations are made on the basis of hydrogen bonds, with torsion angles disregarded. The designations are reported with priority given to categories higher in the list (e.g. if a residue has both high- curvature (S) and helical hydrogen bonds (H), it will be reported as H). Experiments indicate that this function agrees almost completely with the true dssp results (run on dumped pdbs). Slight differences can perhaps be chalked up to unequal placement of hydrogens.

Global Read:
dssp_ns::hbond_bb_pair_score_
Global Write:
dssp_ns::hbond_bb_pair_score_
Remarks
References:
Author
olange: ported from original bblum-rosetta++ version $

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::loops::loop_closure::ccd::helix, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::xyz().

void core::scoring::dssp::Dssp::dssp ( ObjexxFCL::FArray1_char &  dssp_secstruct)
void core::scoring::dssp::Dssp::dssp_featurizer ( ObjexxFCL::FArray1_char &  secstruct)
void core::scoring::dssp::Dssp::dssp_reduced ( ObjexxFCL::FArray1_char &  secstruct)

Referenced by protocols::simple_filters::SSMotifFinder::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::splice::Splice::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::forge::remodel::RemodelMover::apply(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), core::scoring::methods::ProQ_Energy::calculate_feature_vector(), core::scoring::methods::ProQ_Energy::calculate_feature_vector_proq2(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), core::select::util::SelectResiduesByLayer::compute(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), protocols::simple_filters::dssp(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), protocols::aa_composition::find_helices_over_length(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::electron_density::findLoopFromDensity(), protocols::pose_length_moves::PossibleLoop::generate_output_pose(), protocols::indexed_structure_store::SSHashedFragmentStore::get_hits_below_rms(), protocols::pose_length_moves::FixAllLoopsMover::get_loops(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loops(), protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop(), core::scoring::methods::SSElementMotifContactEnergy::get_ss_elements(), protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementLengthFilter::get_ss_elements(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::pose_creation::MergePDBatOverlapMover::increase_range_to_ignore_ss_element(), protocols::pose_creation::MergePDBMover::increase_range_to_ignore_ss_element(), protocols::pose_creation::SliceToMiniProteinMover::parse_ss(), core::select::residue_selector::SSElementSelector::parse_ss(), protocols::splice::SpliceOut::place_cut_site_in_segment(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::splice::AlignEndsMover::reference_positions(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::forge::remodel::RemodelLoopMover::set_ideal_helices(), and protocols::forge::remodel::RemodelMover::setup_remodel_data_for_loop_btw_parametric_components().

void core::scoring::dssp::Dssp::dssp_reduced ( )
void core::scoring::dssp::Dssp::dssp_reduced_IG_as_L ( ObjexxFCL::FArray1_char &  secstruct)
void core::scoring::dssp::Dssp::dssp_reduced_IG_as_L_if_adjcent_H ( ObjexxFCL::FArray1_char &  secstruct)
std::string core::scoring::dssp::Dssp::get_dssp_plus_abego_L_def ( core::pose::Pose const &  pose)
std::string core::scoring::dssp::Dssp::get_dssp_reduced_IG_as_L_secstruct ( )
char core::scoring::dssp::Dssp::get_dssp_secstruct ( core::Size  resid)

Referenced by protocols::simple_moves::WriteSSEMover::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::evolution::AlignmentAAFinder::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::evolution::AlignmentGapInserter::apply(), protocols::pack_interface::ProteinProteinInterfaceUpweighter::apply(), protocols::moves::DsspMover::apply(), protocols::splice::Splice::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), protocols::surface_docking::FullatomRelaxMover::calc_secondary_struct(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), protocols::splice::calculate_rmsd(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::protein_interface_design::filters::SSamountFilter::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute(), protocols::fldsgn::filters::SecondaryStructureCountFilter::compute(), protocols::fldsgn::filters::SecondaryStructureFilter::compute(), core::select::util::SelectResiduesByLayer::compute(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_ss_info(), protocols::hybridization::create_fragment_set(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), protocols::simple_filters::dssp(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), protocols::aa_composition::find_helices_over_length(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::pose_length_moves::PossibleLoop::generate_output_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), protocols::switches::GraftSwitchMover::get_c_terminal_helix(), protocols::simple_filters::HelixHelixAngleFilter::get_helix_start_stop(), protocols::indexed_structure_store::SSHashedFragmentStore::get_hits_below_rms(), protocols::pose_length_moves::FixAllLoopsMover::get_loops(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loops(), protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop(), protocols::switches::GraftSwitchMover::get_n_terminal_helix(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_secstruct(), core::select::residue_selector::SecondaryStructureSelector::get_secstruct(), protocols::fldsgn::SheetConstraintGenerator::get_secstruct(), protocols::fldsgn::filters::SheetTopologyFilter::get_secstruct(), protocols::fldsgn::filters::HSSTripletFilter::get_secstruct(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), protocols::struct_fragment::StructFragmentMover::get_secstruct(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_secstruct(), core::scoring::methods::SSElementMotifContactEnergy::get_ss_elements(), protocols::simple_ddg::SSElementBisectddGFilter::get_ss_elements(), protocols::simple_filters::SSElementLengthFilter::get_ss_elements(), core::scoring::methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), protocols::helix_capper::HelixNCapperMover::get_start_positions(), core::scoring::methods::ProQ_Energy::gss_sc_feature(), protocols::pose_creation::MergePDBatOverlapMover::increase_range_to_ignore_ss_element(), protocols::pose_creation::MergePDBMover::increase_range_to_ignore_ss_element(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::match::SecondaryStructureMPM::modified_match_positions(), protocols::splice::neighbors_in_vector(), protocols::pose_creation::SliceToMiniProteinMover::parse_ss(), core::select::residue_selector::SSElementSelector::parse_ss(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::splice::AlignEndsMover::reference_positions(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), protocols::features::HelixCapFeatures::report_features(), protocols::moves::PyMOLMover::send_ss(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker(), core::scoring::methods::ProQ_Energy::ss_feature(), core::scoring::methods::ProQ_Energy::ss_sc_feature(), and core::scoring::methods::ProQ_Energy::stride_feature().

std::string core::scoring::dssp::Dssp::get_dssp_secstruct ( )
std::string core::scoring::dssp::Dssp::get_dssp_unreduced_secstruct ( )
bool core::scoring::dssp::Dssp::in_paired_strands ( Size  res1,
Size  res2 
) const
void core::scoring::dssp::Dssp::insert_dssp_ss_into_pose ( core::pose::Pose pose,
bool  recompute = true 
)
void core::scoring::dssp::Dssp::insert_edge_ss_into_pose ( core::pose::Pose pose,
bool  recompute = true 
)
void core::scoring::dssp::Dssp::insert_ss_into_pose ( core::pose::Pose pose,
bool  recompute = true 
)

References core::pose::Pose::set_secstruct().

Referenced by protocols::hybridization::HybridizeProtocol::add_template(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::simple_moves::StructProfileMover::apply(), protocols::moves::DsspMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::jumping::assign_ss_dssp(), protocols::protein_interface_design::best_cutpoint(), protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure(), protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure_with_surface(), protocols::seeded_abinitio::SegmentHybridizer::check_and_create_fragments(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::convert_to_centroid(), protocols::legacy_sewing::scoring::LegacyMotifScorer::dump_motif(), protocols::pose_metric_calculators::RotamerRecovery::get_ss(), core::scoring::motif::ResPairMotifQuery::init(), protocols::legacy_sewing::scoring::LegacyPartnerMotifScorer::interface_motif_score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::interface_motif_score(), protocols::sewing::scoring::PartnerMotifScorer::interface_motif_score(), protocols::loops::loopfinder(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::sic_dock::XfoxmScore::score(), protocols::moves::PyMOLMover::send_ss(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), core::scoring::methods::P_AA_ss_Energy::setup_for_minimizing(), core::scoring::methods::P_AA_ss_Energy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), and protocols::hybridization::HybridizeProtocol::update_template().

void core::scoring::dssp::Dssp::insert_ss_into_pose_no_IG_helix ( core::pose::Pose pose,
bool  recompute = true 
)
Size core::scoring::dssp::Dssp::num_pairings ( Size  resi) const
bool core::scoring::dssp::Dssp::paired ( core::Size  res1,
core::Size  res2,
bool  antiparallel 
)
StrandPairingSet const& core::scoring::dssp::Dssp::strand_pairing_set ( )
inline

Member Data Documentation

ObjexxFCL::FArray1D_char core::scoring::dssp::Dssp::dssp_secstruct_
private
ObjexxFCL::FArray2D_float core::scoring::dssp::Dssp::hbond_bb_pair_score_
private
StrandPairingSetOP core::scoring::dssp::Dssp::pair_set_
private

Referenced by strand_pairing_set().


The documentation for this class was generated from the following files: