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

#include <Dssp.hh>

Collaboration diagram for core::scoring::dssp::Dssp:

Public Member Functions
	Dssp (core::pose::Pose const &)
	~Dssp ()
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)
char	get_dssp_secstruct (core::Size resid)
std::string	get_dssp_secstruct ()
float	bb_pair_score (Size res1, Size res2)

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_
core::Size	total_residue_

Detailed Description

Definition at line 55 of file Dssp.hh.

Constructor & Destructor Documentation

core::scoring::dssp::Dssp::Dssp

(

core::pose::Pose const &

pose)

Definition at line 72 of file Dssp.cc.

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::scoring::dssp::Dssp::~Dssp

(

)

Definition at line 81 of file Dssp.cc.

Member Function Documentation

float core::scoring::dssp::Dssp::bb_pair_score	(	Size	res1,
		Size	res2
	)

Definition at line 484 of file Dssp.cc.

void core::scoring::dssp::Dssp::compute ( core::pose::Pose const &  pose)

private

Runs dssp, calculating per-residue secondary structure.

Dssp::compute

Detailed:

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:

Sizes::total_residue_ dssp_ns::hbond_bb_pair_score_

Global Write:

dssp_ns::hbond_bb_pair_score_

Remarks

References:

Author

olange: ported from original bblum-rosetta++ version $

Last Modified: nobu

Definition at line 359 of file Dssp.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::xyz().

void core::scoring::dssp::Dssp::dssp

(

ObjexxFCL::FArray1_char &

dssp_secstruct)

Definition at line 259 of file Dssp.cc.

void core::scoring::dssp::Dssp::dssp_featurizer

(

ObjexxFCL::FArray1_char &

secstruct)

Definition at line 265 of file Dssp.cc.

void core::scoring::dssp::Dssp::dssp_reduced

(

ObjexxFCL::FArray1_char &

secstruct)

Referenced by protocols::protein_interface_design::movers::Splice::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::toolbox::SelectResiduesByLayer::compute(), protocols::electron_density::findLoopFromDensity(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::scoring::packing::PoseBalls::PoseBalls(), and core::io::pdb::write_additional_pdb_data().

void core::scoring::dssp::Dssp::dssp_reduced

(

)

Definition at line 315 of file Dssp.cc.

char core::scoring::dssp::Dssp::get_dssp_secstruct

(

core::Size

resid)

Definition at line 469 of file Dssp.cc.

Referenced by protocols::moves::DsspMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::toolbox::SelectResiduesByLayer::compute(), protocols::hybridization::create_fragment_set(), protocols::match::SecondaryStructureMPM::modified_match_positions(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), and protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts().

std::string core::scoring::dssp::Dssp::get_dssp_secstruct

(

)

Definition at line 474 of file Dssp.cc.

void core::scoring::dssp::Dssp::insert_ss_into_pose

(

core::pose::Pose &

pose)

Definition at line 459 of file Dssp.cc.

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

Referenced by protocols::hybridization::HybridizeProtocol::add_template(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::moves::DsspMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::jumping::assign_ss_dssp(), protocols::protein_interface_design::best_cutpoint(), protocols::surface_docking::SurfaceDockingProtocol::CalcSecondayStruct(), protocols::surface_docking::FullatomRelaxMover::CalcSecondayStruct(), protocols::surface_docking::SurfaceDockingProtocol::CalcSecondayStruct_withSurface(), protocols::seeded_abinitio::SegmentHybridizer::check_and_create_fragments(), protocols::swa::StepWiseScreener::convert_to_centroid(), protocols::swa::protein::StepWiseProteinScreener::convert_to_centroid(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::get_ss(), protocols::loops::loopfinder(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::hybridization::HybridizeProtocol::read_template_structures(), protocols::sic_dock::XfoxmScore::score(), and protocols::fldsgn::BluePrintBDR::set_instruction_blueprint().

bool core::scoring::dssp::Dssp::paired	(	core::Size	res1,
		core::Size	res2,
		bool	antiparallel
	)

Definition at line 453 of file Dssp.cc.

StrandPairingSet const& core::scoring::dssp::Dssp::strand_pairing_set ( )

inline

Definition at line 67 of file Dssp.hh.

References pair_set_.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set().

Member Data Documentation

ObjexxFCL::FArray1D_char core::scoring::dssp::Dssp::dssp_secstruct_

private

Definition at line 83 of file Dssp.hh.

ObjexxFCL::FArray2D_float core::scoring::dssp::Dssp::hbond_bb_pair_score_

private

Definition at line 86 of file Dssp.hh.

StrandPairingSetOP core::scoring::dssp::Dssp::pair_set_

private

Definition at line 84 of file Dssp.hh.

Referenced by strand_pairing_set().

core::Size core::scoring::dssp::Dssp::total_residue_

private

Definition at line 87 of file Dssp.hh.

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

• src/core/scoring/dssp/Dssp.hh
• src/core/scoring/dssp/Dssp.cc