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

#include <Dssp.hh>

Public Member Functions
	Dssp (core::pose::Pose const &, bool const asu_only=false)
	~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 &, bool const asu_only=false)
	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

Dssp()

core::scoring::dssp::Dssp::Dssp	(	core::pose::Pose const &	pose,
		bool const	asu_only = false
	)

~Dssp()

core::scoring::dssp::Dssp::~Dssp ( )

default

Member Function Documentation

bb_pair_score()

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

compute()

void core::scoring::dssp::Dssp::compute ( core::pose::Pose const &  pose, bool const  asu_only = false  )

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::pose::symmetry::extract_asymmetric_unit(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::loops::loop_closure::ccd::helix, core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().

dssp()

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

(

ObjexxFCL::FArray1_char &

dssp_secstruct

)

dssp_featurizer()

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

(

ObjexxFCL::FArray1_char &

secstruct

)

dssp_reduced() [1/2]

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

(

)

dssp_reduced() [2/2]

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

(

ObjexxFCL::FArray1_char &

secstruct

)

Referenced by protocols::simple_filters::SSMotifFinder::apply(), core::energy_methods::ProQ_Energy::calculate_feature_vector(), core::energy_methods::ProQ_Energy::calculate_feature_vector_proq2(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), protocols::electron_density::findLoopFromDensity(), protocols::pose_length_moves::PossibleLoop::generate_output_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), and core::scoring::packing::PoseBalls::PoseBalls().

dssp_reduced_IG_as_L()

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

(

ObjexxFCL::FArray1_char &

secstruct

)

dssp_reduced_IG_as_L_if_adjcent_H()

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

(

ObjexxFCL::FArray1_char &

secstruct

)

get_dssp_plus_abego_L_def()

std::string core::scoring::dssp::Dssp::get_dssp_plus_abego_L_def

(

core::pose::Pose const &

pose

)

References protocols::denovo_design::abego_vector(), core::sequence::ABEGOManager::get_abego_string(), and core::sequence::ABEGOManager::get_symbols().

get_dssp_reduced_IG_as_L_secstruct()

std::string core::scoring::dssp::Dssp::get_dssp_reduced_IG_as_L_secstruct

(

)

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector().

get_dssp_secstruct() [1/2]

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

(

)

get_dssp_secstruct() [2/2]

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

(

core::Size

resid

)

Referenced by protocols::simple_filters::SSMotifFinder::apply(), protocols::protein_interface_design::filters::SSamountFilter::compute(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), 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::switches::GraftSwitchMover::get_n_terminal_helix(), protocols::helix_capper::HelixNCapperMover::get_start_positions(), core::energy_methods::ProQ_Energy::gss_sc_feature(), protocols::match::SecondaryStructureMPM::modified_match_positions(), protocols::features::HelixCapFeatures::report_features(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), core::energy_methods::ProQ_Energy::ss_feature(), core::energy_methods::ProQ_Energy::ss_sc_feature(), and core::energy_methods::ProQ_Energy::stride_feature().

get_dssp_unreduced_secstruct()

std::string core::scoring::dssp::Dssp::get_dssp_unreduced_secstruct

(

)

in_paired_strands()

bool core::scoring::dssp::Dssp::in_paired_strands	(	Size	res1,
		Size	res2
	)		const

insert_dssp_ss_into_pose()

void core::scoring::dssp::Dssp::insert_dssp_ss_into_pose	(	core::pose::Pose &	pose,
		bool	recompute = true
	)

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

insert_edge_ss_into_pose()

void core::scoring::dssp::Dssp::insert_edge_ss_into_pose	(	core::pose::Pose &	pose,
		bool	recompute = true
	)

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

insert_ss_into_pose()

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::topology_broker::TopologyBroker::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::simple_moves::StructProfileMover::apply(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::convert_to_centroid(), core::scoring::motif::ResPairMotifQuery::init(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), and protocols::hybridization::HybridizeProtocol::update_template().

insert_ss_into_pose_no_IG_helix()

void core::scoring::dssp::Dssp::insert_ss_into_pose_no_IG_helix	(	core::pose::Pose &	pose,
		bool	recompute = true
	)

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

Referenced by protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore().

num_pairings()

Size core::scoring::dssp::Dssp::num_pairings

(

Size

resi

)

const

paired()

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

strand_pairing_set()

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

inline

References pair_set_.

Member Data Documentation

dssp_secstruct_

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

private

hbond_bb_pair_score_

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

private

pair_set_

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

private

Referenced by strand_pairing_set().

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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