Rosetta
Public Member Functions | Private Attributes | List of all members
protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector Class Reference

a vector of Poses sorted by the secondary structure of the termini More...

#include <TerminalDSSPSortedPoseVector.hh>

Inheritance diagram for protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector:
Inheritance graph
[legend]

Public Member Functions

 TerminalDSSPSortedPoseVector ()
 
 TerminalDSSPSortedPoseVector (TerminalDSSPSortedPoseVector const &src)
 
 ~TerminalDSSPSortedPoseVector () override
 
TerminalDSSPSortedPoseVectorOP clone () const
 
void parse_motif_file (std::string motif_file)
 
void add_segment_envelopes_from_string (std::string motifs)
 
void populate_from_pdb_list (std::string pdb_list)
 
void populate_from_pdb_list (std::string motif_file, std::string pdb_list)
 
void store_pose (PoseSegmentOP, PoseSegmentOP)
 
void store_pose (PoseWithTerminalSegmentsOfKnownDSSPOP)
 
PoseWithTerminalSegmentsOfKnownDSSPOP get_random_pose (std::string, std::string)
 
utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > get_vector (std::string nterm_secstructs, std::string cterm_secstructs)
 
void set_segment_envelopes (utility::vector1< utility::vector1< SegmentEnvelopeOP >>)
 
void add_to_segment_envelopes (utility::vector1< SegmentEnvelopeOP > new_envelope)
 
void clear_segment_envelopes ()
 
void populate_from_segment_file (std::string, bool clear=false)
 
utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > populate_from_segment_file_and_get_random_vector_set (utility::vector1< std::string > const &paths, std::string const &allowed_n_ter_ss, std::string const &allowed_c_ter_ss, core::Size max_vector_size=5000) const
 Read the segment file, return a vector of segments of max size. More...
 
utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > populate_from_segment_file_and_get_random_vector_set (std::string const &path, std::string const &allowed_n_ter_ss, std::string const &allowed_c_ter_ss, core::Size max_vector_size=5000) const
 Read the segment file, return a vector of segments of max size. More...
 
void create_segment_file (std::string)
 
void populate_all_OP_vector ()
 
utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > get_all_poseOPs ()
 
void clear_all_vectors ()
 
void clear_terminal_vectors ()
 
void purge_missing_density ()
 
void simultaneously_populate_and_write_segment_file (std::string const &motif_filename, std::string const &pdb_list, std::string const &file_path, bool store_reference_pdbs, bool use_pdbs_only, utility::vector1< protocols::filters::FilterOP > const &filters, utility::vector1< core::simple_metrics::SimpleMetricOP > const &metrics, bool output_elements=false)
 Write segment file using a pdb list. Append segment file if needed. More...
 
void simultaneously_populate_and_write_segment_file_pdb (core::pose::Pose const &pose, std::string const &motif_filename, std::string const &file_path, bool store_reference_pdbs, bool use_pdbs_only, utility::vector1< protocols::filters::FilterOP > const &filters, utility::vector1< core::simple_metrics::SimpleMetricOP > const &metrics, bool output_elements=false)
 Write segment file on an individual pose. Append segment file if needed. More...
 
void simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs (core::pose::Pose const &pose, std::string const &file_path, bool store_reference_pdbs, bool use_pdbs_only, utility::vector1< protocols::filters::FilterOP > const &filters, utility::vector1< core::simple_metrics::SimpleMetricOP > const &metrics, bool output_elements)
 
core::Size get_total_size ()
 
utility::vector1< core::pose::PoseCOP > convert_pose_into_segment_vector (core::pose::PoseOP current_pose)
 

Private Attributes

utility::vector1< utility::vector1< SegmentEnvelopeOP > > segment_envelopes_
 
utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > all_poseOPs_
 
std::map< char, std::map< char, utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > > > poseOP_map_
 
std::string nterm_secstructs_
 
std::string cterm_secstructs_
 

Detailed Description

a vector of Poses sorted by the secondary structure of the termini

Constructor & Destructor Documentation

◆ TerminalDSSPSortedPoseVector() [1/2]

protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::TerminalDSSPSortedPoseVector ( )

References segment_envelopes_.

Referenced by clone().

◆ TerminalDSSPSortedPoseVector() [2/2]

protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::TerminalDSSPSortedPoseVector ( TerminalDSSPSortedPoseVector const &  src)
default

◆ ~TerminalDSSPSortedPoseVector()

protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::~TerminalDSSPSortedPoseVector ( )
override

Member Function Documentation

◆ add_segment_envelopes_from_string()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::add_segment_envelopes_from_string ( std::string  motifs)

References add_to_segment_envelopes(), segment_envelopes_, and protocols::sparta::split().

Referenced by parse_motif_file().

◆ add_to_segment_envelopes()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::add_to_segment_envelopes ( utility::vector1< SegmentEnvelopeOP >  new_envelope)

References segment_envelopes_.

Referenced by add_segment_envelopes_from_string().

◆ clear_all_vectors()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::clear_all_vectors ( )

References all_poseOPs_, and clear_terminal_vectors().

Referenced by convert_pose_into_segment_vector(), and simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

◆ clear_segment_envelopes()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::clear_segment_envelopes ( )

References segment_envelopes_.

Referenced by parse_motif_file().

◆ clear_terminal_vectors()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::clear_terminal_vectors ( )

References cterm_secstructs_, nterm_secstructs_, and poseOP_map_.

Referenced by clear_all_vectors(), and purge_missing_density().

◆ clone()

TerminalDSSPSortedPoseVectorOP protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::clone ( ) const

References TerminalDSSPSortedPoseVector().

◆ convert_pose_into_segment_vector()

utility::vector1< core::pose::PoseCOP > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::convert_pose_into_segment_vector ( core::pose::PoseOP  current_pose)

References all_poseOPs_, clear_all_vectors(), protocols::simple_filters::dssp(), populate_all_OP_vector(), purge_missing_density(), segment_envelopes_, and store_pose().

◆ create_segment_file()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::create_segment_file ( std::string  file_path)

References all_poseOPs_, core::conformation::membrane::out, protocols::denovo_design::movers::pdb_filename(), populate_all_OP_vector(), and core::id::to_string().

◆ get_all_poseOPs()

utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::get_all_poseOPs ( )

References all_poseOPs_, and populate_all_OP_vector().

◆ get_random_pose()

PoseWithTerminalSegmentsOfKnownDSSPOP protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::get_random_pose ( std::string  nterm_secstructs,
std::string  cterm_secstructs 
)

References poseOP_map_, and protocols::TR().

◆ get_total_size()

core::Size protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::get_total_size ( )

References cterm_secstructs_, nterm_secstructs_, and poseOP_map_.

◆ get_vector()

utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::get_vector ( std::string  nterm_secstructs,
std::string  cterm_secstructs 
)

References poseOP_map_.

◆ parse_motif_file()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::parse_motif_file ( std::string  motif_file)

References add_segment_envelopes_from_string(), and clear_segment_envelopes().

Referenced by populate_from_pdb_list(), and simultaneously_populate_and_write_segment_file_pdb().

◆ populate_all_OP_vector()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_all_OP_vector ( )

References all_poseOPs_, cterm_secstructs_, nterm_secstructs_, and poseOP_map_.

Referenced by convert_pose_into_segment_vector(), create_segment_file(), get_all_poseOPs(), purge_missing_density(), and simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

◆ populate_from_pdb_list() [1/2]

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_pdb_list ( std::string  motif_file,
std::string  pdb_list 
)

References parse_motif_file(), and populate_from_pdb_list().

◆ populate_from_pdb_list() [2/2]

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_pdb_list ( std::string  pdb_list)

References protocols::simple_filters::dssp(), core::import_pose::pose_from_file(), segment_envelopes_, and store_pose().

Referenced by populate_from_pdb_list().

◆ populate_from_segment_file()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_segment_file ( std::string  file_path,
bool  clear = false 
)

References poseOP_map_, protocols::sparta::split(), and store_pose().

◆ populate_from_segment_file_and_get_random_vector_set() [1/2]

utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_segment_file_and_get_random_vector_set ( std::string const &  path,
std::string const &  allowed_n_ter_ss,
std::string const &  allowed_c_ter_ss,
core::Size  max_vector_size = 5000 
) const

Read the segment file, return a vector of segments of max size.

This function also returns a random permutation of the total set n_ter and c_ter control which SS can be possible for N and C term. This function is to reduce the memory footprint associated with whole PDB segment reads.

References protocols::hybridization::path, and populate_from_segment_file_and_get_random_vector_set().

◆ populate_from_segment_file_and_get_random_vector_set() [2/2]

utility::vector1< PoseWithTerminalSegmentsOfKnownDSSPOP > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_segment_file_and_get_random_vector_set ( utility::vector1< std::string > const &  paths,
std::string const &  allowed_n_ter_ss,
std::string const &  allowed_c_ter_ss,
core::Size  max_vector_size = 5000 
) const

Read the segment file, return a vector of segments of max size.

This function also returns a random permutation of the total set n_ter and c_ter control which SS can be possible for N and C term. This function is to reduce the memory footprint associated with whole PDB segment reads.

References protocols::sparta::split(), and protocols::TR().

Referenced by populate_from_segment_file_and_get_random_vector_set().

◆ purge_missing_density()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::purge_missing_density ( )

References core::chemical::ACETYLATION, all_poseOPs_, clear_terminal_vectors(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::chemical::DIMETHYLATION, core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbonds::HBondSet::nhbonds(), populate_all_OP_vector(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::chemical::SIDECHAIN_CONJUGATION, store_pose(), and protocols::TR().

Referenced by convert_pose_into_segment_vector(), and simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

◆ set_segment_envelopes()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::set_segment_envelopes ( utility::vector1< utility::vector1< SegmentEnvelopeOP >>  segment_envelopes)

References segment_envelopes_.

◆ simultaneously_populate_and_write_segment_file()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file ( std::string const &  motif_filename,
std::string const &  pdb_list,
std::string const &  file_path,
bool  store_reference_pdbs,
bool  use_pdbs_only,
utility::vector1< protocols::filters::FilterOP > const &  filters,
utility::vector1< core::simple_metrics::SimpleMetricOP > const &  metrics,
bool  output_elements = false 
)

Write segment file using a pdb list. Append segment file if needed.

References core::import_pose::pose_from_file(), simultaneously_populate_and_write_segment_file_pdb(), and protocols::TR().

◆ simultaneously_populate_and_write_segment_file_pdb()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file_pdb ( core::pose::Pose const &  pose,
std::string const &  motif_filename,
std::string const &  file_path,
bool  store_reference_pdbs,
bool  use_pdbs_only,
utility::vector1< protocols::filters::FilterOP > const &  filters,
utility::vector1< core::simple_metrics::SimpleMetricOP > const &  metrics,
bool  output_elements = false 
)

Write segment file on an individual pose. Append segment file if needed.

References parse_motif_file(), and simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

Referenced by simultaneously_populate_and_write_segment_file().

◆ simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs()

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs ( core::pose::Pose const &  pose,
std::string const &  file_path,
bool  store_reference_pdbs,
bool  use_pdbs_only,
utility::vector1< protocols::filters::FilterOP > const &  filters,
utility::vector1< core::simple_metrics::SimpleMetricOP > const &  metrics,
bool  output_elements 
)

References all_poseOPs_, clear_all_vectors(), protocols::simple_filters::dssp(), protocols::denovo_design::movers::pdb_filename(), core::pose::Pose::pdb_info(), populate_all_OP_vector(), purge_missing_density(), segment_envelopes_, store_pose(), core::id::to_string(), and protocols::TR().

Referenced by simultaneously_populate_and_write_segment_file_pdb().

◆ store_pose() [1/2]

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::store_pose ( PoseSegmentOP  n_terminal,
PoseSegmentOP  c_terminal 
)

References protocols::simple_filters::dssp(), core::pose::pdbslice(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), and core::pose::set_reasonable_fold_tree().

Referenced by convert_pose_into_segment_vector(), populate_from_pdb_list(), populate_from_segment_file(), purge_missing_density(), and simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

◆ store_pose() [2/2]

void protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::store_pose ( PoseWithTerminalSegmentsOfKnownDSSPOP  pose_to_store)

References cterm_secstructs_, nterm_secstructs_, and poseOP_map_.

Member Data Documentation

◆ all_poseOPs_

utility::vector1<PoseWithTerminalSegmentsOfKnownDSSPOP> protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::all_poseOPs_
private

Referenced by clear_all_vectors(), convert_pose_into_segment_vector(), create_segment_file(), get_all_poseOPs(), populate_all_OP_vector(), purge_missing_density(), and simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs().

◆ cterm_secstructs_

std::string protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::cterm_secstructs_
private

Referenced by clear_terminal_vectors(), get_total_size(), populate_all_OP_vector(), and store_pose().

◆ nterm_secstructs_

std::string protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::nterm_secstructs_
private

Referenced by clear_terminal_vectors(), get_total_size(), populate_all_OP_vector(), and store_pose().

◆ poseOP_map_

std::map< char, std::map<char,utility::vector1<PoseWithTerminalSegmentsOfKnownDSSPOP> > > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::poseOP_map_
private

Referenced by clear_terminal_vectors(), get_random_pose(), get_total_size(), get_vector(), populate_all_OP_vector(), populate_from_segment_file(), and store_pose().

◆ segment_envelopes_

utility::vector1<utility::vector1<SegmentEnvelopeOP> > protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::segment_envelopes_
private

Referenced by add_segment_envelopes_from_string(), add_to_segment_envelopes(), clear_segment_envelopes(), convert_pose_into_segment_vector(), populate_from_pdb_list(), set_segment_envelopes(), simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs(), and TerminalDSSPSortedPoseVector().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 11:00:24 for Rosetta by doxygen 1.9.1