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template_util.cc File Reference

template identification utility functions for protocols/tcr/TCRmodel More...

#include <protocols/tcr/template_util.hh>
#include <basic/Tracer.hh>
#include <protocols/tcr/grafting_util.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/tcrmodel.OptionKeys.gen.hh>
#include <set>
#include <utility/file/file_sys_util.hh>
#include <fstream>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::tcr
 

Functions

static basic::Tracer TR ("protocols.tcr.template_util")
 
bool protocols::tcr::ignore_template (std::string const &tmpltid, std::list< std::set< std::string > > const &ignore_lists)
 Check if a particular structure should be ignored for consideration as template. More...
 
std::pair< core::Real,
std::string > 
protocols::tcr::find_template (std::string const &query, std::string const &db, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &tcr_ss)
 find best scoring template from a fasta sequence file More...
 
std::pair< core::Real,
std::string > 
protocols::tcr::find_template_from_multiple_input_db (std::string const &query, utility::vector1< std::string > const &multidb, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &tcr_ss)
 find templates from one or more template fasta sequence files More...
 
utility::vector1< std::string > protocols::tcr::update_template_files (utility::vector1< std::string > const &file_names, std::string const &tcr_seq_db)
 check and update if template files based on sequence length exists on the template More...
 
void protocols::tcr::initialize_template_db_files (TCRseqInfo::tcrsegs const &atcr, TCRseqInfo::tcrsegs const &btcr, TCRmodel::tcrtmplts &atmplt, TCRmodel::tcrtmplts &btmplt, std::string const &tcr_seq_db)
 initialize template files for all TCR segments More...
 
std::set< std::string > protocols::tcr::create_ignore_list (std::string const query, std::string const blast_db, core::Real const &blast_cutoff)
 create template blacklist by runing blast with cut-off value More...
 
void protocols::tcr::initialize_template_ignore_list (TCRseqInfo::tcrsegs const &atcr, TCRseqInfo::tcrsegs const &btcr, std::list< std::set< std::string > > &ignore_lists, core::Real const &blast_cutoff, std::string const &tcr_seq_db)
 initialize list of template structures to ignore More...
 
void protocols::tcr::setup_template_from_pdbfile (TCRmodel::tmpltinfo &currtmplt)
 read the template structure from user provided PDB file More...
 
void protocols::tcr::setup_cdr_template_from_pdbid (TCRmodel::tmpltinfo &currtmplt, core::Size const cdrstart, core::Size const cdrend, std::string const &tpdb_path)
 get the CDR template structure from user provided PDB ID More...
 
void protocols::tcr::setup_cdr_template_from_db (std::string const &seq, TCRmodel::tmpltinfo &currtmplt, core::Size const cdrstart, core::Size const cdrend, std::string const &tpdb_path, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &tcr_ss)
 Search templates for a CDR loop sequence in the template database. More...
 
void protocols::tcr::setup_cdr_template (std::string const &seq, TCRmodel::tmpltinfo &currtmplt, core::Size const cdrstart, core::Size const cdrend, std::string const &tpdb_path, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &tcr_ss)
 CDR template identification and grafting of template structure. More...
 
void protocols::tcr::setup_fw_template_from_pdbid (TCRmodel::tmpltinfo &currtmplt, TCRseqInfo::tcrposi const &aho_pos, std::string const &tpdb_path)
 helper method to read the template structure from user provided PDB id More...
 
void protocols::tcr::setup_fw_template_from_db (std::string const &seq, TCRseqInfo::tcrposi const &aho_pos, TCRmodel::tmpltinfo &currtmplt, std::string const &tpdb_path, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &tcr_ss)
 Search template structures in the template database. More...
 
void protocols::tcr::setup_fw_template (std::string const &seq, TCRseqInfo::tcrposi const &aho_pos, TCRmodel::tmpltinfo &currtmplt, std::string const &tpdb_path, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &tcr_ss)
 Framework/germline template identification and grafting of template structure. More...
 
std::pair< std::string,
std::string > 
protocols::tcr::get_orientation_template_from_db (std::string const &fra, std::string const &frb, TCRmodel::tmpltinfo const &oritmplt, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &ss)
 orientation template identification and grafting from template db More...
 
void protocols::tcr::setup_orientation_template (TCRseqInfo::tcrsegs const &atcr, TCRseqInfo::tcrsegs const &btcr, TCRmodel::tmpltinfo &oria_tmplt, TCRmodel::tmpltinfo &orib_tmplt, TCRseqInfo::tcrposi const &aaho_posi, TCRseqInfo::tcrposi const &baho_posi, std::string const &tpdb_path, std::list< std::set< std::string > > const &ignore_lists, core::Real const &cutoff, core::sequence::ScoringSchemeOP const &ss)
 parent function for orientation template identification More...
 
void protocols::tcr::dump_templates (TCRmodel::tcrtmplts const &atmplt, TCRmodel::tcrtmplts const &btmplt, bool const use_gma, bool const use_gmb)
 dump all templates found for various tcr segments More...
 

Variables

const core::Real MINSCORE = -99999.0
 MINSCORE const value with large negative number. More...
 
const core::Real MAXRESOLUTION = 10.0
 MAXRESOLUTION const value with large possitive number. More...
 

Detailed Description

template identification utility functions for protocols/tcr/TCRmodel

Author
Ragul (ragul.nosp@m.@umd.nosp@m..edu)

Function Documentation

static basic::Tracer TR ( "protocols.tcr.template_util"  )
static

Variable Documentation

const core::Real MAXRESOLUTION = 10.0

MAXRESOLUTION const value with large possitive number.

used for checking/ignoring templates

also used for initializing template resolution value

Referenced by protocols::tcr::find_template(), and protocols::tcr::get_orientation_template_from_db().

const core::Real MINSCORE = -99999.0

MINSCORE const value with large negative number.

used for checking and ignoring templates

also used for initializing template score value

Referenced by protocols::tcr::find_template(), protocols::tcr::find_template_from_multiple_input_db(), protocols::tcr::get_orientation_template_from_db(), protocols::tcr::setup_cdr_template_from_db(), and protocols::tcr::setup_fw_template_from_db().