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Rosetta
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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 <core/pose/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>#include <protocols/tcr/util.hh>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... | |
template identification utility functions for protocols/tcr/TCRmodel
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static |
| 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().
1.9.1