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protocols::tcr Namespace Reference

Classes

class  TCRmodel
 class for modeling TCR structure with optional refinement/loop modeling More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< TCRloopRefine > 
TCRloopRefineOP
 
typedef
utility::pointer::shared_ptr
< TCRloopRefine const > 
TCRloopRefineCOP
 
typedef
utility::pointer::weak_ptr
< TCRloopRefine > 
TCRloopRefineAP
 
typedef
utility::pointer::weak_ptr
< TCRloopRefine const > 
TCRloopRefineCAP
 
typedef
utility::pointer::shared_ptr
< TCRmodel
TCRmodelOP
 
typedef
utility::pointer::shared_ptr
< TCRmodel const > 
TCRmodelCOP
 
typedef
utility::pointer::weak_ptr
< TCRmodel
TCRmodelAP
 
typedef
utility::pointer::weak_ptr
< TCRmodel const > 
TCRmodelCAP
 
typedef
utility::pointer::shared_ptr
< TCRseqInfo > 
TCRseqInfoOP
 
typedef
utility::pointer::shared_ptr
< TCRseqInfo const > 
TCRseqInfoCOP
 
typedef
utility::pointer::weak_ptr
< TCRseqInfo > 
TCRseqInfoAP
 
typedef
utility::pointer::weak_ptr
< TCRseqInfo const > 
TCRseqInfoCAP
 

Functions

void graft_cdr_to_fw (core::pose::Pose &scafold, core::pose::Pose const &cdr_piece, core::Size const &start, core::Size const &end, core::Size &nter_overhang, core::Size &cter_overhang)
 combine graft cdr structures and framework structure to build crude model More...
 
void graft_framework (TCRmodel::tmpltinfo &currtmplt, std::string const &template_pdb_path, TCRseqInfo::tcrposi const &aho_pos)
 grafting of Framework/germline template structure More...
 
void graft_cdr (TCRmodel::tmpltinfo &currtmplt, std::string const &template_pdb_path, core::Size const &cdr_start, core::Size const &cdr_end)
 grafting of cdr segments of template structure More...
 
void match_template_and_target_sequence (core::pose::Pose const &scafold, std::string const &targetseq, core::pose::Pose &posecopy)
 match template seq with target seq during modeling More...
 
void orient_tcr_chain (core::pose::Pose &fr_piece, core::pose::Pose const &ori_tmplt_chain, TCRseqInfo::tcrposi const &selepos)
 orient TCR alpha/beta chains based on the orientation templates More...
 
void refine_tcr_cdr_loops (core::pose::Pose &tcr_pose, protocols::loops::LoopsOP const &cdrloops)
 loop refine function for CDR loop More...
 
void refine_all_cdr_loops (core::pose::Pose &tcr_pose, TCRseqInfo::tcrposi const &a_posi, TCRseqInfo::tcrposi const &b_posi)
 refine all cdr loops More...
 
void refine_cdr3_loops (core::pose::Pose &tcr_pose, antibody::grafting::CDR_Bounds const &acdr3, antibody::grafting::CDR_Bounds const &bcdr3)
 loop refine function for CDR3 alpha and CDR3 beta loops More...
 
void refine_cdr_loop (core::pose::Pose &tcr_pose, antibody::grafting::CDR_Bounds const &cdr)
 loop refine function for CDR alpha/beta loop More...
 
void remodel_tcr_cdr_loops (core::pose::Pose &tcr_pose, protocols::loops::LoopsOP const &cdr3loops, bool refine)
 loop remodel function for CDR loop More...
 
void ind_remodel_tcr_cdr_loops (core::pose::Pose &tcr_pose, core::Size const loopstart, core::Size const loopend)
 loop rebuild function More...
 
bool 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 > 
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 > 
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 > 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 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 > 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 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 setup_template_from_pdbfile (TCRmodel::tmpltinfo &currtmplt)
 read the template structure from user provided PDB file More...
 
void 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 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 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 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 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 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 > 
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 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 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...
 

Typedef Documentation

typedef utility::pointer::weak_ptr< TCRloopRefine > protocols::tcr::TCRloopRefineAP
typedef utility::pointer::weak_ptr< TCRloopRefine const > protocols::tcr::TCRloopRefineCAP
typedef utility::pointer::shared_ptr< TCRloopRefine const > protocols::tcr::TCRloopRefineCOP
typedef utility::pointer::shared_ptr< TCRloopRefine > protocols::tcr::TCRloopRefineOP
typedef utility::pointer::weak_ptr< TCRmodel > protocols::tcr::TCRmodelAP
typedef utility::pointer::weak_ptr< TCRmodel const > protocols::tcr::TCRmodelCAP
typedef utility::pointer::shared_ptr< TCRmodel const > protocols::tcr::TCRmodelCOP
typedef utility::pointer::shared_ptr< TCRmodel > protocols::tcr::TCRmodelOP
typedef utility::pointer::weak_ptr< TCRseqInfo > protocols::tcr::TCRseqInfoAP
typedef utility::pointer::weak_ptr< TCRseqInfo const > protocols::tcr::TCRseqInfoCAP
typedef utility::pointer::shared_ptr< TCRseqInfo const > protocols::tcr::TCRseqInfoCOP
typedef utility::pointer::shared_ptr< TCRseqInfo > protocols::tcr::TCRseqInfoOP

Function Documentation

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

Referenced by initialize_template_ignore_list().

void protocols::tcr::dump_templates ( TCRmodel::tcrtmplts const &  atmplt,
TCRmodel::tcrtmplts const &  btmplt,
bool const  use_gma,
bool const  use_gmb 
)
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

template choosen by best alignment score b/w input query and seq from template file

References ignore_template(), MAXRESOLUTION, and MINSCORE.

Referenced by find_template_from_multiple_input_db().

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

calls find_template for each file in the list

References find_template(), and MINSCORE.

Referenced by setup_cdr_template_from_db(), and setup_fw_template_from_db().

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 &  tcr_ss 
)

orientation template identification and grafting from template db

References ignore_template(), MAXRESOLUTION, MINSCORE, and protocols::tcr::TCRmodel::tmpltinfo::tdb.

Referenced by setup_orientation_template().

void protocols::tcr::graft_cdr ( TCRmodel::tmpltinfo &  currtmplt,
std::string const &  template_pdb_path,
core::Size const &  cdr_start,
core::Size const &  cdr_end 
)
void protocols::tcr::graft_cdr_to_fw ( core::pose::Pose scafold,
core::pose::Pose const &  cdr_piece,
core::Size const &  start,
core::Size const &  end,
core::Size nter_overhang,
core::Size cter_overhang 
)
void protocols::tcr::graft_framework ( TCRmodel::tmpltinfo &  currtmplt,
std::string const &  template_pdb_path,
TCRseqInfo::tcrposi const &  aho_pos 
)
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.

checks if a template id is present in the ignore list

Referenced by find_template(), and get_orientation_template_from_db().

void protocols::tcr::ind_remodel_tcr_cdr_loops ( core::pose::Pose tcr_pose,
core::Size const  loopstart,
core::Size const  loopend 
)
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 
)
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

ignore list can be created by user provide list with flag -ignore_list

References create_ignore_list(), and protocols::forge::methods::merge().

Referenced by protocols::tcr::TCRmodel::setup_templates().

void protocols::tcr::match_template_and_target_sequence ( core::pose::Pose const &  scafold,
std::string const &  targetseq,
core::pose::Pose posecopy 
)
void protocols::tcr::orient_tcr_chain ( core::pose::Pose fr_piece,
core::pose::Pose const &  ori_tmplt_chain,
TCRseqInfo::tcrposi const &  selepos 
)
void protocols::tcr::refine_all_cdr_loops ( core::pose::Pose tcr_pose,
TCRseqInfo::tcrposi const &  a_posi,
TCRseqInfo::tcrposi const &  b_posi 
)

refine all cdr loops

refinement all cdr loops CDR1, CDR2, CDR3 and HV4 loops

References refine_tcr_cdr_loops().

void protocols::tcr::refine_cdr3_loops ( core::pose::Pose tcr_pose,
antibody::grafting::CDR_Bounds const &  acdr3,
antibody::grafting::CDR_Bounds const &  bcdr3 
)

loop refine function for CDR3 alpha and CDR3 beta loops

References refine_tcr_cdr_loops().

void protocols::tcr::refine_cdr_loop ( core::pose::Pose tcr_pose,
antibody::grafting::CDR_Bounds const &  cdr 
)

loop refine function for CDR alpha/beta loop

References refine_tcr_cdr_loops().

void protocols::tcr::refine_tcr_cdr_loops ( core::pose::Pose tcr_pose,
protocols::loops::LoopsOP const &  cdrloops 
)
void protocols::tcr::remodel_tcr_cdr_loops ( core::pose::Pose tcr_pose,
protocols::loops::LoopsOP const &  cdr3loops,
bool  refine 
)
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.

parent function to get the CDR template from PDB file or PDB ID or template databse

References setup_cdr_template_from_db(), setup_cdr_template_from_pdbid(), setup_template_from_pdbfile(), protocols::tcr::TCRmodel::tmpltinfo::tid, and protocols::tcr::TCRmodel::tmpltinfo::tpdb.

Referenced by protocols::tcr::TCRmodel::setup_templates().

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 
)
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

References graft_cdr(), and protocols::tcr::TCRmodel::tmpltinfo::tid.

Referenced by setup_cdr_template().

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.

parent function to get the FE/GM template from PDB file or PDB ID or template databse

References setup_fw_template_from_db(), setup_fw_template_from_pdbid(), setup_template_from_pdbfile(), protocols::tcr::TCRmodel::tmpltinfo::tid, and protocols::tcr::TCRmodel::tmpltinfo::tpdb.

Referenced by protocols::tcr::TCRmodel::setup_templates().

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 
)
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

for framework/germline template structures

References graft_framework(), and protocols::tcr::TCRmodel::tmpltinfo::tid.

Referenced by setup_fw_template().

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

checks for user provided template pdb id or structure before searching for templates

References get_orientation_template_from_db(), graft_framework(), setup_template_from_pdbfile(), protocols::tcr::TCRmodel::tmpltinfo::tid, and protocols::tcr::TCRmodel::tmpltinfo::tpdb.

Referenced by protocols::tcr::TCRmodel::setup_templates().

void protocols::tcr::setup_template_from_pdbfile ( TCRmodel::tmpltinfo &  currtmplt)
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

Referenced by initialize_template_db_files().