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

TCRloopRefineAP

typedef utility::pointer::weak_ptr< TCRloopRefine > protocols::tcr::TCRloopRefineAP

TCRloopRefineCAP

typedef utility::pointer::weak_ptr< TCRloopRefine const > protocols::tcr::TCRloopRefineCAP

TCRloopRefineCOP

typedef utility::pointer::shared_ptr< TCRloopRefine const > protocols::tcr::TCRloopRefineCOP

TCRloopRefineOP

typedef utility::pointer::shared_ptr< TCRloopRefine > protocols::tcr::TCRloopRefineOP

TCRmodelAP

typedef utility::pointer::weak_ptr< TCRmodel > protocols::tcr::TCRmodelAP

TCRmodelCAP

typedef utility::pointer::weak_ptr< TCRmodel const > protocols::tcr::TCRmodelCAP

TCRmodelCOP

typedef utility::pointer::shared_ptr< TCRmodel const > protocols::tcr::TCRmodelCOP

TCRmodelOP

typedef utility::pointer::shared_ptr< TCRmodel > protocols::tcr::TCRmodelOP

TCRseqInfoAP

typedef utility::pointer::weak_ptr< TCRseqInfo > protocols::tcr::TCRseqInfoAP

TCRseqInfoCAP

typedef utility::pointer::weak_ptr< TCRseqInfo const > protocols::tcr::TCRseqInfoCAP

TCRseqInfoCOP

typedef utility::pointer::shared_ptr< TCRseqInfo const > protocols::tcr::TCRseqInfoCOP

TCRseqInfoOP

typedef utility::pointer::shared_ptr< TCRseqInfo > protocols::tcr::TCRseqInfoOP

Function Documentation

create_ignore_list()

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().

dump_templates()

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

References protocols::tcr::TCRmodel::tcrtmplts::cdr1, protocols::tcr::TCRmodel::tcrtmplts::cdr2hv4, protocols::tcr::TCRmodel::tcrtmplts::cdr3, protocols::tcr::TCRmodel::tcrtmplts::fr, protocols::tcr::TCRmodel::tcrtmplts::gm, protocols::tcr::TCRmodel::tcrtmplts::ori, and protocols::tcr::TCRmodel::tmpltinfo::tpiece.

Referenced by protocols::tcr::TCRmodel::init_from_options(), and protocols::tcr::TCRmodel::setup_templates().

find_template()

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().

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().

get_orientation_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().

graft_cdr()

void protocols::tcr::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

for both alpha and beta chain cdr segment

References protocols::antibody::cdr_end, protocols::antibody::cdr_start, core::sequence::end, core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), protocols::grafting::return_region(), protocols::loops::start, protocols::tcr::TCRmodel::tmpltinfo::tid, and protocols::tcr::TCRmodel::tmpltinfo::tpiece.

Referenced by setup_cdr_template_from_db(), and setup_cdr_template_from_pdbid().

graft_cdr_to_fw()

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
	)

combine graft cdr structures and framework structure to build crude model

uses CCDEndsGraftMover with default overhang residue size of 3

References protocols::grafting::CCDEndsGraftMover::apply(), protocols::grafting::GraftMoverBase::copy_pdbinfo(), core::sequence::end, protocols::grafting::AnchoredGraftMover::final_repack(), protocols::grafting::CCDEndsGraftMover::graft_is_closed(), protocols::grafting::AnchoredGraftMover::idealize_insert(), protocols::grafting::AnchoredGraftMover::set_cycles(), protocols::loops::start, protocols::grafting::AnchoredGraftMover::stop_at_closure(), and protocols::TR().

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

graft_framework()

void protocols::tcr::graft_framework	(	TCRmodel::tmpltinfo &	currtmplt,
		std::string const &	template_pdb_path,
		TCRseqInfo::tcrposi const &	aho_pos
	)

grafting of Framework/germline template structure

for both alpha and beta chain framework and germline segment

References core::pose::Pose::begin(), core::pose::get_chain_id_from_chain(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), protocols::grafting::return_region(), core::pose::Pose::split_by_chain(), protocols::tcr::TCRmodel::tmpltinfo::tid, and protocols::tcr::TCRmodel::tmpltinfo::tpiece.

Referenced by setup_fw_template_from_db(), setup_fw_template_from_pdbid(), and setup_orientation_template().

ignore_template()

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().

ind_remodel_tcr_cdr_loops()

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

loop rebuild function

rebuild loop segment of input pose using given loop start and end position

takes options loop remodel mover type

References protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::scoring::atom_pair_constraint, core::chemical::CENTROID, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), core::chemical::FA_STANDARD, protocols::antibody::simple_one_loop_fold_tree(), and core::pose::Pose::total_residue().

initialize_template_db_files()

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

template files for CDR sequences were choosen by CDR sequence length

References protocols::tcr::TCRmodel::tcrtmplts::cdr1, protocols::tcr::TCRmodel::tcrtmplts::cdr2hv4, protocols::tcr::TCRmodel::tcrtmplts::cdr3, protocols::tcr::TCRmodel::tcrtmplts::fr, protocols::tcr::TCRmodel::tcrtmplts::gm, protocols::tcr::TCRmodel::tcrtmplts::ori, protocols::tcr::TCRmodel::tmpltinfo::tdb, core::id::to_string(), and update_template_files().

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

initialize_template_ignore_list()

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 merge().

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

match_template_and_target_sequence()

void protocols::tcr::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

uses protocols::simple_moves::MutateResidue to mutate residues

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), protocols::ligand_docking::ga_ligand_dock::mutate(), core::conformation::Residue::name1(), core::chemical::name_from_aa(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and protocols::TR().

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

orient_tcr_chain()

void protocols::tcr::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

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), core::scoring::superimpose_pose(), and protocols::TR().

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

refine_all_cdr_loops()

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().

refine_cdr3_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().

refine_cdr_loop()

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().

refine_tcr_cdr_loops()

void protocols::tcr::refine_tcr_cdr_loops	(	core::pose::Pose &	tcr_pose,
		protocols::loops::LoopsOP const &	cdrloops
	)

loop refine function for CDR loop

References protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), and core::scoring::get_score_function().

Referenced by refine_all_cdr_loops(), refine_cdr3_loops(), and refine_cdr_loop().

remodel_tcr_cdr_loops()

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

loop remodel function for CDR loop

References protocols::loops::add_cutpoint_variants(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), core::chemical::CENTROID_t, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), core::chemical::FULL_ATOM_t, core::scoring::get_score_function(), protocols::loops::remove_cutpoint_variants(), and core::util::switch_to_residue_type_set().

setup_cdr_template()

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().

setup_cdr_template_from_db()

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.

References find_template_from_multiple_input_db(), graft_cdr(), MINSCORE, protocols::tcr::TCRmodel::tmpltinfo::tdb, protocols::tcr::TCRmodel::tmpltinfo::tid, protocols::TR(), and protocols::tcr::TCRmodel::tmpltinfo::tscore.

Referenced by setup_cdr_template().

setup_cdr_template_from_pdbid()

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().

setup_fw_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().

setup_fw_template_from_db()

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.

for Framework/Germline templates

References find_template_from_multiple_input_db(), graft_framework(), MINSCORE, protocols::tcr::TCRmodel::tmpltinfo::tdb, protocols::tcr::TCRmodel::tmpltinfo::tid, protocols::TR(), and protocols::tcr::TCRmodel::tmpltinfo::tscore.

Referenced by setup_fw_template().

setup_fw_template_from_pdbid()

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().

setup_orientation_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().

setup_template_from_pdbfile()

void protocols::tcr::setup_template_from_pdbfile

(

TCRmodel::tmpltinfo &

currtmplt

)

read the template structure from user provided PDB file

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::tcr::TCRmodel::tmpltinfo::tid, protocols::tcr::TCRmodel::tmpltinfo::tpdb, and protocols::tcr::TCRmodel::tmpltinfo::tpiece.

Referenced by setup_cdr_template(), setup_fw_template(), and setup_orientation_template().

update_template_files()

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().