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

#include <TCRmodel.hh>

Inheritance diagram for protocols::tcr::TCRmodel:

Classes
struct	tcrtmplts
	tcrtmplts holds the tmpltinfo values for different tcr segments More...

struct	tmpltinfo
	tmpltinfo holds the template information for an individual tcr segment More...

Public Member Functions
	TCRmodel (std::string const &aseq, std::string const &bseq)

	TCRmodel (TCRseqInfoOP tcrinfo)

TCRmodelOP	clone () const
	Clone the pointer. More...

	~TCRmodel () override

void	set_use_gma_templates (bool gma)
	use_gma_templates uses germline segments (germline + cdr3 sequence) for modeling alpha chain More...

void	set_use_gmb_templates (bool gmb)
	use_gma_templates uses germline segments (germline + cdr3 sequence) for modeling beta chain More...

tcrtmplts	atmplt () const
	returns the template information (tmpltinfo) for tcr alpha chain segments More...

tcrtmplts	btmplt () const
	returns the template information (tmpltinfo) for tcr alpha chain segments More...

bool	use_gma_templates () const
	returns true if germline alpha chain sequence is used for modeling More...

bool	use_gmb_templates () const
	returns true if germline beta chain sequence is used for modeling More...

core::pose::PoseOP	tcr_model () const

core::pose::PoseOP	tcr_graft_model () const

core::pose::PoseOP	tcr_loop_model () const

Private Member Functions
void	init_from_options ()
	check for user provided options and assign values. More...

void	set_default ()
	set default values for database path and other members More...

void	setup_templates ()
	Find templates for tcr segments. More...

void	make_model ()
	make_model parent function for assembling the model from templates More...

void	build_graft_model ()
	build the crude model from the grafted templates More...

Private Attributes
tcr::TCRseqInfoOP	tsinfo

tcrtmplts	atmplt_

tcrtmplts	btmplt_

core::Size	nter_overhang_
	No. of overhang residues used for grafting; cterminal & nterminal. More...

core::Size	cter_overhang_

std::string	tseq_db_
	path of the template database seq dir, structure dir More...

std::string	tpdb_db_

bool	use_user_templates_
	use user provide templates; no template identification from template db More...

bool	use_gma_templates_
	use germline templates instead of framework templates for a/b tcr chain More...

bool	use_gmb_templates_

bool	include_ab_templates_
	include antibody templates during template search More...

std::string	ab_db_path_
	templated db path for antibody templates More...

std::list< std::set< std::string > >	ignore_lists_
	list of PDB id's to blacklist as templates More...

core::Real	blastp_identity_cutoff_
	cut-off values More...

core::Real	template_identity_cutoff_

core::pose::PoseOP	tcr_graft_model_
	member poseop's to store modeled poses More...

core::pose::PoseOP	tcr_loop_model_

core::pose::PoseOP	tcr_model_

bool	dump_templates_
	dump all templates More...

bool	skip_modeling_
	More...

bool	minimize_model_
	minimize or relax option for model structure More...

bool	relax_model_

core::scoring::ScoreFunctionOP	scorefxn_

Detailed Description

class for modeling TCR structure with optional refinement/loop modeling

TCRmodel class uses TCRseqInfo for parsing and numbering the sequence TCrmodel takes in tcr a & b chain sequence or TCRseqInfo object directly and do template identification, grafting and assembling of TCR structure Calls various utility functions from util files in protocols/tcr Modeling protool uses either germline segments or framework segments germline segments (germline + cdr3 sequence) framework segments (framework + cdr1+ cdr2 + cdr3 sequence) currently extended cdr2 segment is used (cdr2 extended upto hv4 loop) see also: TCRmodel documentation and publication see also: tcr/TCRseqInfo

Constructor & Destructor Documentation

◆ TCRmodel() [1/2]

protocols::tcr::TCRmodel::TCRmodel	(	std::string const &	aseq,
		std::string const &	bseq
	)

References init_from_options(), make_model(), set_default(), setup_templates(), and tsinfo.

◆ TCRmodel() [2/2]

protocols::tcr::TCRmodel::TCRmodel ( TCRseqInfoOP tcrinfo )

◆ ~TCRmodel()

protocols::tcr::TCRmodel::~TCRmodel ( )

overridedefault

Member Function Documentation

◆ atmplt()

tcrtmplts protocols::tcr::TCRmodel::atmplt ( ) const

inline

returns the template information (tmpltinfo) for tcr alpha chain segments

References atmplt_.

◆ btmplt()

tcrtmplts protocols::tcr::TCRmodel::btmplt ( ) const

inline

returns the template information (tmpltinfo) for tcr alpha chain segments

References btmplt_.

◆ build_graft_model()

void protocols::tcr::TCRmodel::build_graft_model ( )

private

◆ clone()

TCRmodelOP protocols::tcr::TCRmodel::clone ( ) const

Clone the pointer.

◆ init_from_options()

void protocols::tcr::TCRmodel::init_from_options ( )

private

check for user provided options and assign values.

assign values for template files, template cutoffs, model refinement options etc..

Referenced by TCRmodel().

◆ make_model()

void protocols::tcr::TCRmodel::make_model ( )

private

make_model parent function for assembling the model from templates

calls other functions to build graft model, optional refinement and loop modeling

References build_graft_model(), core::pose::Pose::energies(), minimize_model_, relax_model_, skip_modeling_, tcr_graft_model_, tcr_loop_model_, tcr_model_, core::scoring::Energies::total_energies(), core::scoring::total_score, protocols::TR(), and tsinfo.

Referenced by TCRmodel().

◆ set_default()

void protocols::tcr::TCRmodel::set_default ( )

private

set default values for database path and other members

References ab_db_path_, core::pose::Pose::clear(), cter_overhang_, core::scoring::get_score_function(), include_ab_templates_, nter_overhang_, scorefxn_, set_use_gma_templates(), set_use_gmb_templates(), tcr_graft_model_, tcr_loop_model_, tcr_model_, tpdb_db_, protocols::TR(), and tseq_db_.

Referenced by TCRmodel().

◆ set_use_gma_templates()

void protocols::tcr::TCRmodel::set_use_gma_templates ( bool gma )

inline

use_gma_templates uses germline segments (germline + cdr3 sequence) for modeling alpha chain

Setters

if false, (framework + cdr1+ cdr2 + cdr3 sequence) is used for modeling

References use_gma_templates_.

Referenced by set_default(), and setup_templates().

◆ set_use_gmb_templates()

void protocols::tcr::TCRmodel::set_use_gmb_templates ( bool gmb )

inline

use_gma_templates uses germline segments (germline + cdr3 sequence) for modeling beta chain

if false, (framework + cdr1+ cdr2 + cdr3 sequence) is used for modeling

References use_gmb_templates_.

Referenced by set_default(), and setup_templates().

◆ setup_templates()

void protocols::tcr::TCRmodel::setup_templates ( )

private

Find templates for tcr segments.

Checks for user provided template pdb id or structure file before searching for templates from db

Calls individual util functions for identification and grafting of templates for TCR segments

References ab_db_path_, atmplt_, blastp_identity_cutoff_, btmplt_, protocols::tcr::TCRmodel::tcrtmplts::cdr1, protocols::tcr::TCRmodel::tcrtmplts::cdr2hv4, protocols::tcr::TCRmodel::tcrtmplts::cdr3, cter_overhang_, protocols::tcr::dump_templates(), dump_templates_, protocols::tcr::TCRmodel::tcrtmplts::fr, protocols::tcr::TCRmodel::tcrtmplts::gm, ignore_lists_, include_ab_templates_, protocols::tcr::initialize_template_db_files(), protocols::tcr::initialize_template_ignore_list(), nter_overhang_, protocols::tcr::TCRmodel::tcrtmplts::ori, set_use_gma_templates(), set_use_gmb_templates(), protocols::tcr::setup_cdr_template(), protocols::tcr::setup_fw_template(), protocols::tcr::setup_orientation_template(), protocols::tcr::TCRmodel::tmpltinfo::tdb, template_identity_cutoff_, core::id::to_string(), tpdb_db_, tseq_db_, tsinfo, use_gma_templates_, use_gmb_templates_, and use_user_templates_.

Referenced by TCRmodel().

◆ tcr_graft_model()

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_graft_model ( ) const

inline

References tcr_graft_model_.

◆ tcr_loop_model()

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_loop_model ( ) const

inline

References tcr_loop_model_.

◆ tcr_model()

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_model ( ) const

inline

References tcr_model_.

◆ use_gma_templates()

bool protocols::tcr::TCRmodel::use_gma_templates ( ) const

inline

returns true if germline alpha chain sequence is used for modeling

References use_gma_templates_.

◆ use_gmb_templates()

bool protocols::tcr::TCRmodel::use_gmb_templates ( ) const

inline

returns true if germline beta chain sequence is used for modeling

References use_gmb_templates_.

Member Data Documentation

◆ ab_db_path_

std::string protocols::tcr::TCRmodel::ab_db_path_

private

templated db path for antibody templates

Referenced by set_default(), and setup_templates().

◆ atmplt_

tcrtmplts protocols::tcr::TCRmodel::atmplt_

private

Referenced by atmplt(), build_graft_model(), init_from_options(), and setup_templates().

◆ blastp_identity_cutoff_

core::Real protocols::tcr::TCRmodel::blastp_identity_cutoff_

private

cut-off values

cutoff values used to blacklist pdb templates

Referenced by init_from_options(), and setup_templates().

◆ btmplt_

tcrtmplts protocols::tcr::TCRmodel::btmplt_

private

Referenced by btmplt(), build_graft_model(), init_from_options(), and setup_templates().

◆ cter_overhang_

core::Size protocols::tcr::TCRmodel::cter_overhang_

private

Referenced by build_graft_model(), set_default(), and setup_templates().

◆ dump_templates_

bool protocols::tcr::TCRmodel::dump_templates_

private

dump all templates

Referenced by init_from_options(), and setup_templates().

◆ ignore_lists_

std::list< std::set<std::string> > protocols::tcr::TCRmodel::ignore_lists_

private

list of PDB id's to blacklist as templates

list provided by user or created by blast/identity cutoff

Referenced by setup_templates().

◆ include_ab_templates_

bool protocols::tcr::TCRmodel::include_ab_templates_

private

include antibody templates during template search

Referenced by init_from_options(), set_default(), and setup_templates().

◆ minimize_model_

bool protocols::tcr::TCRmodel::minimize_model_

private

minimize or relax option for model structure

Referenced by init_from_options(), and make_model().

◆ nter_overhang_

core::Size protocols::tcr::TCRmodel::nter_overhang_

private

No. of overhang residues used for grafting; cterminal & nterminal.

Referenced by build_graft_model(), set_default(), and setup_templates().

◆ relax_model_

bool protocols::tcr::TCRmodel::relax_model_

private

Referenced by init_from_options(), and make_model().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::tcr::TCRmodel::scorefxn_

private

Referenced by set_default().

◆ skip_modeling_

bool protocols::tcr::TCRmodel::skip_modeling_

private

Referenced by init_from_options(), and make_model().

◆ tcr_graft_model_

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_graft_model_

private

member poseop's to store modeled poses

Referenced by build_graft_model(), make_model(), set_default(), and tcr_graft_model().

◆ tcr_loop_model_

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_loop_model_

private

Referenced by make_model(), set_default(), and tcr_loop_model().

◆ tcr_model_

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_model_

private

Referenced by build_graft_model(), make_model(), set_default(), and tcr_model().

◆ template_identity_cutoff_

core::Real protocols::tcr::TCRmodel::template_identity_cutoff_

private

Referenced by init_from_options(), and setup_templates().

◆ tpdb_db_

std::string protocols::tcr::TCRmodel::tpdb_db_

private

Referenced by set_default(), and setup_templates().

◆ tseq_db_

std::string protocols::tcr::TCRmodel::tseq_db_

private

path of the template database seq dir, structure dir

Referenced by set_default(), and setup_templates().

◆ tsinfo

tcr::TCRseqInfoOP protocols::tcr::TCRmodel::tsinfo

private

Referenced by build_graft_model(), make_model(), setup_templates(), and TCRmodel().

◆ use_gma_templates_

bool protocols::tcr::TCRmodel::use_gma_templates_

private

use germline templates instead of framework templates for a/b tcr chain

Referenced by build_graft_model(), set_use_gma_templates(), setup_templates(), and use_gma_templates().

◆ use_gmb_templates_

bool protocols::tcr::TCRmodel::use_gmb_templates_

private

Referenced by build_graft_model(), set_use_gmb_templates(), setup_templates(), and use_gmb_templates().

◆ use_user_templates_

bool protocols::tcr::TCRmodel::use_user_templates_

private

use user provide templates; no template identification from template db

Referenced by init_from_options(), and setup_templates().

The documentation for this class was generated from the following files:

src/protocols/tcr/TCRmodel.hh
src/protocols/tcr/TCRmodel.cc

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TCRmodel() [1/2]

◆ TCRmodel() [2/2]

◆ ~TCRmodel()

Member Function Documentation

◆ atmplt()

◆ btmplt()

◆ build_graft_model()

◆ clone()

◆ init_from_options()

◆ make_model()

◆ set_default()

◆ set_use_gma_templates()

◆ set_use_gmb_templates()

◆ setup_templates()

◆ tcr_graft_model()

◆ tcr_loop_model()

◆ tcr_model()

◆ use_gma_templates()

◆ use_gmb_templates()

Member Data Documentation

◆ ab_db_path_

◆ atmplt_

◆ blastp_identity_cutoff_

◆ btmplt_

◆ cter_overhang_

◆ dump_templates_

◆ ignore_lists_

◆ include_ab_templates_

◆ minimize_model_

◆ nter_overhang_

◆ relax_model_

◆ scorefxn_

◆ skip_modeling_

◆ tcr_graft_model_

◆ tcr_loop_model_

◆ tcr_model_

◆ template_identity_cutoff_

◆ tpdb_db_

◆ tseq_db_

◆ tsinfo

◆ use_gma_templates_

◆ use_gmb_templates_

◆ use_user_templates_