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protocols::tcr::TCRmodel Class Reference

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

#include <TCRmodel.hh>

Inheritance diagram for protocols::tcr::TCRmodel:
Inheritance graph
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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

protocols::tcr::TCRmodel::TCRmodel ( std::string const &  aseq,
std::string const &  bseq 
)
protocols::tcr::TCRmodel::TCRmodel ( TCRseqInfoOP  tcrinfo)
protocols::tcr::TCRmodel::~TCRmodel ( )
overridedefault

Member Function Documentation

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

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

References atmplt_.

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

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

References btmplt_.

void protocols::tcr::TCRmodel::build_graft_model ( )
private
TCRmodelOP protocols::tcr::TCRmodel::clone ( ) const

Clone the pointer.

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

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

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().

void protocols::tcr::TCRmodel::setup_templates ( )
private
core::pose::PoseOP protocols::tcr::TCRmodel::tcr_graft_model ( ) const
inline

References tcr_graft_model_.

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

References tcr_loop_model_.

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

References tcr_model_.

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

returns true if germline alpha chain sequence is used for modeling

References use_gma_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

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

templated db path for antibody templates

Referenced by set_default(), and setup_templates().

tcrtmplts protocols::tcr::TCRmodel::atmplt_
private
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().

tcrtmplts protocols::tcr::TCRmodel::btmplt_
private
core::Size protocols::tcr::TCRmodel::cter_overhang_
private
bool protocols::tcr::TCRmodel::dump_templates_
private

dump all templates

Referenced by init_from_options(), and setup_templates().

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().

bool protocols::tcr::TCRmodel::include_ab_templates_
private

include antibody templates during template search

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

bool protocols::tcr::TCRmodel::minimize_model_
private

minimize or relax option for model structure

Referenced by init_from_options(), and make_model().

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().

bool protocols::tcr::TCRmodel::relax_model_
private

Referenced by init_from_options(), and make_model().

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

Referenced by set_default().

bool protocols::tcr::TCRmodel::skip_modeling_
private

Referenced by init_from_options(), and make_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().

core::pose::PoseOP protocols::tcr::TCRmodel::tcr_loop_model_
private
core::pose::PoseOP protocols::tcr::TCRmodel::tcr_model_
private
core::Real protocols::tcr::TCRmodel::template_identity_cutoff_
private
std::string protocols::tcr::TCRmodel::tpdb_db_
private

Referenced by set_default(), and setup_templates().

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

path of the template database seq dir, structure dir

Referenced by set_default(), and setup_templates().

tcr::TCRseqInfoOP protocols::tcr::TCRmodel::tsinfo
private
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().

bool protocols::tcr::TCRmodel::use_gmb_templates_
private
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: