tcr

Bindings for protocols::tcr namespace

class pyrosetta.rosetta.protocols.tcr.TCRloopRefine

Bases: pybind11_builtins.pybind11_object

class for modeling/refinement of tcr CDR loops

calls other loop modeling classes/ util functions to do loop rebuilding and refinement The refinement level was choosen based on user provide optional flags TCRloopRefine takes in TCRseqInfo or the parsed tcr segments for corresponding cdr positions for a/b chains

apply(self: pyrosetta.rosetta.protocols.tcr.TCRloopRefine, pose_in: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::tcr::TCRloopRefine::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.tcr.TCRloopRefine, : pyrosetta.rosetta.protocols.tcr.TCRloopRefine) pyrosetta.rosetta.protocols.tcr.TCRloopRefine

C++: protocols::tcr::TCRloopRefine::operator=(const class protocols::tcr::TCRloopRefine &) –> class protocols::tcr::TCRloopRefine &

clone(self: pyrosetta.rosetta.protocols.tcr.TCRloopRefine) pyrosetta.rosetta.protocols.tcr.TCRloopRefine

C++: protocols::tcr::TCRloopRefine::clone() const –> class std::shared_ptr<class protocols::tcr::TCRloopRefine>

set_tcr_loop_model(self: pyrosetta.rosetta.protocols.tcr.TCRloopRefine, tcrloopmodel: bool) None

C++: protocols::tcr::TCRloopRefine::set_tcr_loop_model(bool) –> void

tcr_loop_model(self: pyrosetta.rosetta.protocols.tcr.TCRloopRefine) bool

return true if loop modeling/refinement is applied to the pose

C++: protocols::tcr::TCRloopRefine::tcr_loop_model() const –> bool

class pyrosetta.rosetta.protocols.tcr.TCRmodel

Bases: pybind11_builtins.pybind11_object

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

assign(self: pyrosetta.rosetta.protocols.tcr.TCRmodel, : pyrosetta.rosetta.protocols.tcr.TCRmodel) pyrosetta.rosetta.protocols.tcr.TCRmodel

C++: protocols::tcr::TCRmodel::operator=(const class protocols::tcr::TCRmodel &) –> class protocols::tcr::TCRmodel &

atmplt(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) protocols::tcr::TCRmodel::tcrtmplts

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

C++: protocols::tcr::TCRmodel::atmplt() const –> struct protocols::tcr::TCRmodel::tcrtmplts

btmplt(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) protocols::tcr::TCRmodel::tcrtmplts

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

C++: protocols::tcr::TCRmodel::btmplt() const –> struct protocols::tcr::TCRmodel::tcrtmplts

clone(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) pyrosetta.rosetta.protocols.tcr.TCRmodel

Clone the pointer

C++: protocols::tcr::TCRmodel::clone() const –> class std::shared_ptr<class protocols::tcr::TCRmodel>

set_use_gma_templates(self: pyrosetta.rosetta.protocols.tcr.TCRmodel, gma: bool) None

Setters

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

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

C++: protocols::tcr::TCRmodel::set_use_gma_templates(bool) –> void

set_use_gmb_templates(self: pyrosetta.rosetta.protocols.tcr.TCRmodel, gmb: bool) None

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

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

C++: protocols::tcr::TCRmodel::set_use_gmb_templates(bool) –> void

tcr_graft_model(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) pyrosetta.rosetta.core.pose.Pose

C++: protocols::tcr::TCRmodel::tcr_graft_model() const –> class std::shared_ptr<class core::pose::Pose>

tcr_loop_model(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) pyrosetta.rosetta.core.pose.Pose

C++: protocols::tcr::TCRmodel::tcr_loop_model() const –> class std::shared_ptr<class core::pose::Pose>

tcr_model(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) pyrosetta.rosetta.core.pose.Pose

C++: protocols::tcr::TCRmodel::tcr_model() const –> class std::shared_ptr<class core::pose::Pose>

class tcrtmplts

Bases: pybind11_builtins.pybind11_object

tcrtmplts holds the tmpltinfo values for different tcr segments

orientation(ori), framework(fr), germline(gm), CDR1(cdr1), extended CDR2(cdr2hv4), CDR3(cdr3)

assign(self: pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts, : pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts) pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts

C++: protocols::tcr::TCRmodel::tcrtmplts::operator=(const struct protocols::tcr::TCRmodel::tcrtmplts &) –> struct protocols::tcr::TCRmodel::tcrtmplts &

property cdr1
property cdr2hv4
property cdr3
property fr
property gm
property ori
class tmpltinfo

Bases: pybind11_builtins.pybind11_object

tmpltinfo holds the template information for an individual tcr segment

template pdb id(tid), pdb structure(tpdb), sequence(tseq), alignment score(tscore), pose(tpiece) and template databse used(tdb).

assign(self: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, : pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo) pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo

C++: protocols::tcr::TCRmodel::tmpltinfo::operator=(const struct protocols::tcr::TCRmodel::tmpltinfo &) –> struct protocols::tcr::TCRmodel::tmpltinfo &

property tdb
property tid
property tpdb
property tpiece
property tscore
property tseq
use_gma_templates(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) bool

returns true if germline alpha chain sequence is used for modeling

C++: protocols::tcr::TCRmodel::use_gma_templates() const –> bool

use_gmb_templates(self: pyrosetta.rosetta.protocols.tcr.TCRmodel) bool

returns true if germline beta chain sequence is used for modeling

C++: protocols::tcr::TCRmodel::use_gmb_templates() const –> bool

class pyrosetta.rosetta.protocols.tcr.TCRseqInfo

Bases: pybind11_builtins.pybind11_object

class for parsing/numbering tcr sequences

TCRseqInfo takes in the alpha/beta chain sequence TCR segments are parsed by regular expressions / Aho numbering / ANARCI / user provided numbering TCR segments: Germline, Framework, CDR1, CDR2, CDR2HV4, CDR3 Extended cdr2hv4 segment is used for cdr2. More details can be found in publication/documentation

aaho_posi(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) protocols::tcr::TCRseqInfo::tcrposi

returns standard Aho numbering used for cdr positions for a/b chains

C++: protocols::tcr::TCRseqInfo::aaho_posi() const –> struct protocols::tcr::TCRseqInfo::tcrposi

aseq_posi(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) protocols::tcr::TCRseqInfo::tcrposi

returns cdr positions for input a/b chains

C++: protocols::tcr::TCRseqInfo::aseq_posi() const –> struct protocols::tcr::TCRseqInfo::tcrposi

assign(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo, : pyrosetta.rosetta.protocols.tcr.TCRseqInfo) pyrosetta.rosetta.protocols.tcr.TCRseqInfo

C++: protocols::tcr::TCRseqInfo::operator=(const class protocols::tcr::TCRseqInfo &) –> class protocols::tcr::TCRseqInfo &

atcr(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) protocols::tcr::TCRseqInfo::tcrsegs

returns parsed tcr segments for a/b chains

C++: protocols::tcr::TCRseqInfo::atcr() const –> struct protocols::tcr::TCRseqInfo::tcrsegs

baho_posi(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) protocols::tcr::TCRseqInfo::tcrposi

C++: protocols::tcr::TCRseqInfo::baho_posi() const –> struct protocols::tcr::TCRseqInfo::tcrposi

bseq_posi(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) protocols::tcr::TCRseqInfo::tcrposi

C++: protocols::tcr::TCRseqInfo::bseq_posi() const –> struct protocols::tcr::TCRseqInfo::tcrposi

btcr(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) protocols::tcr::TCRseqInfo::tcrsegs

C++: protocols::tcr::TCRseqInfo::btcr() const –> struct protocols::tcr::TCRseqInfo::tcrsegs

clone(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo) pyrosetta.rosetta.protocols.tcr.TCRseqInfo

C++: protocols::tcr::TCRseqInfo::clone() const –> class std::shared_ptr<class protocols::tcr::TCRseqInfo>

class tcrposi

Bases: pybind11_builtins.pybind11_object

tcrposi holds the start/end position of cdr loops

cap has the start/end of the variable domian sequence

assign(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, : pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi

C++: protocols::tcr::TCRseqInfo::tcrposi::operator=(const struct protocols::tcr::TCRseqInfo::tcrposi &) –> struct protocols::tcr::TCRseqInfo::tcrposi &

property cap
property cdr1
property cdr2hv4
property cdr3
class tcrsegs

Bases: pybind11_builtins.pybind11_object

parsed sequence strings of tcr segments

truncdomain:variable domain sequence, fr:framework sequence, gm:germline sequence

cdr1, cdr2, cdr3 cdr loop sequences

assign(self: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, : pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs) pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs

C++: protocols::tcr::TCRseqInfo::tcrsegs::operator=(const struct protocols::tcr::TCRseqInfo::tcrsegs &) –> struct protocols::tcr::TCRseqInfo::tcrsegs &

property cdr1
property cdr2
property cdr3
property fr
property gm
property truncdomain
pyrosetta.rosetta.protocols.tcr.adjust_position_for_chain(pose_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, chainlen: int) None

adjust pose position for partner chain

add partner chain length to all values

C++: protocols::tcr::adjust_position_for_chain(struct protocols::tcr::TCRseqInfo::tcrposi &, const unsigned long &) –> void

pyrosetta.rosetta.protocols.tcr.assign_CDRs_using_anarci(seq: str, anarci_path: str, a_aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, pose_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, parsedseqs: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs) None

TCR segments were assigned using anarci program and Aho numbering

C++: protocols::tcr::assign_CDRs_using_anarci(const std::string &, const std::string &, struct protocols::tcr::TCRseqInfo::tcrposi &, struct protocols::tcr::TCRseqInfo::tcrposi &, struct protocols::tcr::TCRseqInfo::tcrsegs &) –> void

pyrosetta.rosetta.protocols.tcr.assign_CDRs_using_numbers(seq: str, cdr1seqpos: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, cdr2seqpos: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, cdr3seqpos: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, cap: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, parsedseqs: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, pose_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

TCR segments were assigned using start and end position residue numbers

C++: protocols::tcr::assign_CDRs_using_numbers(const std::string &, const struct protocols::antibody::grafting::CDR_Bounds &, const struct protocols::antibody::grafting::CDR_Bounds &, const struct protocols::antibody::grafting::CDR_Bounds &, const struct protocols::antibody::grafting::CDR_Bounds &, struct protocols::tcr::TCRseqInfo::tcrsegs &, struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.assign_achain_CDRs_using_REGEX(seq: str, parsedseqs: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, pose_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

function to initialize and regular expressions for parsing achain TCR sequence

different functions for achain and bchain due to different regex used

due to compiler issues (reqd adv compilers to compile regex) not passing around regex

C++: protocols::tcr::assign_achain_CDRs_using_REGEX(const std::string &, struct protocols::tcr::TCRseqInfo::tcrsegs &, struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.assign_bchain_CDRs_using_REGEX(seq: str, parsedseqs: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, pose_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

regex intialization for parsing bchain TCR sequence

bchian TCR segments were assigned using regular expression

C++: protocols::tcr::assign_bchain_CDRs_using_REGEX(const std::string &, struct protocols::tcr::TCRseqInfo::tcrsegs &, struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.calculate_identity_score(query: str, content: str) float

calculate percent identity between 2 sequences

C++: protocols::tcr::calculate_identity_score(const std::string &, const std::string &) –> double

pyrosetta.rosetta.protocols.tcr.check_seq_match(query: str, db: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t) bool

check if query/target sequence are same from a input template db fasta file

used for deciding whether germline template can be used instead of framework template

for germline templates only CDR3 loop in grafted into germline template structure

C++: protocols::tcr::check_seq_match(const std::string &, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &) –> bool

pyrosetta.rosetta.protocols.tcr.check_seq_match_from_multiple_input_db(query: str, multidb: pyrosetta.rosetta.utility.vector1_std_string, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t) bool

check if query/target sequence are same from multiple input template db fasta file

calls check_seq_match for each input db file in the list

C++: protocols::tcr::check_seq_match_from_multiple_input_db(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &) –> bool

pyrosetta.rosetta.protocols.tcr.create_ignore_list(query: str, blast_db: str, blast_cutoff: float) pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t

create template blacklist by runing blast with cut-off value

C++: protocols::tcr::create_ignore_list(const std::string &, const std::string &, const double &) –> class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >

pyrosetta.rosetta.protocols.tcr.dump_templates(atmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts, btmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts, use_gma: bool, use_gmb: bool) None

dump all templates found for various tcr segments

C++: protocols::tcr::dump_templates(const struct protocols::tcr::TCRmodel::tcrtmplts &, const struct protocols::tcr::TCRmodel::tcrtmplts &, const bool, const bool) –> void

pyrosetta.rosetta.protocols.tcr.find_template(query: str, db: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) Tuple[float, str]

find best scoring template from a fasta sequence file

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

C++: protocols::tcr::find_template(const std::string &, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> struct std::pair<double, std::string >

pyrosetta.rosetta.protocols.tcr.find_template_from_multiple_input_db(query: str, multidb: pyrosetta.rosetta.utility.vector1_std_string, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) Tuple[float, str]

find templates from one or more template fasta sequence files

calls find_template for each file in the list

C++: protocols::tcr::find_template_from_multiple_input_db(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> struct std::pair<double, std::string >

pyrosetta.rosetta.protocols.tcr.get_cdr_pdb_pos_from_input_pose(inpose: pyrosetta.rosetta.core.pose.Pose, selepos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

find cdr positions (pose numbers) in input pose with AHO numbering scheme

C++: protocols::tcr::get_cdr_pdb_pos_from_input_pose(const class core::pose::Pose &, const struct protocols::tcr::TCRseqInfo::tcrposi &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

pyrosetta.rosetta.protocols.tcr.get_orientation_template_from_db(fra: str, frb: str, oritmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, ss: pyrosetta.rosetta.core.sequence.ScoringScheme) Tuple[str, str]

orientation template identification and grafting from template db

C++: protocols::tcr::get_orientation_template_from_db(const std::string &, const std::string &, const struct protocols::tcr::TCRmodel::tmpltinfo &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> struct std::pair<std::string, std::string >

pyrosetta.rosetta.protocols.tcr.graft_cdr(currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, template_pdb_path: str, cdr_start: int, cdr_end: int) None

grafting of cdr segments of template structure

for both alpha and beta chain cdr segment

C++: protocols::tcr::graft_cdr(struct protocols::tcr::TCRmodel::tmpltinfo &, const std::string &, const unsigned long &, const unsigned long &) –> void

pyrosetta.rosetta.protocols.tcr.graft_cdr_to_fw(scafold: pyrosetta.rosetta.core.pose.Pose, cdr_piece: pyrosetta.rosetta.core.pose.Pose, start: int, end: int, nter_overhang: int, cter_overhang: int) None

combine graft cdr structures and framework structure to build crude model

uses CCDEndsGraftMover with default overhang residue size of 3

C++: protocols::tcr::graft_cdr_to_fw(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long &, const unsigned long &, unsigned long &, unsigned long &) –> void

pyrosetta.rosetta.protocols.tcr.graft_framework(currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, template_pdb_path: str, aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

grafting of Framework/germline template structure

for both alpha and beta chain framework and germline segment

C++: protocols::tcr::graft_framework(struct protocols::tcr::TCRmodel::tmpltinfo &, const std::string &, const struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.ignore_template(tmpltid: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t) bool

Check if a particular structure should be ignored for consideration as template

checks if a template id is present in the ignore list

C++: protocols::tcr::ignore_template(const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &) –> bool

pyrosetta.rosetta.protocols.tcr.ind_remodel_tcr_cdr_loops(tcr_pose: pyrosetta.rosetta.core.pose.Pose, loopstart: int, loopend: int) None

loop rebuild function

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

takes options loop remodel mover type

C++: protocols::tcr::ind_remodel_tcr_cdr_loops(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.tcr.initialize_aho_numbers(a_aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, b_aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

initialize aho numbers

Aho number are standard numbering scheme for TCR structures

template structures are renumbered by Aho numbers, grafting of TCr segments are based on these numbering scheme

C++: protocols::tcr::initialize_aho_numbers(struct protocols::tcr::TCRseqInfo::tcrposi &, struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.initialize_template_db_files(atcr: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, btcr: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, atmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts, btmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts, tcr_seq_db: str) None

initialize template files for all TCR segments

template files for CDR sequences were choosen by CDR sequence length

C++: protocols::tcr::initialize_template_db_files(const struct protocols::tcr::TCRseqInfo::tcrsegs &, const struct protocols::tcr::TCRseqInfo::tcrsegs &, struct protocols::tcr::TCRmodel::tcrtmplts &, struct protocols::tcr::TCRmodel::tcrtmplts &, const std::string &) –> void

pyrosetta.rosetta.protocols.tcr.initialize_template_ignore_list(atcr: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, btcr: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, blast_cutoff: float, tcr_seq_db: str) None

initialize list of template structures to ignore

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

C++: protocols::tcr::initialize_template_ignore_list(const struct protocols::tcr::TCRseqInfo::tcrsegs &, const struct protocols::tcr::TCRseqInfo::tcrsegs &, class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const std::string &) –> void

pyrosetta.rosetta.protocols.tcr.match_template_and_target_sequence(scafold: pyrosetta.rosetta.core.pose.Pose, targetseq: str, posecopy: pyrosetta.rosetta.core.pose.Pose) None

match template seq with target seq during modeling

uses protocols::simple_moves::MutateResidue to mutate residues

C++: protocols::tcr::match_template_and_target_sequence(const class core::pose::Pose &, const std::string &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.tcr.minimize_tcr_model(model_pose: pyrosetta.rosetta.core.pose.Pose) None

minimize the tcr model pose

C++: protocols::tcr::minimize_tcr_model(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.tcr.orient_tcr_chain(fr_piece: pyrosetta.rosetta.core.pose.Pose, ori_tmplt_chain: pyrosetta.rosetta.core.pose.Pose, selepos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

orient TCR alpha/beta chains based on the orientation templates

C++: protocols::tcr::orient_tcr_chain(class core::pose::Pose &, const class core::pose::Pose &, const struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.refine_all_cdr_loops(tcr_pose: pyrosetta.rosetta.core.pose.Pose, a_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, b_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi) None

refine all cdr loops

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

C++: protocols::tcr::refine_all_cdr_loops(class core::pose::Pose &, const struct protocols::tcr::TCRseqInfo::tcrposi &, const struct protocols::tcr::TCRseqInfo::tcrposi &) –> void

pyrosetta.rosetta.protocols.tcr.refine_cdr3_loops(tcr_pose: pyrosetta.rosetta.core.pose.Pose, acdr3: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, bcdr3: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds) None

loop refine function for CDR3 alpha and CDR3 beta loops

C++: protocols::tcr::refine_cdr3_loops(class core::pose::Pose &, const struct protocols::antibody::grafting::CDR_Bounds &, const struct protocols::antibody::grafting::CDR_Bounds &) –> void

pyrosetta.rosetta.protocols.tcr.refine_cdr_loop(tcr_pose: pyrosetta.rosetta.core.pose.Pose, cdr: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds) None

loop refine function for CDR alpha/beta loop

C++: protocols::tcr::refine_cdr_loop(class core::pose::Pose &, const struct protocols::antibody::grafting::CDR_Bounds &) –> void

pyrosetta.rosetta.protocols.tcr.refine_tcr_cdr_loops(tcr_pose: pyrosetta.rosetta.core.pose.Pose, cdrloops: pyrosetta.rosetta.protocols.loops.Loops) None

loop refine function for CDR loop

C++: protocols::tcr::refine_tcr_cdr_loops(class core::pose::Pose &, const class std::shared_ptr<class protocols::loops::Loops> &) –> void

pyrosetta.rosetta.protocols.tcr.relax_tcr_model(model_pose: pyrosetta.rosetta.core.pose.Pose) None

relax the tcr model pose

C++: protocols::tcr::relax_tcr_model(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.tcr.remodel_tcr_cdr_loops(tcr_pose: pyrosetta.rosetta.core.pose.Pose, cdr3loops: pyrosetta.rosetta.protocols.loops.Loops, refine: bool) None

loop remodel function for CDR loop

C++: protocols::tcr::remodel_tcr_cdr_loops(class core::pose::Pose &, const class std::shared_ptr<class protocols::loops::Loops> &, bool) –> void

pyrosetta.rosetta.protocols.tcr.repack_tcr_model(model_pose: pyrosetta.rosetta.core.pose.Pose) None

repack the tcr model pose

C++: protocols::tcr::repack_tcr_model(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.tcr.run_blast(query: str, blast_db: str) None

run blast to find templates

used for blacklisting pdb’s based on cutoff

C++: protocols::tcr::run_blast(const std::string &, const std::string &) –> void

pyrosetta.rosetta.protocols.tcr.score_alignment(query: str, content: str, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) float

calculte alignment score b/w 2 sequences of same length

PAM30 pssm matrix is used for scoring the AA pairs

C++: protocols::tcr::score_alignment(const std::string &, const std::string &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> double

pyrosetta.rosetta.protocols.tcr.setup_cdr_template(seq: str, currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, cdrstart: int, cdrend: int, tpdb_path: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) None

CDR template identification and grafting of template structure

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

C++: protocols::tcr::setup_cdr_template(const std::string &, struct protocols::tcr::TCRmodel::tmpltinfo &, const unsigned long, const unsigned long, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> void

pyrosetta.rosetta.protocols.tcr.setup_cdr_template_from_db(seq: str, currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, cdrstart: int, cdrend: int, tpdb_path: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) None

Search templates for a CDR loop sequence in the template database

C++: protocols::tcr::setup_cdr_template_from_db(const std::string &, struct protocols::tcr::TCRmodel::tmpltinfo &, const unsigned long, const unsigned long, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> void

pyrosetta.rosetta.protocols.tcr.setup_cdr_template_from_pdbid(currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, cdrstart: int, cdrend: int, tpdb_path: str) None

get the CDR template structure from user provided PDB ID

C++: protocols::tcr::setup_cdr_template_from_pdbid(struct protocols::tcr::TCRmodel::tmpltinfo &, const unsigned long, const unsigned long, const std::string &) –> void

pyrosetta.rosetta.protocols.tcr.setup_fw_template(seq: str, aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, tpdb_path: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) None

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

C++: protocols::tcr::setup_fw_template(const std::string &, const struct protocols::tcr::TCRseqInfo::tcrposi &, struct protocols::tcr::TCRmodel::tmpltinfo &, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> void

pyrosetta.rosetta.protocols.tcr.setup_fw_template_from_db(seq: str, aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, tpdb_path: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, tcr_ss: pyrosetta.rosetta.core.sequence.ScoringScheme) None

Search template structures in the template database

for Framework/Germline templates

C++: protocols::tcr::setup_fw_template_from_db(const std::string &, const struct protocols::tcr::TCRseqInfo::tcrposi &, struct protocols::tcr::TCRmodel::tmpltinfo &, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> void

pyrosetta.rosetta.protocols.tcr.setup_fw_template_from_pdbid(currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, aho_pos: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, tpdb_path: str) None

helper method to read the template structure from user provided PDB id

for framework/germline template structures

C++: protocols::tcr::setup_fw_template_from_pdbid(struct protocols::tcr::TCRmodel::tmpltinfo &, const struct protocols::tcr::TCRseqInfo::tcrposi &, const std::string &) –> void

pyrosetta.rosetta.protocols.tcr.setup_orientation_template(atcr: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, btcr: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs, oria_tmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, orib_tmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo, aaho_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, baho_posi: pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi, tpdb_path: str, ignore_lists: pyrosetta.rosetta.std.list_std_set_std_string_std_less_std_string_std_allocator_std_string_std_allocator_std_set_std_string_std_less_std_string_std_allocator_std_string_t, cutoff: float, ss: pyrosetta.rosetta.core.sequence.ScoringScheme) None

parent function for orientation template identification

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

C++: protocols::tcr::setup_orientation_template(const struct protocols::tcr::TCRseqInfo::tcrsegs &, const struct protocols::tcr::TCRseqInfo::tcrsegs &, struct protocols::tcr::TCRmodel::tmpltinfo &, struct protocols::tcr::TCRmodel::tmpltinfo &, const struct protocols::tcr::TCRseqInfo::tcrposi &, const struct protocols::tcr::TCRseqInfo::tcrposi &, const std::string &, const class std::list<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, class std::allocator<class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > &, const double &, const class std::shared_ptr<class core::sequence::ScoringScheme> &) –> void

pyrosetta.rosetta.protocols.tcr.setup_template_from_pdbfile(currtmplt: pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo) None

read the template structure from user provided PDB file

C++: protocols::tcr::setup_template_from_pdbfile(struct protocols::tcr::TCRmodel::tmpltinfo &) –> void

pyrosetta.rosetta.protocols.tcr.string_to_CDRbounds(position: str) pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds

convert string to numbers used in CDR_bounds

C++: protocols::tcr::string_to_CDRbounds(const std::string &) –> struct protocols::antibody::grafting::CDR_Bounds

pyrosetta.rosetta.protocols.tcr.update_template_files(file_names: pyrosetta.rosetta.utility.vector1_std_string, tcr_seq_db: str) pyrosetta.rosetta.utility.vector1_std_string

check and update if template files based on sequence length exists on the template

C++: protocols::tcr::update_template_files(const class utility::vector1<std::string, class std::allocator<std::string > > &, const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >