tcr¶
Bindings for protocols::tcr namespace
- class pyrosetta.rosetta.protocols.tcr.TCRloopRefine¶
Bases:
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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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 > >