grafting

Bindings for protocols::antibody::grafting namespace

class pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain

Bases: pybind11_builtins.pybind11_object

Hold information about heavy or light antibody chain. This include:

  • loop info (though CDR_Bounds cdr*)

  • sequnce

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain

C++: protocols::antibody::grafting::AntibodyChain::operator=(const struct protocols::antibody::grafting::AntibodyChain &) –> struct protocols::antibody::grafting::AntibodyChain &

property cdr1
cdr1_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) str

Calculate CDR sequence

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::AntibodyChain::cdr1_sequence() const –> std::string

property cdr2
cdr2_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) str

C++: protocols::antibody::grafting::AntibodyChain::cdr2_sequence() const –> std::string

property cdr3
cdr3_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) str

C++: protocols::antibody::grafting::AntibodyChain::cdr3_sequence() const –> std::string

property sequence
validate(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) None

validate CDR sequence’s

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::AntibodyChain::validate() const –> void

class pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering

Bases: pybind11_builtins.pybind11_object

all(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering) pyrosetta.rosetta.utility.vector0_std_string

C++: protocols::antibody::grafting::AntibodyChainNumbering::all() –> class utility::vector0<std::string, class std::allocator<std::string > >

property cdr1
property cdr2
property cdr3
property fr1
property fr2
property fr3
property fr4
validate(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework, chain_id: str) None

Check if numbering array length match content of AntibodyChain and AntibodyFramework

throws _AE_unexpected_region_length_ if mismatch detected

C++: protocols::antibody::grafting::AntibodyChainNumbering::validate(const struct protocols::antibody::grafting::AntibodyChain &, const struct protocols::antibody::grafting::AntibodyFramework &, const std::string &) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework

C++: protocols::antibody::grafting::AntibodyFramework::operator=(const struct protocols::antibody::grafting::AntibodyFramework &) –> struct protocols::antibody::grafting::AntibodyFramework &

property fr1
property fr1_begin
property fr1_end
property fr2
property fr2_begin
property fr2_end
property fr3
property fr3_begin
property fr3_end
property fr4
property fr4_begin
property fr4_end
update_sequences(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework, chain_sequence: str) None

update fr1/4 sequences.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::AntibodyFramework::update_sequences(std::string) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.AntibodyNumbering

Bases: pybind11_builtins.pybind11_object

property heavy
property light
class pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence

Bases: pybind11_builtins.pybind11_object

Hold info about whole antibody sequence: heavy and light chains. This is basially a convenience class

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence

C++: protocols::antibody::grafting::AntibodySequence::operator=(const struct protocols::antibody::grafting::AntibodySequence &) –> struct protocols::antibody::grafting::AntibodySequence &

h1_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) str

Calculate CDR sequence

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::AntibodySequence::h1_sequence() const –> std::string

h2_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) str

C++: protocols::antibody::grafting::AntibodySequence::h2_sequence() const –> std::string

h3_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) str

C++: protocols::antibody::grafting::AntibodySequence::h3_sequence() const –> std::string

property heavy
heavy_framework(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework

Calculate Framework sequence’s by using CDR’s CDR_Bounds info

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::AntibodySequence::heavy_framework() const –> struct protocols::antibody::grafting::AntibodyFramework

l1_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) str

C++: protocols::antibody::grafting::AntibodySequence::l1_sequence() const –> std::string

l2_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) str

C++: protocols::antibody::grafting::AntibodySequence::l2_sequence() const –> std::string

l3_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) str

C++: protocols::antibody::grafting::AntibodySequence::l3_sequence() const –> std::string

property light
light_framework(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework

C++: protocols::antibody::grafting::AntibodySequence::light_framework() const –> struct protocols::antibody::grafting::AntibodyFramework

class pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, : pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds) pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds

C++: protocols::antibody::grafting::CDR_Bounds::operator=(const struct protocols::antibody::grafting::CDR_Bounds &) –> struct protocols::antibody::grafting::CDR_Bounds &

property begin
defined(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds) bool

Check if current value of begin/end could be valid for some sequence

C++: protocols::antibody::grafting::CDR_Bounds::defined() const –> bool

property end
size(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds) int

return size of region

C++: protocols::antibody::grafting::CDR_Bounds::size() const –> unsigned long

valid(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, sequence: str) bool

Check if current value of begin/end if valid for given sequence. Always return true if CDR undefined.

C++: protocols::antibody::grafting::CDR_Bounds::valid(const std::string &) const –> bool

validate(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds, sequence: str) None

validate CDR sequence

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::CDR_Bounds::validate(const std::string &) const –> void

class pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector

Bases: pyrosetta.rosetta.basic.Reporter

Base class for antibody CDR detector. Sub-class it to implement particular input file/cmdline or prediction

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector) pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector

C++: protocols::antibody::grafting::CDR_Detector::operator=(const class protocols::antibody::grafting::CDR_Detector &) –> class protocols::antibody::grafting::CDR_Detector &

detect(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

Detect CDR’s

_AE_cdr_detection_failed_ if for some of the loops detection is failed

C++: protocols::antibody::grafting::CDR_Detector::detect(struct protocols::antibody::grafting::AntibodySequence &) –> void

detect_heavy_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

C++: protocols::antibody::grafting::CDR_Detector::detect_heavy_chain(struct protocols::antibody::grafting::AntibodySequence &) –> void

detect_light_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

C++: protocols::antibody::grafting::CDR_Detector::detect_light_chain(struct protocols::antibody::grafting::AntibodySequence &) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer

Bases: pybind11_builtins.pybind11_object

Use RegEx and antibody sequence information to detect CDR’s

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer, : pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer) pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer

C++: protocols::antibody::grafting::Chothia_Numberer::operator=(const class protocols::antibody::grafting::Chothia_Numberer &) –> class protocols::antibody::grafting::Chothia_Numberer &

number(self: pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework, light_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyNumbering

Detect CDR’s

_AE_unexpected_cdr_region_ (sub-class of _AE_numbering_failed_) if numbering is fails

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::Chothia_Numberer::number(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::AntibodyFramework &, const struct protocols::antibody::grafting::AntibodyFramework &) –> struct protocols::antibody::grafting::AntibodyNumbering

number_heavy_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering

C++: protocols::antibody::grafting::Chothia_Numberer::number_heavy_chain(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::AntibodyFramework &) –> struct protocols::antibody::grafting::AntibodyChainNumbering

number_light_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, light_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering

C++: protocols::antibody::grafting::Chothia_Numberer::number_light_chain(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::AntibodyFramework &) –> struct protocols::antibody::grafting::AntibodyChainNumbering

class pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL, : pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL) pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL

C++: protocols::antibody::grafting::FRH_FRL::operator=(const struct protocols::antibody::grafting::FRH_FRL &) –> struct protocols::antibody::grafting::FRH_FRL &

property frh1
property frh2
property frh3
property frh4
property frl1
property frl2
property frl3
property frl4
class pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

Bases: pyrosetta.rosetta.utility.excn.Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception, : pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception) pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

C++: protocols::antibody::grafting::Grafting_Base_Exception::operator=(const class protocols::antibody::grafting::Grafting_Base_Exception &) –> class protocols::antibody::grafting::Grafting_Base_Exception &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector

Bases: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector

Use input JSON (in same format as output report) to detect the CDR begin/end points

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector) pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector

C++: protocols::antibody::grafting::Json_based_CDR_Detector::operator=(const class protocols::antibody::grafting::Json_based_CDR_Detector &) –> class protocols::antibody::grafting::Json_based_CDR_Detector &

detect(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

Detect CDR’s

_AE_cdr_detection_failed_ if for some of the loops detection is failed

C++: protocols::antibody::grafting::CDR_Detector::detect(struct protocols::antibody::grafting::AntibodySequence &) –> void

detect_heavy_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

C++: protocols::antibody::grafting::Json_based_CDR_Detector::detect_heavy_chain(struct protocols::antibody::grafting::AntibodySequence &) –> void

detect_light_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

C++: protocols::antibody::grafting::Json_based_CDR_Detector::detect_light_chain(struct protocols::antibody::grafting::AntibodySequence &) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.Numberer

Bases: pybind11_builtins.pybind11_object

Base class for antibody CDR detector. Sub-class it to implement particular detection methods

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.Numberer, : pyrosetta.rosetta.protocols.antibody.grafting.Numberer) pyrosetta.rosetta.protocols.antibody.grafting.Numberer

C++: protocols::antibody::grafting::Numberer::operator=(const class protocols::antibody::grafting::Numberer &) –> class protocols::antibody::grafting::Numberer &

number(self: pyrosetta.rosetta.protocols.antibody.grafting.Numberer, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework, light_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework) pyrosetta.rosetta.protocols.antibody.grafting.AntibodyNumbering

Number CDR’s

_AE_unexpected_cdr_region_ (or it sub-class) if numbering is fails

_AE_cdr_undefined_ if reuested CDR regions is not defined.

_AE_invalid_cdr_region_ if CDR sequence out of bound of Chain sequence

C++: protocols::antibody::grafting::Numberer::number(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::AntibodyFramework &, const struct protocols::antibody::grafting::AntibodyFramework &) –> struct protocols::antibody::grafting::AntibodyNumbering

class pyrosetta.rosetta.protocols.antibody.grafting.RegExManager

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_antibody_grafting_RegExManager_t

This class is a singleton and manages CarbohydratesInfo data that should only be read from the database one time and shared among all instances of CarbohydrateInfo.

H1_pattern(self: pyrosetta.rosetta.protocols.antibody.grafting.RegExManager) str

C++: protocols::antibody::grafting::RegExManager::H1_pattern() const –> std::string

H3_pattern(self: pyrosetta.rosetta.protocols.antibody.grafting.RegExManager) str

C++: protocols::antibody::grafting::RegExManager::H3_pattern() const –> std::string

L1_pattern(self: pyrosetta.rosetta.protocols.antibody.grafting.RegExManager) str

C++: protocols::antibody::grafting::RegExManager::L1_pattern() const –> std::string

L3_pattern(self: pyrosetta.rosetta.protocols.antibody.grafting.RegExManager) str

C++: protocols::antibody::grafting::RegExManager::L3_pattern() const –> std::string

static get_instance() protocols::antibody::grafting::RegExManager

C++: utility::SingletonBase<protocols::antibody::grafting::RegExManager>::get_instance() –> class protocols::antibody::grafting::RegExManager *

class pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector

Bases: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector

Use RegEx and antibody sequence information to detect CDR’s

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector) pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector

C++: protocols::antibody::grafting::RegEx_based_CDR_Detector::operator=(const class protocols::antibody::grafting::RegEx_based_CDR_Detector &) –> class protocols::antibody::grafting::RegEx_based_CDR_Detector &

detect(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

Detect CDR’s

_AE_cdr_detection_failed_ if for some of the loops detection is failed

C++: protocols::antibody::grafting::CDR_Detector::detect(struct protocols::antibody::grafting::AntibodySequence &) –> void

detect_heavy_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

C++: protocols::antibody::grafting::RegEx_based_CDR_Detector::detect_heavy_chain(struct protocols::antibody::grafting::AntibodySequence &) –> void

detect_light_chain(self: pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) None

C++: protocols::antibody::grafting::RegEx_based_CDR_Detector::detect_light_chain(struct protocols::antibody::grafting::AntibodySequence &) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result

C++: protocols::antibody::grafting::SCS_Antibody_Database_Result::operator=(const struct protocols::antibody::grafting::SCS_Antibody_Database_Result &) –> struct protocols::antibody::grafting::SCS_Antibody_Database_Result &

property bio_type
property frh
property frl
property h1
property h2
property h3
property l1
property l2
property l3
property light_type
property padded
property pdb
property resolution
property struct_source
class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base

Bases: pyrosetta.rosetta.basic.Reporter

add_filter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, filter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::add_filter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base

C++: protocols::antibody::grafting::SCS_Base::operator=(const class protocols::antibody::grafting::SCS_Base &) –> class protocols::antibody::grafting::SCS_Base &

pad_results(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible

C++: protocols::antibody::grafting::SCS_Base::pad_results(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &, struct protocols::antibody::grafting::SCS_Results &) –> void

raw_select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template without filtering or sorting. In general you probably need to call select(…) instead

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_Base::raw_select(const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template, filter it and sort. Try to provide at least ‘n’ templates if possible

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_Base::select(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

set_sorter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, sorter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::set_sorter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_Comparator::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator

C++: protocols::antibody::grafting::SCS_BlastComparator::operator=(const class protocols::antibody::grafting::SCS_BlastComparator &) –> class protocols::antibody::grafting::SCS_BlastComparator &

compare(*args, **kwargs)

Overloaded function.

  1. compare(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, a: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result, b: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result) -> bool

C++: protocols::antibody::grafting::SCS_BlastComparator::compare(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::SCS_Result &, const struct protocols::antibody::grafting::SCS_Result &) const –> bool

  1. compare(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, a: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult, b: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult) -> bool

C++: protocols::antibody::grafting::SCS_BlastComparator::compare(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::SCS_BlastResult &, const struct protocols::antibody::grafting::SCS_BlastResult &) const –> bool

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_Comparator::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution

C++: protocols::antibody::grafting::SCS_BlastComparator_BitScore_Resolution::operator=(const class protocols::antibody::grafting::SCS_BlastComparator_BitScore_Resolution &) –> class protocols::antibody::grafting::SCS_BlastComparator_BitScore_Resolution &

compare(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, a: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult, b: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult) bool

C++: protocols::antibody::grafting::SCS_BlastComparator_BitScore_Resolution::compare(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::SCS_BlastResult &, const struct protocols::antibody::grafting::SCS_BlastResult &) const –> bool

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_OCD &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_OCD &

get_n_orientational_templates(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) int

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::get_n_orientational_templates() const –> unsigned long

get_ocd_cutoff(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) float

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::get_ocd_cutoff() const –> double

init_from_options(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::init_from_options() –> void

set_n_orientational_templates(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, n: int) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::set_n_orientational_templates(unsigned long) –> void

set_ocd_cutoff(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD, cutoff: float) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_OCD::set_ocd_cutoff(double) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_alignment_length::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length

C++: protocols::antibody::grafting::SCS_BlastFilter_by_alignment_length::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_alignment_length &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_alignment_length &

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_outlier::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier

C++: protocols::antibody::grafting::SCS_BlastFilter_by_outlier::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_outlier &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_outlier &

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_pdbid::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid

C++: protocols::antibody::grafting::SCS_BlastFilter_by_pdbid::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_pdbid &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_pdbid &

get_pdb_names(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid) pyrosetta.rosetta.utility.vector0_std_string

C++: protocols::antibody::grafting::SCS_BlastFilter_by_pdbid::get_pdb_names() const –> class utility::vector0<std::string, class std::allocator<std::string > >

init_from_options(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_pdbid::init_from_options() –> void

set_pdb_names(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid, pdb_names: pyrosetta.rosetta.utility.vector0_std_string) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_pdbid::set_pdb_names(class utility::vector0<std::string, class std::allocator<std::string > >) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity &

get_sid_cutoff_cdr(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) float

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::get_sid_cutoff_cdr() const –> double

get_sid_cutoff_fr(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) float

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::get_sid_cutoff_fr() const –> double

init_from_options(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::init_from_options() –> void

set_sid_cutoff_cdr(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, cutoff: float) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::set_sid_cutoff_cdr(double) –> void

set_sid_cutoff_fr(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity, cutoff: float) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_identity::set_sid_cutoff_fr(double) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_length::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length

C++: protocols::antibody::grafting::SCS_BlastFilter_by_sequence_length::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_sequence_length &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_sequence_length &

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_template_bfactor::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor

C++: protocols::antibody::grafting::SCS_BlastFilter_by_template_bfactor::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_template_bfactor &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_template_bfactor &

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_template_resolution::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution

C++: protocols::antibody::grafting::SCS_BlastFilter_by_template_resolution::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_by_template_resolution &) –> class protocols::antibody::grafting::SCS_BlastFilter_by_template_resolution &

get_resolution_cutoff(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution) float

C++: protocols::antibody::grafting::SCS_BlastFilter_by_template_resolution::get_resolution_cutoff() const –> double

set_resolution_cutoff(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution, cutoff: float) None

C++: protocols::antibody::grafting::SCS_BlastFilter_by_template_resolution::set_resolution_cutoff(double) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_BlastFilter_nonmatching_prolines::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines

C++: protocols::antibody::grafting::SCS_BlastFilter_nonmatching_prolines::operator=(const class protocols::antibody::grafting::SCS_BlastFilter_nonmatching_prolines &) –> class protocols::antibody::grafting::SCS_BlastFilter_nonmatching_prolines &

find_positions(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines, str: str, query: str) pyrosetta.rosetta.utility.vector0_unsigned_long

C++: protocols::antibody::grafting::SCS_BlastFilter_nonmatching_prolines::find_positions(std::string, char) const –> class utility::vector0<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs

add_filter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, filter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::add_filter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus

C++: protocols::antibody::grafting::SCS_BlastPlus::operator=(const class protocols::antibody::grafting::SCS_BlastPlus &) –> class protocols::antibody::grafting::SCS_BlastPlus &

init_from_options(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus) None

set working dir/output-prefix for intermediate files based on command-line options

C++: protocols::antibody::grafting::SCS_BlastPlus::init_from_options() –> void

pad_results(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible

C++: protocols::antibody::grafting::SCS_BlastPlus::pad_results(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &, struct protocols::antibody::grafting::SCS_Results &) –> void

raw_select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_LoopOverSCs::raw_select(const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template, filter it and sort. Try to provide at least ‘n’ templates if possible

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_Base::select(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

set_blastp_executable(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus, blastp: str) None

set path to NCBI-Blast+ executable

C++: protocols::antibody::grafting::SCS_BlastPlus::set_blastp_executable(const std::string &) –> void

set_database_path(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, database: str) None

set path to antibody grafting database root, should point to tools/antibody

C++: protocols::antibody::grafting::SCS_LoopOverSCs::set_database_path(const std::string &) –> void

set_output_prefix(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus, prefix: str) None

set custom working dir/output-prefix for intermediate files

C++: protocols::antibody::grafting::SCS_BlastPlus::set_output_prefix(const std::string &) –> void

set_sorter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, sorter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::set_sorter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result

property alignment_length
assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult) pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult

C++: protocols::antibody::grafting::SCS_BlastResult::operator=(const struct protocols::antibody::grafting::SCS_BlastResult &) –> struct protocols::antibody::grafting::SCS_BlastResult &

property bio_type
property bit_score
property frh
property frl
property h1
property h2
property h3
property identity
property l1
property l2
property l3
property light_type
property padded
property pdb
property resolution
property struct_source
class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_Comparator::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator

C++: protocols::antibody::grafting::SCS_Comparator::operator=(const class protocols::antibody::grafting::SCS_Comparator &) –> class protocols::antibody::grafting::SCS_Comparator &

compare(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, a: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result, b: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result) bool

C++: protocols::antibody::grafting::SCS_Comparator::compare(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::SCS_Result &, const struct protocols::antibody::grafting::SCS_Result &) const –> bool

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

Bases: pybind11_builtins.pybind11_object

apply(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor, antibody_sequence: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, results: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

C++: protocols::antibody::grafting::SCS_Functor::apply(const struct protocols::antibody::grafting::AntibodySequence &, class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>) const –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor

C++: protocols::antibody::grafting::SCS_Functor::operator=(const class protocols::antibody::grafting::SCS_Functor &) –> class protocols::antibody::grafting::SCS_Functor &

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Helper

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_antibody_grafting_SCS_Helper_t

This class is a singleton and manages data that is necessary for SCS filters and should be read only once

static get_ab_OCDs() pyrosetta.rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t

Return a map of pdb to map of pdb to a float (OCD distance between the two pdbs)

C++: protocols::antibody::grafting::SCS_Helper::get_ab_OCDs() –> class std::map<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > > > >

static get_ab_cdr_bfactors() pyrosetta.rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t

Return a map of pdb to map of CDR to bool (true if bfactor cutoff is NOT met)

C++: protocols::antibody::grafting::SCS_Helper::get_ab_cdr_bfactors() –> class std::map<std::string, class std::map<std::string, bool, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, bool> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, bool, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, bool> > > > > >

static get_ab_region_outliers() pyrosetta.rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t

Return a map of pdb to map of CDR to bool (true if region is outlier)

C++: protocols::antibody::grafting::SCS_Helper::get_ab_region_outliers() –> class std::map<std::string, class std::map<std::string, bool, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, bool> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, bool, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, bool> > > > > >

static get_instance() protocols::antibody::grafting::SCS_Helper

C++: utility::SingletonBase<protocols::antibody::grafting::SCS_Helper>::get_instance() –> class protocols::antibody::grafting::SCS_Helper *

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base

add_filter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, filter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::add_filter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs) pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs

C++: protocols::antibody::grafting::SCS_LoopOverSCs::operator=(const class protocols::antibody::grafting::SCS_LoopOverSCs &) –> class protocols::antibody::grafting::SCS_LoopOverSCs &

init_from_options(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs) None

set working dir/output-prefix for intermediate files based on command-line options

C++: protocols::antibody::grafting::SCS_LoopOverSCs::init_from_options() –> void

pad_results(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible

C++: protocols::antibody::grafting::SCS_Base::pad_results(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &, struct protocols::antibody::grafting::SCS_Results &) –> void

raw_select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_LoopOverSCs::raw_select(const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template, filter it and sort. Try to provide at least ‘n’ templates if possible

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_Base::select(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

set_database_path(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, database: str) None

set path to antibody grafting database root, should point to tools/antibody

C++: protocols::antibody::grafting::SCS_LoopOverSCs::set_database_path(const std::string &) –> void

set_sorter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, sorter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::set_sorter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base

Proxy-like class for SCS_Base that alter SCS results: - for results not in ‘regions_’ return top result obtained from source_ - for results in ‘regions_’ return N best results

add_filter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, filter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::add_filter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate) pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate

C++: protocols::antibody::grafting::SCS_MultiTemplate::operator=(const class protocols::antibody::grafting::SCS_MultiTemplate &) –> class protocols::antibody::grafting::SCS_MultiTemplate &

pad_results(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, : int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible

C++: protocols::antibody::grafting::SCS_MultiTemplate::pad_results(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &, struct protocols::antibody::grafting::SCS_Results &) –> void

raw_select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template without filtering or sorting. In general you probably need to call select(…) instead

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_MultiTemplate::raw_select(const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template, filter it and sort. Try to provide at least ‘n’ templates if possible

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_MultiTemplate::select(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

set_multi_template_regions(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, regions: pyrosetta.rosetta.utility.vector0_std_string) None

specify mutable regions for multi-template selection mode.

C++: protocols::antibody::grafting::SCS_MultiTemplate::set_multi_template_regions(const class utility::vector0<std::string, class std::allocator<std::string > > &) –> void

set_sorter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, sorter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::set_sorter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result

Bases: pybind11_builtins.pybind11_object

Base struct for any SCS single result. Hold information of selected template

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result

C++: protocols::antibody::grafting::SCS_Result::operator=(const struct protocols::antibody::grafting::SCS_Result &) –> struct protocols::antibody::grafting::SCS_Result &

property padded
property pdb
class pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet

Bases: pybind11_builtins.pybind11_object

property frh
property frl
property h1
property h2
property h3
property l1
property l2
property l3
property orientation
class pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector

Bases: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t

append(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: protocols::antibody::grafting::SCS_Result) None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector) pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector

C++: protocols::antibody::grafting::SCS_ResultVector::operator=(const struct protocols::antibody::grafting::SCS_ResultVector &) –> struct protocols::antibody::grafting::SCS_ResultVector &

back(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) protocols::antibody::grafting::SCS_Result

access the last element

capacity(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) None

clears the contents

count(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: protocols::antibody::grafting::SCS_Result) int

counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: int) None

erases element at index

extend(othervec)
front(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) protocols::antibody::grafting::SCS_Result

access the first element

l(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) int

lower index

max_size(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) -> protocols::antibody::grafting::SCS_Result

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: int) -> protocols::antibody::grafting::SCS_Result

remove and return item at index

remove(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: protocols::antibody::grafting::SCS_Result) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: int) None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t, arg0: int) None

changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t) int

upper index

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Bases: pybind11_builtins.pybind11_object

property frh
property frl
get_result_set(*args, **kwargs)

Overloaded function.

  1. get_result_set(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results, row: int) -> protocols::antibody::grafting::SCS_ResultSet

  2. get_result_set(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results, row: int, strict: bool) -> protocols::antibody::grafting::SCS_ResultSet

Create result set from ‘row’ element of each SCS_ResultVector vector

if strict is true the throw if no resuls found otherwise use empty OP

std::out_of_range if for some of the row is not present and strict==true

C++: protocols::antibody::grafting::SCS_Results::get_result_set(unsigned long, bool) –> struct protocols::antibody::grafting::SCS_ResultSet

property h1
property h2
property h3
property l1
property l2
property l3
property orientation
class pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs

add_filter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, filter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::add_filter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix) pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix

C++: protocols::antibody::grafting::SCS_SubstitutionMatrix::operator=(const class protocols::antibody::grafting::SCS_SubstitutionMatrix &) –> class protocols::antibody::grafting::SCS_SubstitutionMatrix &

init_from_options(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix) None

set working dir/output-prefix for intermediate files based on command-line options

C++: protocols::antibody::grafting::SCS_SubstitutionMatrix::init_from_options() –> void

pad_results(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) None

Pad results vectors for each region (if possible) by adding arbitraty but compatible templates so at least n templates for each region is avalible

C++: protocols::antibody::grafting::SCS_Base::pad_results(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &, struct protocols::antibody::grafting::SCS_Results &) –> void

raw_select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_LoopOverSCs::raw_select(const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

select(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, n: int, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results

Select CDR’s template, filter it and sort. Try to provide at least ‘n’ templates if possible

_AE_scs_failed_ on failure

C++: protocols::antibody::grafting::SCS_Base::select(unsigned long, const struct protocols::antibody::grafting::AntibodySequence &) –> class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>

set_database_path(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs, database: str) None

set path to antibody grafting database root, should point to tools/antibody

C++: protocols::antibody::grafting::SCS_LoopOverSCs::set_database_path(const std::string &) –> void

set_sorter(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, sorter: protocols::antibody::grafting::SCS_Functor) None

C++: protocols::antibody::grafting::SCS_Base::set_sorter(class std::shared_ptr<const class protocols::antibody::grafting::SCS_Functor>) –> void

class pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult

Bases: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result

assign(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult) pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult

C++: protocols::antibody::grafting::SCS_SubstitutionMatrixResult::operator=(const struct protocols::antibody::grafting::SCS_SubstitutionMatrixResult &) –> struct protocols::antibody::grafting::SCS_SubstitutionMatrixResult &

property bio_type
property frh
property frl
property h1
property h2
property h3
property l1
property l2
property l3
property light_type
property padded
property pdb
property resolution
property score
property sid
property struct_source
class pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_) pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_

C++: protocols::antibody::grafting::_AE_cdr_detection_failed_::operator=(const class protocols::antibody::grafting::_AE_cdr_detection_failed_ &) –> class protocols::antibody::grafting::_AE_cdr_detection_failed_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_) pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_

C++: protocols::antibody::grafting::_AE_cdr_undefined_::operator=(const class protocols::antibody::grafting::_AE_cdr_undefined_ &) –> class protocols::antibody::grafting::_AE_cdr_undefined_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_) pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_

C++: protocols::antibody::grafting::_AE_grafting_failed_::operator=(const class protocols::antibody::grafting::_AE_grafting_failed_ &) –> class protocols::antibody::grafting::_AE_grafting_failed_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_) pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_

C++: protocols::antibody::grafting::_AE_invalid_cdr_region_::operator=(const class protocols::antibody::grafting::_AE_invalid_cdr_region_ &) –> class protocols::antibody::grafting::_AE_invalid_cdr_region_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_) pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_

C++: protocols::antibody::grafting::_AE_json_cdr_detection_failed_::operator=(const class protocols::antibody::grafting::_AE_json_cdr_detection_failed_ &) –> class protocols::antibody::grafting::_AE_json_cdr_detection_failed_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_) pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_

C++: protocols::antibody::grafting::_AE_numbering_failed_::operator=(const class protocols::antibody::grafting::_AE_numbering_failed_ &) –> class protocols::antibody::grafting::_AE_numbering_failed_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_

Bases: pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_) pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_

C++: protocols::antibody::grafting::_AE_scs_failed_::operator=(const class protocols::antibody::grafting::_AE_scs_failed_ &) –> class protocols::antibody::grafting::_AE_scs_failed_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_

Bases: pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_, : pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_) pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_

C++: protocols::antibody::grafting::_AE_unexpected_region_length_::operator=(const class protocols::antibody::grafting::_AE_unexpected_region_length_ &) –> class protocols::antibody::grafting::_AE_unexpected_region_length_ &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

pyrosetta.rosetta.protocols.antibody.grafting.antibody_grafting_usable() bool

Check if regex library is functional

C++: protocols::antibody::grafting::antibody_grafting_usable() –> bool

pyrosetta.rosetta.protocols.antibody.grafting.calculate_frh_frl(: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL

Calculate frh+frl pair by trimming fr* and removing ‘less-preserved’ regions

C++: protocols::antibody::grafting::calculate_frh_frl(const struct protocols::antibody::grafting::AntibodySequence &) –> struct protocols::antibody::grafting::FRH_FRL

pyrosetta.rosetta.protocols.antibody.grafting.graft_cdr_loops(*args, **kwargs)

Overloaded function.

  1. graft_cdr_loops(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : protocols::antibody::grafting::SCS_ResultSet, output_prefix: str, suffix: str, database: str) -> pyrosetta.rosetta.core.pose.Pose

  2. graft_cdr_loops(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : protocols::antibody::grafting::SCS_ResultSet, output_prefix: str, suffix: str, database: str, optimal_graft: bool) -> pyrosetta.rosetta.core.pose.Pose

  3. graft_cdr_loops(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : protocols::antibody::grafting::SCS_ResultSet, output_prefix: str, suffix: str, database: str, optimal_graft: bool, optimize_cdrs: bool) -> pyrosetta.rosetta.core.pose.Pose

graft cdr-loops using best scs-results and write results into specified output_prefix

C++: protocols::antibody::grafting::graft_cdr_loops(const struct protocols::antibody::grafting::AntibodySequence &, const struct protocols::antibody::grafting::SCS_ResultSet &, const std::string &, const std::string &, const std::string &, bool, bool) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.antibody.grafting.parse_plain_text_with_columns(*args, **kwargs)

Overloaded function.

  1. parse_plain_text_with_columns(file_name: str) -> pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

  2. parse_plain_text_with_columns(file_name: str, legend_prefix: str) -> pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

  3. parse_plain_text_with_columns(file_name: str, legend_prefix: str, legend_separator: str) -> pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

  4. parse_plain_text_with_columns(file_name: str, legend_prefix: str, legend_separator: str, data_prefix: str) -> pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

  5. parse_plain_text_with_columns(file_name: str, legend_prefix: str, legend_separator: str, data_prefix: str, data_separator: str) -> pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t

helper function to parse plain text for BLAST result and filter data

C++: protocols::antibody::grafting::parse_plain_text_with_columns(std::string, std::string, char, std::string, char) –> class utility::vector0<class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >, class std::allocator<class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > > >

pyrosetta.rosetta.protocols.antibody.grafting.populate_results_from_db(result: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result, db: pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t) None

C++: protocols::antibody::grafting::populate_results_from_db(const class std::shared_ptr<struct protocols::antibody::grafting::SCS_Antibody_Database_Result> &, const class std::map<std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > > > > &) –> void

pyrosetta.rosetta.protocols.antibody.grafting.result_sizes(*args, **kwargs)

Overloaded function.

  1. result_sizes(r: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results) -> str

  2. result_sizes(r: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results, width: int) -> str

filter helper function: generate string with results sizes

C++: protocols::antibody::grafting::result_sizes(class std::shared_ptr<struct protocols::antibody::grafting::SCS_Results>, int) –> std::string

pyrosetta.rosetta.protocols.antibody.grafting.trim_framework(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, heavy_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework, light_fr: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework) None

Calculate antibody framework regions (frh1…frl4) and Trim it by removing less-preserved elements

C++: protocols::antibody::grafting::trim_framework(const struct protocols::antibody::grafting::AntibodySequence &, struct protocols::antibody::grafting::AntibodyFramework &, struct protocols::antibody::grafting::AntibodyFramework &) –> void