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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain, sequence_: str) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain, arg0: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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

cdr2_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) → str¶: C++: protocols::antibody::grafting::AntibodyChain::cdr2_sequence() const –> std::string

cdr3_sequence(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain) → str¶: C++: protocols::antibody::grafting::AntibodyChain::cdr3_sequence() const –> std::string

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.AntibodySequence¶

Bases: pybind11_builtins.pybind11_object

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, heavy_: str, light_: str) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, arg0: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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

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_Detector¶

Bases: pyrosetta.rosetta.basic.Reporter

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector, arg0: pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) → None¶

Detect CDR’s

_AE_cdr_detection_failed_ if for some of the loops detection failed

C++: protocols::antibody::grafting::CDR_Detector::detect(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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.Numberer¶

Bases: pybind11_builtins.pybind11_object

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.Numberer) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.Numberer, arg0: pyrosetta.rosetta.protocols.antibody.grafting.Numberer) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector, arg0: pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.RegEx_based_CDR_Detector, : pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence) → None¶

Detect CDR’s

_AE_cdr_detection_failed_ if for some of the loops detection failed

C++: protocols::antibody::grafting::RegEx_based_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_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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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> > > > > >

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> > > > > >

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> > > > > >

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_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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, arg0: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, arg0: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, arg1: pyrosetta.rosetta.utility.vector0_std_string) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate, source: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base, regions: pyrosetta.rosetta.utility.vector0_std_string, report: pyrosetta.rosetta.basic.Report) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result) -> None
__init__(self: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result, arg0: pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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.

graft_cdr_loops(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet, output_prefix: str, suffix: str, database: str) -> pyrosetta.rosetta.core.pose.Pose
graft_cdr_loops(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet, output_prefix: str, suffix: str, database: str, optimal_graft: bool) -> pyrosetta.rosetta.core.pose.Pose
graft_cdr_loops(A: pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence, : pyrosetta.rosetta.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 class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, bool, bool) –> class std::shared_ptr<class core::pose::Pose>

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

Overloaded function.

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
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
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
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
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(class std::basic_string<char>, class std::basic_string<char>, char, class std::basic_string<char>, 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<class std::basic_string<char>, class std::map<class std::basic_string<char>, class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::basic_string<char> > > >, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::map<class std::basic_string<char>, class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::basic_string<char> > > > > > > &) –> void

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

Overloaded function.

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