io

Bindings for core::io namespace

class pyrosetta.rosetta.core.io.AtomInformation

Bases: pybind11_builtins.pybind11_object

Only fields that are present in the PDB file will be initialized; others will have the default value. This class basically reflects the structure of ‘ATOM’ lines in PDB file format.

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.AtomInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.AtomInformation, arg0: pyrosetta.rosetta.core.io.AtomInformation) -> 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__(self: pyrosetta.rosetta.core.io.AtomInformation) → str
__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.core.io.AtomInformation, : pyrosetta.rosetta.core.io.AtomInformation) → pyrosetta.rosetta.core.io.AtomInformation

C++: core::io::AtomInformation::operator=(const struct core::io::AtomInformation &) –> struct core::io::AtomInformation &

class pyrosetta.rosetta.core.io.CisPeptideInformation

Bases: pybind11_builtins.pybind11_object

Labonte <JWLabonte.edu>

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.CisPeptideInformation, arg0: pyrosetta.rosetta.core.io.CisPeptideInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.CisPeptideInformation) -> 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.core.io.CisPeptideInformation, : pyrosetta.rosetta.core.io.CisPeptideInformation) → pyrosetta.rosetta.core.io.CisPeptideInformation

C++: core::io::CisPeptideInformation::operator=(const struct core::io::CisPeptideInformation &) –> struct core::io::CisPeptideInformation &

class pyrosetta.rosetta.core.io.HELIXInformation

Bases: pybind11_builtins.pybind11_object

Steven Lewis smlewi.com

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.HELIXInformation, arg0: pyrosetta.rosetta.core.io.HELIXInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.HELIXInformation) -> 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.core.io.HELIXInformation, : pyrosetta.rosetta.core.io.HELIXInformation) → pyrosetta.rosetta.core.io.HELIXInformation

C++: core::io::HELIXInformation::operator=(const struct core::io::HELIXInformation &) –> struct core::io::HELIXInformation &

class pyrosetta.rosetta.core.io.HeaderInformation

Bases: pybind11_builtins.pybind11_object

Information stored in the header records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z

class ExperimentalTechnique

Bases: pybind11_builtins.pybind11_object

Fields for the EXPDTA Record

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

  1. __eq__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique, arg0: pyrosetta.rosetta.core.io.ExperimentalTechnique) -> bool
  2. __eq__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique, arg0: int) -> bool
__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique) → tuple
__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique) → int
__init__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique, arg0: int) → None
__init_subclass__()

This method is called when a class is subclassed.

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

__int__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique) → int
__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

  1. __ne__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique, arg0: pyrosetta.rosetta.core.io.ExperimentalTechnique) -> bool
  2. __ne__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique, arg0: int) -> bool
__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique) → str
__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.io.ExperimentalTechnique, arg0: tuple) → None
__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).

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.HeaderInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.HeaderInformation, arg0: pyrosetta.rosetta.core.io.HeaderInformation) -> 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.core.io.HeaderInformation, : pyrosetta.rosetta.core.io.HeaderInformation) → pyrosetta.rosetta.core.io.HeaderInformation

C++: core::io::HeaderInformation::operator=(const class core::io::HeaderInformation &) –> class core::io::HeaderInformation &

classification(self: pyrosetta.rosetta.core.io.HeaderInformation) → str

C++: core::io::HeaderInformation::classification() const –> std::string

clear_compounds(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::clear_compounds() –> void

clear_experimental_techniques(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::clear_experimental_techniques() –> void

clear_keywords(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::clear_keywords() –> void

clear_title(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::clear_title() –> void

compound_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) → bool

C++: core::io::HeaderInformation::compound_in_progress() const –> bool

compound_token_to_string(token: pyrosetta.rosetta.core.io.CompoundToken) → str

C++: core::io::HeaderInformation::compound_token_to_string(enum core::io::HeaderInformation::CompoundToken) –> std::string

compounds(self: pyrosetta.rosetta.core.io.HeaderInformation) → pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t

C++: core::io::HeaderInformation::compounds() const –> const class utility::vector1<struct std::pair<enum core::io::HeaderInformation::CompoundToken, std::string >, class std::allocator<struct std::pair<enum core::io::HeaderInformation::CompoundToken, std::string > > > &

deposition_date(*args, **kwargs)

Overloaded function.

  1. deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation) -> str

C++: core::io::HeaderInformation::deposition_date() const –> std::string

  1. deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation, yy: int, mm: int, dd: int) -> None
get the deposition date using the format of two digit numbers
for the year, month and day of the month

C++: core::io::HeaderInformation::deposition_date(unsigned long &, unsigned long &, unsigned long &) const –> void

experimental_technique_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) → bool

C++: core::io::HeaderInformation::experimental_technique_in_progress() const –> bool

experimental_technique_to_string(technique: pyrosetta.rosetta.core.io.ExperimentalTechnique) → str

C++: core::io::HeaderInformation::experimental_technique_to_string(enum core::io::HeaderInformation::ExperimentalTechnique) –> std::string

experimental_techniques(self: pyrosetta.rosetta.core.io.HeaderInformation) → pyrosetta.rosetta.std.list_core_io_HeaderInformation_ExperimentalTechnique_t

C++: core::io::HeaderInformation::experimental_techniques() const –> const class std::list<enum core::io::HeaderInformation::ExperimentalTechnique, class std::allocator<enum core::io::HeaderInformation::ExperimentalTechnique> > &

finalize_compound_records(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::finalize_compound_records() –> void

finalize_experimental_technique_records(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::finalize_experimental_technique_records() –> void

finalize_keyword_records(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::finalize_keyword_records() –> void

finalize_parse(self: pyrosetta.rosetta.core.io.HeaderInformation) → None

C++: core::io::HeaderInformation::finalize_parse() –> void

idCode(self: pyrosetta.rosetta.core.io.HeaderInformation) → str

C++: core::io::HeaderInformation::idCode() const –> std::string

is_experimental_technique(self: pyrosetta.rosetta.core.io.HeaderInformation, technique: pyrosetta.rosetta.core.io.ExperimentalTechnique) → bool

C++: core::io::HeaderInformation::is_experimental_technique(enum core::io::HeaderInformation::ExperimentalTechnique) const –> bool

keyword_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) → bool

C++: core::io::HeaderInformation::keyword_in_progress() const –> bool

keywords(self: pyrosetta.rosetta.core.io.HeaderInformation) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: core::io::HeaderInformation::keywords() const –> const class std::list<std::string, class std::allocator<std::string > > &

parse_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) → bool

C++: core::io::HeaderInformation::parse_in_progress() const –> bool

store_classification(self: pyrosetta.rosetta.core.io.HeaderInformation, classification: str) → None

C++: core::io::HeaderInformation::store_classification(const class std::basic_string<char> &) –> void

store_compound(*args, **kwargs)

Overloaded function.

  1. store_compound(self: pyrosetta.rosetta.core.io.HeaderInformation, compound: str) -> None

C++: core::io::HeaderInformation::store_compound(const class std::basic_string<char> &) –> void

  1. store_compound(self: pyrosetta.rosetta.core.io.HeaderInformation, token: pyrosetta.rosetta.core.io.CompoundToken, value: str) -> None

C++: core::io::HeaderInformation::store_compound(enum core::io::HeaderInformation::CompoundToken, const class std::basic_string<char> &) –> void

store_deposition_date(*args, **kwargs)

Overloaded function.

  1. store_deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation, deposition_date: str) -> None

Store the deposition date using the format like “84-DEC-18”

C++: core::io::HeaderInformation::store_deposition_date(const class std::basic_string<char> &) –> void

  1. store_deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation, yy: int, mm: int, dd: int) -> None
Store the deposition date using the format of two digit numbers
for the year, month and day of the month.

C++: core::io::HeaderInformation::store_deposition_date(unsigned long, unsigned long, unsigned long) –> void

store_experimental_technique(self: pyrosetta.rosetta.core.io.HeaderInformation, technique: pyrosetta.rosetta.core.io.ExperimentalTechnique) → None

C++: core::io::HeaderInformation::store_experimental_technique(enum core::io::HeaderInformation::ExperimentalTechnique) –> void

store_experimental_techniques(self: pyrosetta.rosetta.core.io.HeaderInformation, exp: str) → None
the list of techniques string following the technqiue
field in the EXPDTA record of the pdb format and store the techniques

C++: core::io::HeaderInformation::store_experimental_techniques(const class std::basic_string<char> &) –> void

store_idCode(self: pyrosetta.rosetta.core.io.HeaderInformation, id_code: str) → None

C++: core::io::HeaderInformation::store_idCode(const class std::basic_string<char> &) –> void

store_keywords(self: pyrosetta.rosetta.core.io.HeaderInformation, keywords: str) → None

C++: core::io::HeaderInformation::store_keywords(const class std::basic_string<char> &) –> void

store_title(self: pyrosetta.rosetta.core.io.HeaderInformation, title: str) → None

Append title record onto current title string

C++: core::io::HeaderInformation::store_title(const class std::basic_string<char> &) –> void

string_to_compound_token(token: str) → pyrosetta.rosetta.core.io.CompoundToken

C++: core::io::HeaderInformation::string_to_compound_token(const class std::basic_string<char> &) –> enum core::io::HeaderInformation::CompoundToken

string_to_experimental_technique(technique: str) → pyrosetta.rosetta.core.io.ExperimentalTechnique

C++: core::io::HeaderInformation::string_to_experimental_technique(const class std::basic_string<char> &) –> enum core::io::HeaderInformation::ExperimentalTechnique

title(self: pyrosetta.rosetta.core.io.HeaderInformation) → str

C++: core::io::HeaderInformation::title() const –> const std::string &

class pyrosetta.rosetta.core.io.LinkInformation

Bases: pybind11_builtins.pybind11_object

Labonte <JWLabonte.edu>

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.LinkInformation, arg0: pyrosetta.rosetta.core.io.LinkInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.LinkInformation) -> 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__(self: pyrosetta.rosetta.core.io.LinkInformation) → str
__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.core.io.LinkInformation, : pyrosetta.rosetta.core.io.LinkInformation) → pyrosetta.rosetta.core.io.LinkInformation

C++: core::io::LinkInformation::operator=(const struct core::io::LinkInformation &) –> struct core::io::LinkInformation &

class pyrosetta.rosetta.core.io.ModifiedResidueInformation

Bases: pybind11_builtins.pybind11_object

Labonte <JWLabonte.edu>

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.ModifiedResidueInformation, arg0: pyrosetta.rosetta.core.io.ModifiedResidueInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.ModifiedResidueInformation) -> 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.core.io.ModifiedResidueInformation, : pyrosetta.rosetta.core.io.ModifiedResidueInformation) → pyrosetta.rosetta.core.io.ModifiedResidueInformation

C++: core::io::ModifiedResidueInformation::operator=(const struct core::io::ModifiedResidueInformation &) –> struct core::io::ModifiedResidueInformation &

class pyrosetta.rosetta.core.io.NomenclatureManager

Bases: pyrosetta.rosetta.utility.SingletonBase_core_io_NomenclatureManager_t

This class is a singleton and manages AltCodeMap data that should only be read from the database one time and shared among all processes constructing Poses.

__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).

annotated_sequence_from_IUPAC_sequence(seq: str) → str

C++: core::io::NomenclatureManager::annotated_sequence_from_IUPAC_sequence(const class std::basic_string<char> &) –> std::string

annotated_sequence_from_modomics_oneletter_sequence(seq: str) → str

C++: core::io::NomenclatureManager::annotated_sequence_from_modomics_oneletter_sequence(const class std::basic_string<char> &) –> std::string

decide_is_d_aa(name3: str) → bool

C++: core::io::NomenclatureManager::decide_is_d_aa(const class std::basic_string<char> &) –> bool

decide_is_known_achiral(name3: str) → bool

C++: core::io::NomenclatureManager::decide_is_known_achiral(const class std::basic_string<char> &) –> bool

decide_is_l_aa(name3: str) → bool

C++: core::io::NomenclatureManager::decide_is_l_aa(const class std::basic_string<char> &) –> bool

get_instance() → core::io::NomenclatureManager

C++: utility::SingletonBase<core::io::NomenclatureManager>::get_instance() –> class core::io::NomenclatureManager *

is_NA(name3: str) → bool

C++: core::io::NomenclatureManager::is_NA(const class std::basic_string<char> &) –> bool

is_metal(name3: str) → bool

C++: core::io::NomenclatureManager::is_metal(const class std::basic_string<char> &) –> bool

is_old_DNA(name3: str) → bool

C++: core::io::NomenclatureManager::is_old_DNA(const class std::basic_string<char> &) –> bool

is_old_RNA(name3: str) → bool

C++: core::io::NomenclatureManager::is_old_RNA(const class std::basic_string<char> &) –> bool

is_sugar(name3: str) → bool

C++: core::io::NomenclatureManager::is_sugar(const class std::basic_string<char> &) –> bool

pdb_code_from_rosetta_name(self: pyrosetta.rosetta.core.io.NomenclatureManager, rosetta_name: str) → str

C++: core::io::NomenclatureManager::pdb_code_from_rosetta_name(const class std::basic_string<char> &) –> std::string

rosetta_names_from_pdb_code(pdb_code: str) → Tuple[str, str]
Return a pair of Rosetta names (3-letter code and base ResidueType name, if available) from the
given PDB 3-letter code.

C++: core::io::NomenclatureManager::rosetta_names_from_pdb_code(const class std::basic_string<char> &) –> struct std::pair<std::string, std::string >

class pyrosetta.rosetta.core.io.ResidueInformation

Bases: pybind11_builtins.pybind11_object

Subset of data from “ATOM” lines that is shared by all atoms in a residue. This class is used for temporary storage of information during Pose building and “unbuilding”.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.io.ResidueInformation, that: pyrosetta.rosetta.core.io.ResidueInformation) → bool

C++: core::io::ResidueInformation::operator==(const class core::io::ResidueInformation &) const –> bool

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.ResidueInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.ResidueInformation, ai: pyrosetta.rosetta.core.io.AtomInformation) -> None
  3. __init__(self: pyrosetta.rosetta.core.io.ResidueInformation, arg0: pyrosetta.rosetta.core.io.ResidueInformation) -> 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__(self: pyrosetta.rosetta.core.io.ResidueInformation, that: pyrosetta.rosetta.core.io.ResidueInformation) → bool

C++: core::io::ResidueInformation::operator!=(const class core::io::ResidueInformation &) const –> bool

__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).

append_atom(self: pyrosetta.rosetta.core.io.ResidueInformation, atoms: pyrosetta.rosetta.core.io.AtomInformation) → None

C++: core::io::ResidueInformation::append_atom(const struct core::io::AtomInformation &) –> void

append_atoms(self: pyrosetta.rosetta.core.io.ResidueInformation, source: pyrosetta.rosetta.core.io.ResidueInformation) → None

C++: core::io::ResidueInformation::append_atoms(const class core::io::ResidueInformation &) –> void

assign(self: pyrosetta.rosetta.core.io.ResidueInformation, : pyrosetta.rosetta.core.io.ResidueInformation) → pyrosetta.rosetta.core.io.ResidueInformation

C++: core::io::ResidueInformation::operator=(const class core::io::ResidueInformation &) –> class core::io::ResidueInformation &

atoms(self: pyrosetta.rosetta.core.io.ResidueInformation) → pyrosetta.rosetta.utility.vector1_core_io_AtomInformation

C++: core::io::ResidueInformation::atoms() const –> const class utility::vector1<struct core::io::AtomInformation, class std::allocator<struct core::io::AtomInformation> > &

chainID(*args, **kwargs)

Overloaded function.

  1. chainID(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::chainID() const –> char

  1. chainID(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::chainID(char) –> void

iCode(*args, **kwargs)

Overloaded function.

  1. iCode(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::iCode() const –> char

  1. iCode(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::iCode(char) –> void

rename_atom(self: pyrosetta.rosetta.core.io.ResidueInformation, orig_name: str, new_name: str) → None

C++: core::io::ResidueInformation::rename_atom(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

resName(*args, **kwargs)

Overloaded function.

  1. resName(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::resName() const –> const std::string &

  1. resName(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::resName(const class std::basic_string<char> &) –> void

resSeq(*args, **kwargs)

Overloaded function.

  1. resSeq(self: pyrosetta.rosetta.core.io.ResidueInformation) -> int

C++: core::io::ResidueInformation::resSeq() const –> int

  1. resSeq(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: int) -> None

C++: core::io::ResidueInformation::resSeq(int) –> void

resid(self: pyrosetta.rosetta.core.io.ResidueInformation) → str

Returns a short, printable designation for this residue.

C++: core::io::ResidueInformation::resid() const –> std::string

rosetta_resName(self: pyrosetta.rosetta.core.io.ResidueInformation) → str

C++: core::io::ResidueInformation::rosetta_resName() const –> const std::string &

segmentID(*args, **kwargs)

Overloaded function.

  1. segmentID(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::segmentID() const –> const std::string &

  1. segmentID(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::segmentID(const class std::basic_string<char> &) –> void

set_temp(self: pyrosetta.rosetta.core.io.ResidueInformation, atomname: str, val: float) → None

C++: core::io::ResidueInformation::set_temp(const class std::basic_string<char> &, const double &) –> void

set_xyz(self: pyrosetta.rosetta.core.io.ResidueInformation, atomname: str, vect: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: core::io::ResidueInformation::set_xyz(const class std::basic_string<char> &, const class numeric::xyzVector<double> &) –> void

temps(self: pyrosetta.rosetta.core.io.ResidueInformation) → pyrosetta.rosetta.std.map_std_string_double

C++: core::io::ResidueInformation::temps() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

terCount(*args, **kwargs)

Overloaded function.

  1. terCount(self: pyrosetta.rosetta.core.io.ResidueInformation) -> int

C++: core::io::ResidueInformation::terCount() const –> int

  1. terCount(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: int) -> None

C++: core::io::ResidueInformation::terCount(int) –> void

xyz(self: pyrosetta.rosetta.core.io.ResidueInformation) → pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t

A convenience accessor for the coordinates.

C++: core::io::ResidueInformation::xyz() const –> const class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > &

class pyrosetta.rosetta.core.io.SHEETInformation

Bases: pybind11_builtins.pybind11_object

Steven Lewis smlewi.com

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.SHEETInformation, arg0: pyrosetta.rosetta.core.io.SHEETInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.SHEETInformation) -> 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.core.io.SHEETInformation, : pyrosetta.rosetta.core.io.SHEETInformation) → pyrosetta.rosetta.core.io.SHEETInformation

C++: core::io::SHEETInformation::operator=(const struct core::io::SHEETInformation &) –> struct core::io::SHEETInformation &

class pyrosetta.rosetta.core.io.SSBondInformation

Bases: pybind11_builtins.pybind11_object

Watkins

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.SSBondInformation, arg0: pyrosetta.rosetta.core.io.SSBondInformation) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.SSBondInformation) -> 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.core.io.SSBondInformation, : pyrosetta.rosetta.core.io.SSBondInformation) → pyrosetta.rosetta.core.io.SSBondInformation

C++: core::io::SSBondInformation::operator=(const struct core::io::SSBondInformation &) –> struct core::io::SSBondInformation &

class pyrosetta.rosetta.core.io.StructFileRep

Bases: pybind11_builtins.pybind11_object

This class is designed to store information about a structure in a “non-Rosetta” way, such that it can serve as an intermediary between various file formats and a Pose.

This class is intended to be light, consisting primarily of simple accessors.

HELIXInformations(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation

C++: core::io::StructFileRep::HELIXInformations() –> class utility::vector1<struct core::io::HELIXInformation, class std::allocator<struct core::io::HELIXInformation> > &

SHEETInformations(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation

C++: core::io::StructFileRep::SHEETInformations() –> class utility::vector1<struct core::io::SHEETInformation, class std::allocator<struct core::io::SHEETInformation> > &

__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.

  1. __init__(self: pyrosetta.rosetta.core.io.StructFileRep) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.StructFileRep, arg0: pyrosetta.rosetta.core.io.StructFileRep) -> 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__(self: pyrosetta.rosetta.core.io.StructFileRep) → str
__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).

additional_string_output(self: pyrosetta.rosetta.core.io.StructFileRep) → str

C++: core::io::StructFileRep::additional_string_output() –> std::string &

append_to_additional_string_output(self: pyrosetta.rosetta.core.io.StructFileRep, input_string: str) → None

Append more string data to the additional_string_output_ string in the SFR.

C++: core::io::StructFileRep::append_to_additional_string_output(const class std::basic_string<char> &) –> void

assign(self: pyrosetta.rosetta.core.io.StructFileRep, : pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.core.io.StructFileRep

C++: core::io::StructFileRep::operator=(const class core::io::StructFileRep &) –> class core::io::StructFileRep &

chain_sequences(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t

C++: core::io::StructFileRep::chain_sequences() –> class std::map<char, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<char>, class std::allocator<struct std::pair<const char, class utility::vector1<std::string, class std::allocator<std::string > > > > > &

chains(self: pyrosetta.rosetta.core.io.StructFileRep) → utility::vector0<utility::vector0<core::io::AtomInformation, std::allocator<core::io::AtomInformation> >, std::allocator<utility::vector0<core::io::AtomInformation, std::allocator<core::io::AtomInformation> > > >

C++: core::io::StructFileRep::chains() –> class utility::vector0<utility::vector0<core::io::AtomInformation> > &

cispep_map(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_core_io_CisPeptideInformation

C++: core::io::StructFileRep::cispep_map() –> class std::map<std::string, struct core::io::CisPeptideInformation, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::CisPeptideInformation> > > &

clone(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.core.io.StructFileRep

Create a copy and return an owning pointer to the copy.

C++: core::io::StructFileRep::clone() const –> class std::shared_ptr<class core::io::StructFileRep>

crystinfo(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.core.io.CrystInfo

C++: core::io::StructFileRep::crystinfo() –> class core::io::CrystInfo &

filename(self: pyrosetta.rosetta.core.io.StructFileRep) → str

C++: core::io::StructFileRep::filename() –> std::string &

foldtree_string(self: pyrosetta.rosetta.core.io.StructFileRep) → str

C++: core::io::StructFileRep::foldtree_string() –> std::string &

header(self: pyrosetta.rosetta.core.io.StructFileRep) → core::io::HeaderInformation

C++: core::io::StructFileRep::header() –> class std::shared_ptr<class core::io::HeaderInformation> &

heterogen_formulae(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::heterogen_formulae() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

heterogen_names(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::heterogen_names() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

heterogen_synonyms(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t

C++: core::io::StructFileRep::heterogen_synonyms() –> class std::map<std::string, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<std::string, class std::allocator<std::string > > > > > &

C++: core::io::StructFileRep::link_map() –> class std::map<std::string, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> > > > > &

modeltag(self: pyrosetta.rosetta.core.io.StructFileRep) → str

C++: core::io::StructFileRep::modeltag() –> std::string &

modres_map(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_core_io_ModifiedResidueInformation

C++: core::io::StructFileRep::modres_map() –> class std::map<std::string, struct core::io::ModifiedResidueInformation, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::ModifiedResidueInformation> > > &

pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::pdb_comments() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

pose_cache_float_data(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_float

C++: core::io::StructFileRep::pose_cache_float_data() –> class std::map<std::string, float, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, float> > > &

pose_cache_string_data(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::pose_cache_string_data() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

remarks(self: pyrosetta.rosetta.core.io.StructFileRep) → core::io::Remarks

C++: core::io::StructFileRep::remarks() –> class std::shared_ptr<class core::io::Remarks> &

residue_type_base_names(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_std_pair_std_string_std_string_t

C++: core::io::StructFileRep::residue_type_base_names() –> class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > > &

score_table_filename(self: pyrosetta.rosetta.core.io.StructFileRep) → str

C++: core::io::StructFileRep::score_table_filename() –> std::string &

score_table_labels(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::StructFileRep::score_table_labels() –> class utility::vector1<std::string, class std::allocator<std::string > > &

score_table_lines(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.utility.vector1_std_vector_std_string_std_allocator_std_string_t

C++: core::io::StructFileRep::score_table_lines() –> class utility::vector1<class std::vector<std::string, class std::allocator<std::string > >, class std::allocator<class std::vector<std::string, class std::allocator<std::string > > > > &

score_table_weights(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.utility.vector1_double

C++: core::io::StructFileRep::score_table_weights() –> class utility::vector1<double, class std::allocator<double> > &

ssbond_map(self: pyrosetta.rosetta.core.io.StructFileRep) → pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t

C++: core::io::StructFileRep::ssbond_map() –> class std::map<std::string, class utility::vector1<struct core::io::SSBondInformation, class std::allocator<struct core::io::SSBondInformation> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<struct core::io::SSBondInformation, class std::allocator<struct core::io::SSBondInformation> > > > > &

C++: core::io::explicit_links_from_sfr_linkage(const class std::map<class std::basic_string<char>, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> >, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> > > > > &, const class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &) –> class std::map<std::string, class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > > > > >

pyrosetta.rosetta.core.io.fix_glycan_order(rinfos: pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation, glycan_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions, known_links: pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t) → pyrosetta.rosetta.utility.vector1_unsigned_long

Reorganize the given glycan residues such that they’re in tree order

Not 100% great, as it won’t move any non-glycan residue, which may result in a funky order if there are non-glycans interspersed with the glycan residues Return the positions (in the rinfos) of the known (non-reducing) ends of the glycan chains

C++: core::io::fix_glycan_order(class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::io::StructFileRepOptions &, class std::map<class std::basic_string<char>, class std::map<class std::basic_string<char>, struct std::pair<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>, struct std::pair<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>, struct std::pair<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>, struct std::pair<class std::basic_string<char>, class std::basic_string<char> > > > > > > >) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

Is the LinkInformation in the given vector?

C++: core::io::link_in_vector(const class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> > &, const struct core::io::LinkInformation &) –> bool

pyrosetta.rosetta.core.io.pose_data_cache_from_sfr(*args, **kwargs)

Overloaded function.

  1. pose_data_cache_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> str

Extract the pose data cache from the SFR as a string representation for PDB output.

C++: core::io::pose_data_cache_from_sfr(const class core::io::StructFileRep &) –> std::string

  1. pose_data_cache_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, out: pyrosetta.rosetta.std.stringstream) -> None

Extract the pose data cache from the SFR as a string representation for PDB output.

C++: core::io::pose_data_cache_from_sfr(const class core::io::StructFileRep &, class std::basic_stringstream<char> &) –> void

pyrosetta.rosetta.core.io.pose_energies_from_sfr(*args, **kwargs)

Overloaded function.

  1. pose_energies_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> str

Extract the pose energies table from an SFR as a string representation for PDB output.

C++: core::io::pose_energies_from_sfr(const class core::io::StructFileRep &) –> std::string

  1. pose_energies_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, out: pyrosetta.rosetta.std.stringstream) -> None

Extract the pose energies table from an SFR as a string representation for PDB output.

C++: core::io::pose_energies_from_sfr(const class core::io::StructFileRep &, class std::basic_stringstream<char> &) –> void

pyrosetta.rosetta.core.io.pose_from_pose(*args, **kwargs)

Overloaded function.

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::io::StructFileRepOptions &) –> void

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::io::StructFileRepOptions &) –> void

pyrosetta.rosetta.core.io.read_alternative_3_letter_codes_from_database_file(filename: str) → pyrosetta.rosetta.std.map_std_string_std_tuple_std_string_std_string_utility_vector1_std_string_std_allocator_std_string_t
Return a mapping of alternative PDB 3-letter codes to a paired set including the Rosetta 3-letter code and,
optionally, any HETNAM information for the residue desired.

C++: core::io::read_alternative_3_letter_codes_from_database_file(const class std::basic_string<char> &) –> class std::map<std::string, class std::tuple<std::string, std::string, class utility::vector1<std::string, class std::allocator<std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::tuple<std::string, std::string, class utility::vector1<std::string, class std::allocator<std::string > > > > > >

pyrosetta.rosetta.core.io.reorder_glycan_residues(rinfos: pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation, correct_order: pyrosetta.rosetta.utility.vector1_unsigned_long, glycan_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None
Bring glycans into the correct order, which corresponds to connectivity of each glycan tree
This requires reordering rinfos and rosetta_residue_name3s.

C++: core::io::reorder_glycan_residues(class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

Do these link information correspond to the same connection (ignoring order)

C++: core::io::same_link(const struct core::io::LinkInformation &, const struct core::io::LinkInformation &) –> bool