raw_data

Bindings for core::io::raw_data namespace

class pyrosetta.rosetta.core.io.raw_data.DisulfideFile

Bases: pybind11_builtins.pybind11_object

Parses and stores a disulfide file.

Initiallizing a DisulfideFile is a lightweight operation. The heavy lifting occurs the first time disulfides() is called. This parses the file and caches the resulting pairs of residues. Subsequent calls to disulfides() are fast since they don’t reparse the file but merely reinterpret the results in terms of the specified.

The disulfide file format is pretty flexible. It looks for three kinds of lines:

  • ‘12 42’ Lines with two integers are interpreted as a disulfide bond, indexed by internal rosetta residue number, i.e. the 12th and 42nd residues from the start of the pose.

  • ‘12A 42A’ If a single character is appended to the numbers, DisulfideFile assumes that these refer to the pdb number and chain, i.e. the residues of chain A numbered 12 and 42 in the pdb.

  • ‘SSBOND 1 CYS A 12 CYS A 42’ The

    PDB format for disulfide bond annotations.

All lines not matching these criteria are silently ignored. This implies that whole pdb files can usually be used unaltered as disulfide files, since the SSBOND entries are extracted and all else is ignored.

Question from rhiju, 2014 – I don’t see handling of ‘12A’ or SSBOND cases in
DisulfideFile.cc – is someone going to check that in?
__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.raw_data.DisulfideFile, filename: str) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, arg0: pyrosetta.rosetta.core.io.raw_data.DisulfideFile) -> 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).

disulfides(*args, **kwargs)

Overloaded function.

  1. disulfides(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, disulfides: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None

Get a list of disulfide bonds declared in the file

C++: core::io::raw_data::DisulfideFile::disulfides(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> void

  1. disulfides(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, disulfides: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Get a list of disulfide bonds declared in the file
(renumbered to rosetta numbering if necessary)

C++: core::io::raw_data::DisulfideFile::disulfides(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class core::pose::Pose &) const –> void

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

Accessor for the filename

C++: core::io::raw_data::DisulfideFile::filename() const –> const std::string &

read_in_and_set_disulfides(self: pyrosetta.rosetta.core.io.raw_data.DisulfideFile, pose: pyrosetta.rosetta.core.pose.Pose) → None
Get a list of disulfide bonds declared in the file
(renumbered to rosetta numbering if necessary)

also manually set the disulfides in the conformation of the provided pose (this is a necessary workaround for dealing with multiple disulfide specification files in PyRosetta

C++: core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(class core::pose::Pose &) –> void

class pyrosetta.rosetta.core.io.raw_data.RawFileData

Bases: pybind11_builtins.pybind11_object

Abstract base class for classes that writes different types of silent-files that contain a mixture of Struct objects which are expected to be uniquely identified by some sort of string-based tag.

__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.raw_data.RawFileData) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, arg0: pyrosetta.rosetta.core.io.raw_data.RawFileData) -> 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.raw_data.RawFileData, : pyrosetta.rosetta.core.io.raw_data.RawFileData) → pyrosetta.rosetta.core.io.raw_data.RawFileData

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

begin(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the start of the members of this container.

C++: core::io::raw_data::RawFileData::begin() –> class core::io::raw_data::RawFileData::iterator

begin_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::begin_const() const –> class core::io::raw_data::RawFileData::const_iterator

clear_structure_map(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → None

Remove all of the RawStruct objects from this object.

C++: core::io::raw_data::RawFileData::clear_structure_map() –> void

end(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::iterator

Returns an iterator to the end of the members of this container.

C++: core::io::raw_data::RawFileData::end() –> class core::io::raw_data::RawFileData::iterator

end_const(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → core::io::raw_data::RawFileData::const_iterator

C++: core::io::raw_data::RawFileData::end_const() const –> class core::io::raw_data::RawFileData::const_iterator

nres(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int
Returns the number of residues in the first structure in this object. Not
guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::nres() const –> int

read_tags_fast(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str) → pyrosetta.rosetta.utility.vector1_std_string
quickly read a list of tags from a silent-input file. Only checks lines beginning
with SCORE: strings.

C++: core::io::raw_data::RawFileData::read_tags_fast(const class std::basic_string<char> &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

sequence(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → str
Returns the sequence of the first structure in this object. Not
guaranteed to be fixed for all structures in this container.

C++: core::io::raw_data::RawFileData::sequence() const –> std::string

size(self: pyrosetta.rosetta.core.io.raw_data.RawFileData) → int

Returns the number of structures contained in this container.

C++: core::io::raw_data::RawFileData::size() const –> int

write_all(self: pyrosetta.rosetta.core.io.raw_data.RawFileData, filename: str, score_map: pyrosetta.rosetta.std.map_std_string_double) → None

write all RawStruct objects in the structure_map_ to the given filename.

C++: core::io::raw_data::RawFileData::write_all(const class std::basic_string<char> &, const class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &) –> void

class pyrosetta.rosetta.core.io.raw_data.RawStruct

Bases: pybind11_builtins.pybind11_object

__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.raw_data.RawStruct, arg0: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> 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.raw_data.RawStruct, : pyrosetta.rosetta.core.io.raw_data.RawStruct) → pyrosetta.rosetta.core.io.raw_data.RawStruct

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

decoy_tag(*args, **kwargs)

Overloaded function.

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag() –> std::string

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, tag: str) -> None

sets the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag(class std::basic_string<char>) –> void

fill_pose(*args, **kwargs)

Overloaded function.

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Fill a Pose with the conformation information in this RawStruct and the FA_STANDARD
ResidueTypeSet. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::RawStruct::fill_pose(class core::pose::Pose &) –> void

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
Fill a Pose with the conformation information in this RawStruct and the ResidueTypeSet
provided by the caller. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::RawStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

get_debug_rmsd(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) → float
Do some sort of comparison between the actual RMSD of this silent-struct and
the cached coordinates. Used for RawStruct objects that are rebuild from torsions or other shortened representations of data.

C++: core::io::raw_data::RawStruct::get_debug_rmsd() –> double

nres(*args, **kwargs)

Overloaded function.

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> int

data access methods.

C++: core::io::raw_data::RawStruct::nres() –> unsigned long

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, nres: int) -> None

returns the number of residues in this RawStruct

C++: core::io::raw_data::RawStruct::nres(unsigned long) –> void

print_conformation(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::raw_data::RawStruct::print_conformation(class std::basic_ostream<char> &) const –> void

print_header(*args, **kwargs)

Overloaded function.

  1. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None
  2. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None
  3. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string, print_sequence: bool) -> None
print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines
SEQUENCE: <protein sequence>: <list of score-types>.

C++: core::io::raw_data::RawStruct::print_header(class std::basic_ostream<char> &, const class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &, const 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> > > > &, bool) const –> void

print_scores(*args, **kwargs)

Overloaded function.

  1. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None
  2. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

print out a SCORE line to the given ozstream.

C++: core::io::raw_data::RawStruct::print_scores(class std::basic_ostream<char> &, const class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &, const 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> > > > &) const –> void

sequence(*args, **kwargs)

Overloaded function.

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence() –> std::string

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, sequence: str) -> None

sets the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence(class std::basic_string<char>) –> void

class pyrosetta.rosetta.core.io.raw_data.ScoreStructText

Bases: pyrosetta.rosetta.core.io.raw_data.RawStruct

__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.raw_data.ScoreStructText) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, arg0: pyrosetta.rosetta.core.pose.Pose) -> None

doc

  1. __init__(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, : pyrosetta.rosetta.core.pose.Pose, tag: str) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, arg0: pyrosetta.rosetta.core.io.raw_data.ScoreStructText) -> 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.raw_data.ScoreStructText, : pyrosetta.rosetta.core.io.raw_data.ScoreStructText) → pyrosetta.rosetta.core.io.raw_data.ScoreStructText

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

decoy_tag(*args, **kwargs)

Overloaded function.

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag() –> std::string

  1. decoy_tag(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, tag: str) -> None

sets the tag associated with this RawStruct

C++: core::io::raw_data::RawStruct::decoy_tag(class std::basic_string<char>) –> void

fill_pose(*args, **kwargs)

Overloaded function.

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, : pyrosetta.rosetta.core.pose.Pose) -> None
Fill a Pose with the conformation information in this RawStruct and the FA_STANDARD
ResidueTypeSet. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::ScoreStructText::fill_pose(class core::pose::Pose &) –> void

  1. fill_pose(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, : pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
Fill a Pose with the conformation information in this RawStruct and the ResidueTypeSet
provided by the caller. This is a virtual method which must be implemented by classes derived from RawStruct.

C++: core::io::raw_data::ScoreStructText::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

get_debug_rmsd(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText) → float

C++: core::io::raw_data::ScoreStructText::get_debug_rmsd() –> double

nres(*args, **kwargs)

Overloaded function.

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> int

data access methods.

C++: core::io::raw_data::RawStruct::nres() –> unsigned long

  1. nres(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, nres: int) -> None

returns the number of residues in this RawStruct

C++: core::io::raw_data::RawStruct::nres(unsigned long) –> void

print_conformation(self: pyrosetta.rosetta.core.io.raw_data.ScoreStructText, out: pyrosetta.rosetta.std.ostream) → None

C++: core::io::raw_data::ScoreStructText::print_conformation(class std::basic_ostream<char> &) const –> void

print_header(*args, **kwargs)

Overloaded function.

  1. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None
  2. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None
  3. print_header(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string, print_sequence: bool) -> None
print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines
SEQUENCE: <protein sequence>: <list of score-types>.

C++: core::io::raw_data::RawStruct::print_header(class std::basic_ostream<char> &, const class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &, const 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> > > > &, bool) const –> void

print_scores(*args, **kwargs)

Overloaded function.

  1. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double) -> None
  2. print_scores(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, out: pyrosetta.rosetta.std.ostream, score_map: pyrosetta.rosetta.std.map_std_string_double, string_map: pyrosetta.rosetta.std.map_std_string_std_string) -> None

print out a SCORE line to the given ozstream.

C++: core::io::raw_data::RawStruct::print_scores(class std::basic_ostream<char> &, const class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &, const 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> > > > &) const –> void

sequence(*args, **kwargs)

Overloaded function.

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct) -> str

returns the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence() –> std::string

  1. sequence(self: pyrosetta.rosetta.core.io.raw_data.RawStruct, sequence: str) -> None

sets the sequence for this RawStruct

C++: core::io::raw_data::RawStruct::sequence(class std::basic_string<char>) –> void