pdb

Bindings for core::io::pdb namespace

class pyrosetta.rosetta.core.io.pdb.RecordCollection

Bases: pyrosetta.rosetta.utility.SingletonBase_core_io_pdb_RecordCollection_t

This class is a singleton and manages the definitions of PDB Records, which should only be read from the database one time.

__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() → core::io::pdb::RecordCollection

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

is_valid_record_type(type: str) → bool

Is the given string a valid 6-letter PDB record type?

C++: core::io::pdb::RecordCollection::is_valid_record_type(const class std::basic_string<char> &) –> bool

class pyrosetta.rosetta.core.io.pdb.RecordType

Bases: pybind11_builtins.pybind11_object

Enumerators for all of the record types used in PDB files, according to: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

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

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

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

Return self>value.

__hash__(self: pyrosetta.rosetta.core.io.pdb.RecordType) → int
__init__(self: pyrosetta.rosetta.core.io.pdb.RecordType, 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.pdb.RecordType) → int
__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

  1. __ne__(self: pyrosetta.rosetta.core.io.pdb.RecordType, arg0: pyrosetta.rosetta.core.io.pdb.RecordType) -> bool
  2. __ne__(self: pyrosetta.rosetta.core.io.pdb.RecordType, 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.pdb.RecordType) → str
__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.io.pdb.RecordType, 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).

pyrosetta.rosetta.core.io.pdb.build_pose_from_pdb_as_is(*args, **kwargs)

Overloaded function.

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None
Builds a pose into <pose>, without repacking or optimizing
hydrogens; using the full-atom ResidueTypeSet

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class std::basic_string<char> &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None
Builds a pose into <pose>, without repacking or optimizing
hydrogens; using the full-atom ResidueTypeSet and a set of options.

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class std::basic_string<char> &, const class core::io::StructFileReaderOptions &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class std::basic_string<char> &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class std::basic_string<char> &, const class core::io::StructFileReaderOptions &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, file_contents: pyrosetta.rosetta.std.istream, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class std::basic_string<char> &, class std::basic_istream<char> &, const class core::io::StructFileReaderOptions &) –> void

pyrosetta.rosetta.core.io.pdb.create_pdb_contents_from_sfr(*args, **kwargs)

Overloaded function.

  1. create_pdb_contents_from_sfr(sfr: core::io::StructFileRep) -> str
  2. create_pdb_contents_from_sfr(sfr: core::io::StructFileRep, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

Create a full .pdb as a string given a StructFileRep object.

C++: core::io::pdb::create_pdb_contents_from_sfr(const class core::io::StructFileRep &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> std::string

pyrosetta.rosetta.core.io.pdb.create_sfr_from_pdb_file_contents(*args, **kwargs)

Overloaded function.

  1. create_sfr_from_pdb_file_contents(pdb_contents: str, options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from .pdb file contents with options.

C++: core::io::pdb::create_sfr_from_pdb_file_contents(const class std::basic_string<char> &, const class core::io::StructFileReaderOptions &) –> class core::io::StructFileRep

  1. create_sfr_from_pdb_file_contents(pdb_contents: str) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from .pdb file contents.

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

pyrosetta.rosetta.core.io.pdb.dump_pdb(*args, **kwargs)

Overloaded function.

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str) -> bool
Writes <pose> to a PDB file, returns false if an error occurs
Use default StructFileRepOptions

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const class std::basic_string<char> &) –> bool

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

Writes <pose> to a PDB file, returns false if an error occurs

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const class std::basic_string<char> &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> bool

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> None
Writes <pose> to a given stream in PDB file format
Use default StructFileRepOptions

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, class std::basic_ostream<char> &) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes <pose> to a given stream in PDB file format

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, class std::basic_ostream<char> &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None
  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

This version takes an AtomID mask.

Used by Will’s motif hash stuff, I think.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, class std::basic_ostream<char> &, const class core::id::AtomID_Map<bool> &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

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

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: utility::io::ozstream) -> None
  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: utility::io::ozstream, filename: str) -> None
Writes a pose to a given stream in PDB file format, optionally

appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It’s an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

The pose to turn into a PDB.

Additional data to append to the PDB file data (from the job).

The output stream that the PDB file data will be written to.

(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Vikram K. Mulligan (vmullig.edu).

Jared Adolf-Bryfogle (jadolfbr.com)

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const class std::basic_string<char> &, class utility::io::ozstream &, const class std::basic_string<char> &) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: str) -> None
  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: str, filename: str) -> None
Writes a pose to a given string in PDB file format, optionally

appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It’s an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

The pose to turn into a PDB.

Additional data to append to the PDB file data from the Job.

The output string that the PDB file data will be written to.

(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Vikram K. Mulligan (vmullig.edu).

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const class std::basic_string<char> &, class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.io.pdb.dump_pdb_residue(*args, **kwargs)

Overloaded function.

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue) -> str
  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str
  3. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.io.StructFileRepOptions, start_atom_number: int) -> str

PyRosetta-Compatible; Writes pdb data for the given residue, beginning from the given atom number

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, class std::shared_ptr<const class core::io::StructFileRepOptions>, unsigned long) –> std::string

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int) -> str
  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

PyRosetta-Compatible; Writes pdb data for the given residue, incrementing atom_number counter

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, unsigned long &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> std::string

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, out: pyrosetta.rosetta.std.ostream) -> None
  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes pdb data for the given residue, incrementing atom_number counter

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, unsigned long &, class std::basic_ostream<char> &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream) -> None
  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream, start_atom_number: int) -> None
  3. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream, start_atom_number: int, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes pdb data for the given residue, beginning from the given atom number

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, class std::basic_ostream<char> &, unsigned long, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.store_base_residue_type_name_in_sfr(hetID: str, text_field: str, sfr: pyrosetta.rosetta.core.io.StructFileRep) → None

Parse .pdb HETNAM text field to extract full resID and convert into SFR data.

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