pose_to_sfr

Bindings for core::io::pose_to_sfr namespace

class pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter

Bases: pybind11_builtins.pybind11_object

A class to convert a pose to a StructFileRep.

The StructFileRep is a data structure that serves as an intermediate between Protein Databank file formats (PDB and mmCIF) and Rosetta objects (poses). This was implemented at the 2016 Chemical XRW (eXtreme Rosetta Workshop), at which this class was popularly referred to as the “pose unbuilder”.

__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.pose_to_sfr.PoseToStructFileRepConverter) -> None
  2. __init__(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, options_in: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None
  3. __init__(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, arg0: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) -> 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).

append_residue_to_sfr(*args, **kwargs)

Overloaded function.

  1. append_residue_to_sfr(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) -> None

Append pdb information to StructFileRep for a single residue.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(const class core::pose::Pose &, const unsigned long) –> void

  1. append_residue_to_sfr(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, new_atom_num: int, new_tercount: int) -> None

Start atom numbering from given n. Increments N

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(const class core::pose::Pose &, const unsigned long, unsigned long &, const unsigned long) –> void

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

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

get_connectivity_annotation_info(*args, **kwargs)

Overloaded function.

  1. get_connectivity_annotation_info(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose) -> None
  2. get_connectivity_annotation_info(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, fresh_pdb_info: pyrosetta.rosetta.core.pose.PDBInfo) -> None
Get connectivity annotation information from the Pose object and create LinkInformation and
SSBondInformation data as appropriate.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(const class core::pose::Pose &, const class std::shared_ptr<class core::pose::PDBInfo> &) –> void

Overloaded function.

  1. get_link_record(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, ii: int, conn: int) -> pyrosetta.rosetta.core.io.LinkInformation
  2. get_link_record(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, ii: int, conn: int, fresh_pdb_info: pyrosetta.rosetta.core.pose.PDBInfo) -> pyrosetta.rosetta.core.io.LinkInformation

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(const class core::pose::Pose &, unsigned long, unsigned long, const class std::shared_ptr<class core::pose::PDBInfo> &) –> struct core::io::LinkInformation

get_parametric_info(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, remarks: pyrosetta.rosetta.core.io.Remarks, pose: pyrosetta.rosetta.core.pose.Pose) → None

Get parametric information from the Pose object and add it to the PDB remarks.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(class std::shared_ptr<class core::io::Remarks>, const class core::pose::Pose &) –> void

get_ssbond_record(*args, **kwargs)

Overloaded function.

  1. get_ssbond_record(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, ii: int, conn: int) -> pyrosetta.rosetta.core.io.SSBondInformation
  2. get_ssbond_record(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, ii: int, conn: int, fresh_pdb_info: pyrosetta.rosetta.core.pose.PDBInfo) -> pyrosetta.rosetta.core.io.SSBondInformation

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(const class core::pose::Pose &, unsigned long, unsigned long, const class std::shared_ptr<class core::pose::PDBInfo> &) –> struct core::io::SSBondInformation

grab_additional_pose_data(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose) → None

Get additional pose data.

This is rewritten from the old core/io/pdb/file_data.cc:write_additional_pdb_data() function. This was a catch-all for dumping out all sorts of protocol-specific stuff (e.g. membrane info).

Vikram K. Mulligan (vmullig.edu)

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_additional_pose_data(const class core::pose::Pose &) –> void

grab_pose_cache_data(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose) → None
Grab all the data that is in pose datacache as string/value pairs
Arbitrary Float data Arbitrary String data

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_cache_data(const class core::pose::Pose &) –> void

grab_pose_energies_table(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose) → None

Grab all the data that makes the pose energies table

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(const class core::pose::Pose &) –> void

init_from_pose(*args, **kwargs)

Overloaded function.

  1. init_from_pose(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Fill StructFileRep object using information from given Pose object.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(const class core::pose::Pose &) –> void

  1. init_from_pose(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Fill StructFileRep object using information from given Pose object and a set of options.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(const class core::pose::Pose &, const class core::io::StructFileRepOptions &) –> void

  1. init_from_pose(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
Fill StructFileRep object using information from given Pose object,
for a specified subset of residues

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

  1. init_from_pose(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None
Fill StructFileRep object using information from given Pose object,
for a specified subset of residues and atoms

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(const class core::pose::Pose &, const class core::id::AtomID_Map<bool> &) –> void

  1. init_from_pose(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None
Fill StructFileRep object using information from given Pose object,
for a specified subset of residues and atoms

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(const class core::pose::Pose &, const class core::id::AtomID_Map<bool> &, const class core::io::StructFileRepOptions &) –> void

new_sfr(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) → pyrosetta.rosetta.core.io.StructFileRep
Resets the PoseToStructFileRepConverter object, and reinitializes
it with a fresh StruftFileRep object, returning an owning pointer to the new object.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::new_sfr() –> class std::shared_ptr<class core::io::StructFileRep>

sfr(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) → pyrosetta.rosetta.core.io.StructFileRep

Non-const access to the StructFileRep object.

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr() –> class std::shared_ptr<class core::io::StructFileRep>

pyrosetta.rosetta.core.io.pose_to_sfr.restrict_prec(inval: float) → str

C++: core::io::pose_to_sfr::restrict_prec(double) –> std::string