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”.

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, new_chainIDs: pyrosetta.rosetta.utility.vector1_char) -> None

  2. get_connectivity_annotation_info(self: pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose: pyrosetta.rosetta.core.pose.Pose, new_chainIDs: pyrosetta.rosetta.utility.vector1_char, 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 utility::vector1<char, class std::allocator<char> > &, 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, new_chainIDs: pyrosetta.rosetta.utility.vector1_char) -> 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, new_chainIDs: pyrosetta.rosetta.utility.vector1_char, 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 utility::vector1<char, class std::allocator<char> > &, 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

Simple Metric 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

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

Grab RAW simple_metric data for SM IO

C++: core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_simple_metric_data(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