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- builtins.object
-
- PoseToStructFileRepConverter
class PoseToStructFileRepConverter(builtins.object) |
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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". |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) -> NoneType
2. __init__(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, options_in : rosetta.core.io.StructFileRepOptions) -> NoneType
3. __init__(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- append_residue_to_sfr(...) from builtins.PyCapsule
- append_residue_to_sfr(*args, **kwargs)
Overloaded function.
1. append_residue_to_sfr(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, resnum : int) -> NoneType
Append pdb information to StructFileRep for a single residue.
2. append_residue_to_sfr(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, resnum : int, new_atom_num : int, new_tercount : int) -> NoneType
Start atom numbering from given n. Increments N
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) -> rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter
- get_connectivity_annotation_info(...) from builtins.PyCapsule
- get_connectivity_annotation_info(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose) -> NoneType
Get connectivity annotation information from the Pose object and create LinkInformation and
SSBondInformation data as appropriate.
- get_link_record(...) from builtins.PyCapsule
- get_link_record(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, ii : int, conn : int) -> rosetta.core.io.LinkInformation
- get_parametric_info(...) from builtins.PyCapsule
- get_parametric_info(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, remarks : rosetta.core.io.Remarks, pose : rosetta.core.pose.Pose) -> NoneType
Get parametric information from the Pose object and add it to the PDB remarks.
- get_ssbond_record(...) from builtins.PyCapsule
- get_ssbond_record(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, ii : int, conn : int) -> rosetta.core.io.SSBondInformation
- grab_additional_pose_data(...) from builtins.PyCapsule
- grab_additional_pose_data(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose) -> NoneType
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)
- init_from_pose(...) from builtins.PyCapsule
- init_from_pose(*args, **kwargs)
Overloaded function.
1. init_from_pose(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose) -> NoneType
Fill StructFileRep object using information from given Pose object.
2. init_from_pose(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, options : rosetta.core.io.StructFileRepOptions) -> NoneType
Fill StructFileRep object using information from given Pose object and a set of options.
3. init_from_pose(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, residue_indices : rosetta.utility.vector1_unsigned_long) -> NoneType
Fill StructFileRep object using information from given Pose object,
for a specified subset of residues
4. init_from_pose(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, mask : rosetta.core.id.AtomID_Map_bool_t) -> NoneType
Fill StructFileRep object using information from given Pose object,
for a specified subset of residues and atoms
5. init_from_pose(self : rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter, pose : rosetta.core.pose.Pose, mask : rosetta.core.id.AtomID_Map_bool_t, options : rosetta.core.io.StructFileRepOptions) -> NoneType
Fill StructFileRep object using information from given Pose object,
for a specified subset of residues and atoms
- new_sfr(...) from builtins.PyCapsule
- new_sfr(rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) -> rosetta.core.io.StructFileRep
Resets the PoseToStructFileRepConverter object, and reinitializes
it with a fresh StruftFileRep object, returning an owning pointer to the
new object.
- sfr(...) from builtins.PyCapsule
- sfr(rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter) -> rosetta.core.io.StructFileRep
Non-const access to the StructFileRep object.
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