Source code for atomium.files.file

"""Contains the File class."""

from math import inf
from copy import deepcopy
from ..models import Model

[docs]class File: """When a file is parsed, the result is a ``File``. It contains the structure of interest, as well as meta information.""" def __init__(self): self._filetype = None self._code = None self._title = None self._deposition_date = None self._classification = None self._keywords = [] self._authors = [] self._technique = None self._source_organism = None self._expression_system = None self._resolution = None self._rvalue = None self._rfree = None self._assemblies = [] self._models = [] def __repr__(self): return "<{}{}File>".format( self._code if self._code else "", "." + self._filetype + " " if self._filetype else "", ) @property def filetype(self): """The filetype that this File was created from, such as .pdb or .cif. :rtype: ``str``""" return self._filetype @filetype.setter def filetype(self, filetype): self._filetype = filetype @property def code(self): """The unique database identifer for this structure. :rtype: ``str``""" return self._code @code.setter def code(self, code): self._code = code @property def title(self): """The structure's text description. :rtype: ``str``""" return self._title @title.setter def title(self, title): self._title = title @property def deposition_date(self): """The date the structure was submitted for publication. :rtype: ````""" return self._deposition_date @deposition_date.setter def deposition_date(self, deposition_date): self._deposition_date = deposition_date @property def classification(self): """The structure's formal classification. :rtype: ``str``""" return self._classification @classification.setter def classification(self, classification): self._classification = classification @property def keywords(self): """The structure's keyword descriptors. :rtype: ``list``""" return self._keywords @property def authors(self): """The structure's authors. :rtype: ``list``""" return self._authors @property def technique(self): """The structure's experimental technique. :rtype: ``str``""" return self._technique @technique.setter def technique(self, technique): self._technique = technique @property def source_organism(self): """The structure's original organism. :rtype: ``float``""" return self._source_organism @source_organism.setter def source_organism(self, source_organism): self._source_organism = source_organism @property def expression_system(self): """The organism the structure was expressed in. :rtype: ``float``""" return self._expression_system @expression_system.setter def expression_system(self, expression_system): self._expression_system = expression_system @property def resolution(self): """The structure's resolution. :rtype: ``float``""" return self._resolution @resolution.setter def resolution(self, resolution): self._resolution = resolution @property def rvalue(self): """The structure's R-value. :rtype: ``float``""" return self._rvalue @rvalue.setter def rvalue(self, rvalue): self._rvalue = rvalue @property def rfree(self): """The structure's R-free value. :rtype: ``float``""" return self._rfree @rfree.setter def rfree(self, rfree): self._rfree = rfree @property def assemblies(self): """The structure's assembly instructions. :rtype: ``list``""" return self._assemblies @property def models(self): """The structure's models. :rtype: ``list``""" return self._models @property def model(self): """The structure's primary :py:class:`.Model`. :rtype: ``Model``""" if self._models: return self._models[0]
[docs] def generate_assembly(self, id): """Creates a :py:class:`.Model` from the current model and the instructions contained in one of the Pdb's assemblies, which you specify. :param int id: The assembly to use to generate the assembly. :raises ValueError: if you give an ID which doesn't correspond to a\ assembly. :rtype: ``Model``""" model = self._models[0] for assembly in self._assemblies: if assembly["id"] == id: break else: raise ValueError("No assembly with ID {}".format(id)) new_chains = [] for transformation in assembly["transformations"]: chains = [model.chain(id_) for id_ in transformation["chains"]] chains = [c for c in chains if c is not None] for chain in chains: new_chain = chain.copy() new_chain.transform(transformation["matrix"]) new_chain.translate(transformation["vector"]) new_chains.append(new_chain) return Model(*new_chains)
@property def best_assembly(self): """Returns the 'best' biological assembly for this Pdb - the one with the lowest (most negative) delta energy. If there are no assemblies, ``None`` is returned. :rtype: ``Model``""" sorted_mol = sorted( self._assemblies, key=lambda b: inf if b["delta_energy"] is None else b["delta_energy"] ) if sorted_mol: return sorted_mol[0]
[docs] def generate_best_assembly(self): """Generates the 'best' biological assembly for this Pdb - the one with the lowest (most negative) delta energy. If there are no assemblies, the original model will be returned. :rtype: ``Model``""" best = self.best_assembly if best: return self.generate_assembly(best["id"]) else: return self._models[0]
[docs] def save(self, path): """Saves the File to the location specified. The file extension in the path given will be used to determine what file type to save as. Currently supported extensions are .pdb and .xyz (.cif coming soon). :param str path: The path to save to.""" filestring = "" if path.endswith(".xyz"): from .xyz import file_to_xyz_string filestring = file_to_xyz_string(self) elif path.endswith(".pdb"): from .pdb import file_to_pdb_string filestring = file_to_pdb_string(self) else: raise ValueError("{} has an unknown file extension".format(path)) with open(path, "w") as f: f.write(filestring)