Source code for

# -*- coding: utf-8 -*-
Base classes for structure data (:mod:``)

.. currentmodule::

from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'

from abc import ABCMeta, abstractmethod

from sknano.core import get_fpath
from sknano.core.atoms import StructureAtom as Atom, StructureAtoms as Atoms
from sknano.core.crystallography import StructureData
# from sknano.utils.analysis import StructureAnalyzer
from sknano.version import version

default_comment_line = \
    'Structure data generated using scikit-nano version {}'.format(version)
default_structure_format = 'xyz'
supported_structure_formats = ('xyz', 'data', 'dump')

__all__ = ['Atom', 'Atoms',

[docs]class StructureIO(StructureData): """Base class for structure data file input and output. Parameters ---------- fpath : {None, str}, optional """ def __init__(self, fpath=None, fname=None, **kwargs): super().__init__() self.comment_line = default_comment_line if fpath is None and fname is not None: fpath = fname self.fpath = fpath self.kwargs = kwargs @property def comment_line(self): """Comment line.""" return self._comment_line @comment_line.setter def comment_line(self, value): """Set the comment line string. Parameters ---------- value : str """ if not isinstance(value, str): raise TypeError('Expected a string.') self._comment_line = value @comment_line.deleter def comment_line(self): del self._comment_line def __deepcopy__(self, memo): from copy import deepcopy cp = self.__class__(None) memo[id(self)] = cp for attr in dir(self): if not attr.startswith('_'): setattr(cp, attr, deepcopy(getattr(self, attr), memo)) return cp
[docs]class StructureReader: """Structure data reader base class.""" @classmethod
[docs] def read(cls, fpath, structure_format=None, **kwargs): """Read structure data from file. Parameters ---------- fpath : str structure_format : {None, str} """ if (structure_format is None and fpath.endswith('.data')) or \ structure_format == 'data': from ._lammps_data_format import DATAReader return DATAReader(fpath, **kwargs) elif (structure_format is None and fpath.endswith('.dump')) or \ structure_format == 'dump': from ._lammps_dump_format import DUMPReader return DUMPReader(fpath, **kwargs) elif (structure_format is None and fpath.endswith('.xyz')) or \ structure_format == 'xyz': from ._xyz_format import XYZReader return else: raise StructureIOError("Unable to determine `structure_format`")
[docs]class StructureWriter: """Structure data writer base class.""" @classmethod
[docs] def write(cls, fname=None, structure_format=None, **kwargs): """Write structure data to file. Parameters ---------- fname : str, optional structure_format : {None, str}, optional """ if fname is None and structure_format is None: structure_format = default_structure_format if fname is None: fname = get_fpath(fname='structure_data', ext=structure_format, add_fnum=True) if (structure_format is None and fname.endswith('.data')) or \ structure_format == 'data': from ._lammps_data_format import DATAWriter DATAWriter.write(fname=fname, **kwargs) elif (structure_format is None and fname.endswith('.dump')) or \ structure_format == 'dump': from ._lammps_dump_format import DUMPWriter DUMPWriter.write(fname=fname, **kwargs) # elif (structure_format is None and fname.endswith('.xyz')) or \ # structure_format == 'xyz': else: from ._xyz_format import XYZWriter XYZWriter.write(fname=fname, **kwargs)
[docs]class StructureConverter(metaclass=ABCMeta): """Abstract base class for converting structure data. Parameters ---------- infile : str outfile : str """ def __init__(self, infile=None, outfile=None, **kwargs): self.infile = infile self.outfile = outfile self.kwargs = kwargs @abstractmethod
[docs] def convert(self): """Convert structure data from one format to another format.""" raise NotImplementedError('Subclasses of `StructureConverter` need ' 'to implement the `convert` method.')
[docs]class StructureFormatSpec: """Base class for defining a format specification. Parameters ---------- """ def __init__(self, **kwargs): pass
[docs]class StructureIOError(Exception): """Base class for `StructureIO` errors.""" pass