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"""Classes to associate extra files with the system.
Typically, one or more :class:`Repository` objects are created and
added to :attr:`modelcif.System.repositories`."""
import posixpath
import warnings
class Repository:
"""An online location where associated files can be found.
These objects are typically added to
:attr:`modelcif.System.repositories`.
:param str url_root: URL root that prefixes each file's path.
For example, if url_root is ``https://example.com`` then
a :class:`File` with path ``test.txt`` can be found at
``https://example.com/test.txt``. If the files are not
available online, None can be used here.
:param list files: A list of :class:`File` objects.
"""
def __init__(self, url_root, files):
self.url_root = url_root
self.files = files
def get_url(self, f):
"""Get the full URL for the given :class:`File`"""
return posixpath.join(self.url_root or '', f.path)
class File:
"""A single associated file. These objects can be added to a
:class:`Repository` or a :class:`ZipFile`.
:param str path: File name.
:param str details: Any additional information about the file.
:param data: If available, the data (e.g. sequence, structure,
alignment) that are stored in the file.
:type data: :class:`~modelcif.data.Data`
"""
file_type = 'file'
file_content = 'other'
file_format = 'other'
def __init__(self, path, details=None, data=None):
self.path, self.details, self.data = path, details, data
class CIFFile(File):
"""An associated file in mmCIF or BinaryCIF format.
See :class:`File` for more details.
:param str path: File name that will be used to construct URLs in the
main mmCIF file (see :class:`Repository` or :class:`ZipFile`).
:param str details: Any additional information about the file.
:param data: If available, the data (e.g. sequence, structure,
alignment) that are stored in the file.
:type data: :class:`~modelcif.data.Data`
:param list categories: If given, any mmCIF category names in this list
are written out to ``local_path`` by
:func:`modelcif.dumper.write` instead of to the primary file
handle.
:param list copy_categories: If given, any mmCIF category names in this
list are written out to both ``local_path`` by
:func:`modelcif.dumper.write` and the primary file handle.
:param str entry_id: Unique identifier for the associated file,
if written (by specifying ``categories`` or ``copy_categories``).
:param str entry_details: A comment to be added to the associated file,
if written (by specifying ``categories`` or ``copy_categories``).
:param str local_path: File name that will be used for ``categories``
or ``copy_categories``. If not given, it defaults to the same
as ``path``. (The file is always written directly to the local
disk, even if this object is placed inside a :class:`ZipFile`.)
:param bool binary: If False (the default), any output file is written
in mmCIF format; if True, the file is written in BinaryCIF.
"""
_binary_ff_map = {True: 'bcif', False: 'cif'}
file_format = property(lambda self: self._binary_ff_map[self.binary],
doc="Format of the file (BinaryCIF or mmCIF)")
def __init__(self, path, details=None, categories=[], copy_categories=[],
entry_id='model', entry_details=None, local_path=None,
binary=False, data=None):
super(CIFFile, self).__init__(path, details, data)
self.categories = categories
self.copy_categories = copy_categories
self.id = entry_id
self.entry_details = entry_details
self.local_path = local_path or path
self.binary = binary
class QAMetricsFile(CIFFile):
"""An associated file in CIF format containing QA metrics.
See :class:`CIFFile` for more details.
"""
file_content = 'QA metrics'
# Map old class name to new equivalent
class LocalPairwiseQAScoresFile(QAMetricsFile):
def __init__(self, *args, **keys):
warnings.warn("LocalPairwiseQAScoresFile is deprecated. "
"Use QAMetricsFile instead.", stacklevel=2)
super(LocalPairwiseQAScoresFile, self).__init__(*args, **keys)
class ZipFile(File):
"""An associated archive file in zip format, containing other files.
See :class:`File` for more details.
:param list files: A list of the :class:`File` objects contained
within this archive. Note that an archive cannot contain another
archive.
"""
file_type = 'archive'
file_content = 'archive with multiple files'
file_format = 'zip'
def __init__(self, path, details=None, files=[], data=None):
super(ZipFile, self).__init__(path, details, data)
self.files = files
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