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#!/usr/bin/env python
"""Classes for reading macromolecular structure files in different formats."""
import xml.dom.minidom
from cogent.parse import pdb
from cogent.parse.sequence import format_from_filename
from cogent.parse.record import FileFormatError
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
def FromFilenameStructureParser(filename, format=None, **kw):
"""
Returns a structure parser for a specified format for given filename.
Arguments:
- filename: name of the structure file
- format: the structure file format
"""
format = format_from_filename(filename, format)
f = open(filename, 'U')
return FromFileStructureParser(f, format, **kw)
def FromFileStructureParser(f, format, dialign_recode=False, **kw):
"""
Returns a structure parser for a specified format for given filename.
Arguments:
- filename: name of the structure file
- format: the structure file format
"""
if not type(f) is file:
raise TypeError('%s is not a file' % f)
format = format.lower()
if format in XML_PARSERS:
doctype = format
format = 'xml'
else:
doctype = None
if format == 'xml':
source = dom = xml.dom.minidom.parse(f)
if doctype is None:
doctype = str(dom.doctype.name).lower()
if doctype not in XML_PARSERS:
raise FileFormatError("Unsupported XML doctype %s" % doctype)
parser = XML_PARSERS[doctype]
else:
if format not in PARSERS:
raise FileFormatError("Unsupported file format %s" % format)
parser = PARSERS[format]
source = f
return parser(source, **kw)
PARSERS = {
'pdb': pdb.PDBParser,
}
XML_PARSERS = {
}
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