"""
This module contains the metaclass for defining and registering a particular
file format. Any class with this metaclass will be added to the registry and
therefore automatically be added to the 'automatic' file type identification.
The following static class functions will trigger special behavior:
- id_format(file) : Takes a filename to identify the type, and return True
if the file is that format or False if not.
- parse(file) : Takes a file name or file-like object, parse through the
whole thing and return it. If this method is not found, the constructor is
called directly.
Note, id_format must be IMPLEMENTED for each class added to the registry, not
simply inherited from a base class (unless that base class is not a metaclass of
FileFormatType)
"""
from __future__ import division, print_function, absolute_import
from contextlib import closing
from parmed.utils.io import genopen
from parmed.utils.six import iteritems
from parmed.exceptions import FormatNotFound
import os
PARSER_REGISTRY = dict()
PARSER_ARGUMENTS = dict()
[docs]def load_file(filename, *args, **kwargs):
"""
Identifies the file format of the specified file and returns its parsed
contents.
Parameters
----------
filename : str
The name of the file to try to parse. If the filename starts with
http:// or https:// or ftp://, it is treated like a URL and the file will be
loaded directly from its remote location on the web
structure : object, optional
For some classes, such as the Mol2 file class, the default return object
is not a Structure, but can be made to return a Structure if the
``structure=True`` keyword argument is passed. To facilitate writing
easy code, the ``structure`` keyword is always processed and only passed
on to the correct file parser if that parser accepts the structure
keyword. There is no default, as each parser has its own default.
natom : int, optional
This is needed for some coordinate file classes, but not others. This is
treated the same as ``structure``, above. It is the # of atoms expected
hasbox : bool, optional
Same as ``structure``, but indicates whether the coordinate file has
unit cell dimensions
skip_bonds : bool, optional
Same as ``structure``, but indicates whether or not bond searching will
be skipped if the topology file format does not contain bond information
(like PDB, GRO, and PQR files).
*args : other positional arguments
Some formats accept positional arguments. These will be passed along
**kwargs : other options
Some formats can only be instantiated with other options besides just a
file name.
Returns
-------
object
The returned object is the result of the parsing function of the class
associated with the file format being parsed
Notes
-----
Compressed files are supported and detected by filename extension. This
applies both to local and remote files. The following names are supported:
- ``.gz`` : gzip compressed file
- ``.bz2`` : bzip2 compressed file
SDF file is loaded via `rdkit` package.
Examples
--------
Load a Mol2 file
>>> load_file('tripos1.mol2')
<ResidueTemplate DAN: 31 atoms; 33 bonds; head=None; tail=None>
Load a Mol2 file as a Structure
>>> load_file('tripos1.mol2', structure=True)
<Structure 31 atoms; 1 residues; 33 bonds; NOT parametrized>
Load an Amber topology file
>>> load_file('trx.prmtop', xyz='trx.inpcrd')
<AmberParm 1654 atoms; 108 residues; 1670 bonds; parametrized>
Load a CHARMM PSF file
>>> load_file('ala_ala_ala.psf')
<CharmmPsfFile 33 atoms; 3 residues; 32 bonds; NOT parametrized>
Load a PDB and CIF file
>>> load_file('4lzt.pdb')
<Structure 1164 atoms; 274 residues; 0 bonds; PBC (triclinic); NOT parametrized>
>>> load_file('4LZT.cif')
<Structure 1164 atoms; 274 residues; 0 bonds; PBC (triclinic); NOT parametrized>
Load a Gromacs topology file -- only works with Gromacs installed
>>> load_file('1aki.ff99sbildn.top')
<GromacsTopologyFile 40560 atoms [9650 EPs]; 9779 residues; 30934 bonds; parametrized>
Load a SDF file -- only works with rdkit installed
>>> load_file('mol.sdf', structure=True)
<Structure 34 atoms; 1 residues; 66 bonds; NOT parametrized>
Raises
------
IOError
If ``filename`` does not exist
parmed.exceptions.FormatNotFound
If no suitable file format can be identified, a TypeError is raised
TypeError
If the identified format requires additional arguments that are not
provided as keyword arguments in addition to the file name
"""
global PARSER_REGISTRY, PARSER_ARGUMENTS
# Check that the file actually exists and that we can read it
if filename.startswith('http://') or filename.startswith('https://')\
or filename.startswith('ftp://'):
# This raises IOError if it does not exist; assert silences linters
with closing(genopen(filename)) as f:
assert f
elif not os.path.exists(filename):
raise IOError('%s does not exist' % filename)
elif not os.access(filename, os.R_OK):
raise IOError('%s does not have read permissions set' % filename)
for name, cls in iteritems(PARSER_REGISTRY):
if not hasattr(cls, 'id_format'):
continue
try:
if cls.id_format(filename):
break
except UnicodeDecodeError:
continue
else:
# We found no file format
raise FormatNotFound('Could not identify file format')
# We found a file format that is compatible. Parse it!
other_args = PARSER_ARGUMENTS[name]
for arg in other_args:
if not arg in kwargs:
raise TypeError('%s constructor expects %s keyword argument' %
name, arg)
# Pass on the following keywords IFF the target function accepts a target
# keyword. Otherwise, get rid of it: structure, natom, hasbox, skip_bonds
if hasattr(cls, 'parse'):
_prune_argument(cls.parse, kwargs, 'structure')
_prune_argument(cls.parse, kwargs, 'natom')
_prune_argument(cls.parse, kwargs, 'hasbox')
_prune_argument(cls.parse, kwargs, 'skip_bonds')
return cls.parse(filename, *args, **kwargs)
elif hasattr(cls, 'open_old'):
_prune_argument(cls.open_old, kwargs, 'structure')
_prune_argument(cls.open_old, kwargs, 'natom')
_prune_argument(cls.open_old, kwargs, 'hasbox')
_prune_argument(cls.open_old, kwargs, 'skip_bonds')
return cls.open_old(filename, *args, **kwargs)
elif hasattr(cls, 'open'):
_prune_argument(cls.open, kwargs, 'structure')
_prune_argument(cls.open, kwargs, 'natom')
_prune_argument(cls.open, kwargs, 'hasbox')
_prune_argument(cls.open, kwargs, 'skip_bonds')
return cls.open(filename, *args, **kwargs)
_prune_argument(cls.__init__, kwargs, 'structure')
_prune_argument(cls.__init__, kwargs, 'natom')
_prune_argument(cls.__init__, kwargs, 'hasbox')
_prune_argument(cls.__init__, kwargs, 'skip_bonds')
return cls(filename, *args, **kwargs)
def _prune_argument(func, kwargs, keyword):
if keyword in kwargs:
if (keyword not in
func.__code__.co_varnames[:func.__code__.co_argcount]):
kwargs.pop(keyword)