def get_reader_for(filename, format=None):
"""Return the appropriate trajectory reader class for `filename`.
Parameters
----------
filename
filename of the input trajectory or coordinate file. Also can
handle a few special cases, see notes below.
format : str or :class:`Reader` (optional)
Define the desired format. Can be a string to request a given
Reader.
If a class is passed, it will be assumed that this is
a Reader and will be returned.
Returns
-------
:class:`Reader`
A Reader object
Raises
------
ValueError
If no appropriate Reader is found
Notes
-----
There are a number of special cases that can be handled:
- If `filename` is a numpy array,
:class:`~MDAnalysis.coordinates.memory.MemoryReader` is returned.
- If `filename` is an MMTF object,
:class:`~MDAnalysis.coordinates.MMTF.MMTFReader` is returned.
- If `filename` is an iterable of filenames,
:class:`~MDAnalysis.coordinates.chain.ChainReader` is returned.
Automatic detection is disabled when an explicit `format` is provided,
unless a list of filenames is given, in which case
:class:`~MDAnalysis.coordinates.chain.ChainReader` is returned and `format`
passed to the :class:`~MDAnalysis.coordinates.chain.ChainReader`.
"""
# check if format is actually a Reader
if inspect.isclass(format):
return format
# ChainReader gets returned even if format is specified
if not isinstance(filename, np.ndarray) and util.iterable(
filename) and not isstream(filename):
format = 'CHAIN'
# Only guess if format is not specified
elif format is None:
# Checks for specialised formats
if isinstance(filename, np.ndarray):
# memoryreader slurps numpy arrays
format = 'MEMORY'
elif isinstance(filename, mmtf.MMTFDecoder):
# mmtf slurps mmtf object
format = 'MMTF'
else:
# else let the guessing begin!
format = util.guess_format(filename)
format = format.upper()
try:
return _READERS[format]
except KeyError:
raise ValueError(
"Unknown coordinate trajectory format '{0}' for '{1}'. The FORMATs \n"
" {2}\n"
" are implemented in MDAnalysis.\n"
" See https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1\n"
" Use the format keyword to explicitly set the format: 'Universe(...,format=FORMAT)'\n"
" For missing formats, raise an issue at "
"http://issues.mdanalysis.org".format(format, filename,
_READERS.keys()))
def test_StringIO_read(self):
with open(datafiles.PSF, "r") as f:
obj = StringIO(f.read())
assert_equal(util.isstream(obj), True)
obj.close()
def test_StringIO_write(self):
obj = StringIO()
assert_equal(util.isstream(obj), True)
obj.close()
def test_iterator(self):
obj = (i for i in range(3))
assert_equal(util.isstream(obj), False)
def test_file(self):
with open(datafiles.PSF) as obj:
assert_equal(util.isstream(obj), True)
def test_string(self):
obj = datafiles.PSF # filename
assert_equal(util.isstream(obj), False)
def test_list(self):
obj = [1, 2, 3]
assert_equal(util.isstream(obj), False)
def test_StringIO_read(self):
with open(datafiles.PSF, "r") as f:
obj = StringIO.StringIO(f)
assert_equal(util.isstream(obj), True)
obj.close()
def test_StringIO_write(self):
obj = StringIO.StringIO()
assert_equal(util.isstream(obj), True)
obj.close()
def test_file(self):
with open(datafiles.PSF) as obj:
assert_equal(util.isstream(obj), True)
def test_iterator(self):
obj = (i for i in xrange(3))
assert_equal(util.isstream(obj), False)
def test_list(self):
obj = [1, 2, 3]
assert_equal(util.isstream(obj), False)
def test_string(self):
obj = datafiles.PSF # filename
assert_equal(util.isstream(obj), False)
def get_reader_for(filename, format=None):
"""Return the appropriate trajectory reader class for `filename`.
Parameters
----------
filename
filename of the input trajectory or coordinate file. Also can
handle a few special cases, see notes below.
format : str or :class:`Reader` (optional)
Define the desired format. Can be a string to request a given
Reader.
If a class is passed, it will be assumed that this is
a Reader and will be returned.
Returns
-------
:class:`Reader`
A Reader object
Raises
------
ValueError
If no appropriate Reader is found
Notes
-----
There are a number of special cases that can be handled:
- If `filename` is a numpy array,
:class:`~MDAnalysis.coordinates.memory.MemoryReader` is returned.
- If `filename` is an MMTF object,
:class:`~MDAnalysis.coordinates.MMTF.MMTFReader` is returned.
- If `filename` is an iterable of filenames,
:class:`~MDAnalysis.coordinates.chain.ChainReader` is returned.
Automatic detection is disabled when an explicit `format` is provided,
unless a list of filenames is given, in which case
:class:`~MDAnalysis.coordinates.chain.ChainReader` is returned and `format`
passed to the :class:`~MDAnalysis.coordinates.chain.ChainReader`.
"""
# check if format is actually a Reader
if inspect.isclass(format):
return format
# ChainReader gets returned even if format is specified
if not isinstance(filename, np.ndarray) and util.iterable(filename) and not isstream(filename):
format = 'CHAIN'
# Only guess if format is not specified
elif format is None:
# Checks for specialised formats
if isinstance(filename, np.ndarray):
# memoryreader slurps numpy arrays
format = 'MEMORY'
elif isinstance(filename, mmtf.MMTFDecoder):
# mmtf slurps mmtf object
format = 'MMTF'
else:
# else let the guessing begin!
format = util.guess_format(filename)
format = format.upper()
try:
return _READERS[format]
except KeyError:
raise ValueError(
"Unknown coordinate trajectory format '{0}' for '{1}'. The FORMATs \n"
" {2}\n"
" are implemented in MDAnalysis.\n"
" See https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1\n"
" Use the format keyword to explicitly set the format: 'Universe(...,format=FORMAT)'\n"
" For missing formats, raise an issue at "
"http://issues.mdanalysis.org".format(
format, filename, _READERS.keys()))
