def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext=native_str("stream"))
self._version = kwargs.get("charmm_version", 41)
width = 4 if self._version < 36 else 8
if self._version >= 36:
self.fmt = ("""
IC EDIT
DIST %-{width}s %{width}d %-{width}s %-{width}s %{width}d %-{width}s%{width}.1f
END
""".format(width=width))
else:
self.fmt = ("""
IC EDIT
DIST BYNUM %{width}d BYNUM %{width}d %{width}.1f
END
""".format(width=width))
date = time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime())
user = environ["USER"]
self._title = kwargs.get(
"title", (
"* Created by fluctmatch on {date}".format(date=date),
"* User: {user}".format(user=user),
))
if not util.iterable(self._title):
self._title = util.asiterable(self._title)
def testNamedStream(self):
ns = util.NamedStream(cStringIO.StringIO(), self.filename)
fn = util.filename(ns, ext=self.ext)
# assert_equal replace by this if loop to avoid segfault on some systems
if fn != ns:
raise AssertionError("fn and ns are different")
assert_equal(str(fn), self.filename2)
assert_equal(ns.name, self.filename2)
def test_named_stream(self):
ns = util.NamedStream(StringIO(), self.filename)
fn = util.filename(ns, ext=self.ext)
# assert_equal replace by this if loop to avoid segfault on some systems
if fn != ns:
pytest.fail("fn and ns are different")
assert str(fn) == self.filename2
assert ns.name == self.filename2
def testNamedStream(self):
ns = util.NamedStream(StringIO(), self.filename)
fn = util.filename(ns, ext=self.ext)
# assert_equal replace by this if loop to avoid segfault on some systems
if fn != ns:
raise AssertionError("fn and ns are different")
assert_equal(str(fn), self.filename2)
assert_equal(ns.name, self.filename2)
def __init__(self, filename):
self.filename = util.filename(filename, ext="prm")
self._prmbuffers = dict(
ATOMS=StringIO(),
BONDS=StringIO(),
ANGLES=StringIO(),
DIHEDRALS=StringIO(),
IMPROPER=StringIO(),
)
def __init__(self, filename, **kwargs):
"""
Parameters
----------
filename : str or :class:`~MDAnalysis.lib.util.NamedStream`
name of the output file or a stream
"""
super().__init__(filename, **kwargs)
self.filename = util.filename(filename, ext="cor")
self.crd = None
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext="prm")
self._version = kwargs.get("charmm_version", 41)
self._nonbonded = kwargs.get("nonbonded", False)
date = time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime())
user = environ["USER"]
self._title = kwargs.get("title", (
"* Created by fluctmatch on {date}".format(date=date),
"* User: {user}".format(user=user),
))
if not util.iterable(self._title):
self._title = util.asiterable(self._title)
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext="ic")
self._intcor = None
self._extended = kwargs.get("extended", True)
self._resid = kwargs.get("resid", True)
self.key = "EXTENDED" if self._extended else "STANDARD"
self.key += "_RESID" if self._resid else ""
date = time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime())
user = environ["USER"]
self._title = kwargs.get(
"title", (
"* Created by fluctmatch on {date}".format(date=date),
"* User: {user}".format(user=user),
))
if not util.iterable(self._title):
self._title = util.asiterable(self._title)
def __init__(self, filename, convert_units=True, **kwargs):
"""Set up a DATAWriter
Parameters
----------
filename : str
output filename
convert_units : bool, optional
units are converted to the MDAnalysis base format; [``True``]
"""
self.filename = util.filename(filename, ext='data')
self.convert_units = convert_units
self.units = {'time': 'fs', 'length': 'Angstrom'}
self.units['length'] = kwargs.pop('lengthunit', self.units['length'])
self.units['time'] = kwargs.pop('timeunit', self.units['time'])
self.units['velocity'] = kwargs.pop('velocityunit',
self.units['length']+'/'+self.units['time'])
def test_string(self, name, ext, keep, actual_name):
file_name = util.filename(name, ext, keep)
assert file_name == actual_name
def __init__(self, filename):
self.filename = util.filename(filename, ext="ic")
def testStringRootExtKeep(self):
fn = util.filename(self.root, ext=self.ext, keep=True)
assert_equal(fn, self.filename2)
def testStringRootExt(self):
fn = util.filename(self.root, ext=self.ext)
assert_equal(fn, self.filename2)
def testStringKeep(self):
fn = util.filename(self.filename, ext=self.ext, keep=True)
assert_equal(fn, self.filename)
def testStringRootExtKeep(self):
fn = util.filename(self.root, ext=self.ext, keep=True)
assert_equal(fn, self.filename2)
def testStringRootExt(self):
fn = util.filename(self.root, ext=self.ext)
assert_equal(fn, self.filename2)
def testStringKeep(self):
fn = util.filename(self.filename, ext=self.ext, keep=True)
assert_equal(fn, self.filename)
def testStringNoExt(self):
fn = util.filename(self.filename)
assert_equal(fn, self.filename)
def __init__(self, filename, **kwargs):
super().__init__(filename, **kwargs)
self.filename = util.filename(filename, ext="par")
def cli(data_dir, logfile, outdir, prefix, tbltype, ressep, verbose, start, end, trimmed, trimcut):
pt = paramtable.ParamTable(
prefix=prefix,
tbltype=tbltype,
ressep=ressep,
datadir=data_dir,
start=start,
end=end,
trimmed=trimmed,
trimcut=trimcut
)
# Setup logger
logging.config.dictConfig({
"version": 1,
"disable_existing_loggers": False, # this fixes the problem
"formatters": {
"standard": {
"class": "logging.Formatter",
"format": "%(name)-12s %(levelname)-8s %(message)s",
},
"detailed": {
"class": "logging.Formatter",
"format":
"%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
"datefmt": "%m-%d-%y %H:%M",
},
},
"handlers": {
"console": {
"class": "logging.StreamHandler",
"level": "INFO",
"formatter": "standard",
},
"file": {
"class": "logging.FileHandler",
"filename": logfile,
"level": "INFO",
"mode": "w",
"formatter": "detailed",
}
},
"root": {
"level": "INFO",
"handlers": ["console", "file"]
},
})
logger = logging.getLogger(__name__)
pt.run(verbose=verbose)
# Write the various tables to different files.
fn = path.join(outdir, filename(tbltype.lower(), ext="txt", keep=True))
pt.write(fn)
if tbltype == "Kb":
fn = path.join(outdir, filename("perres", ext="txt"))
with open(fn, mode="wb") as output:
logger.info("Writing per-residue data to {}.".format(fn))
table = pt.per_residue.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(table.encode())
logger.info("Table successfully written.")
fn = path.join(outdir, filename("interactions", ext="txt"))
with open(fn, mode="wb") as output:
logger.info("Writing interactions to {}.".format(fn))
table = pt.interactions.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(table.encode())
logger.info("Table successfully written.")
def testStringNoExt(self):
fn = util.filename(self.filename)
assert_equal(fn, self.filename)