def _process_plot_kwargs(self, kwargs):
import matplotlib.colors
from itertools import cycle
kw = {}
frames = kwargs.pop('frames', None)
if frames is None:
frames = numpy.sort(self.profiles.keys()[::kwargs.pop('step', 1)])
else:
frames = asiterable(frames)
kw['frames'] = frames
kw['yshift'] = kwargs.pop('yshift', 0.0)
kw['rmax'] = kwargs.pop('rmax', None)
kw['label'] = kwargs.pop('label', True)
if kw['label'] == "_nolegend_":
kw['label'] = False
elif kw['label'] is None:
kw['label'] = True
color = kwargs.pop('color', None)
if color is None:
cmap = kwargs.pop('cmap', matplotlib.cm.jet)
normalize = matplotlib.colors.normalize(vmin=numpy.min(frames), vmax=numpy.max(frames))
colors = cmap(normalize(frames))
else:
colors = cycle(asiterable(color))
kw['colors'] = colors
kw['linestyles'] = cycle(asiterable(kwargs.pop('linestyle', '-')))
return kw, kwargs
def _process_plot_kwargs(self, kwargs):
import matplotlib.colors
from itertools import cycle
kw = {}
frames = kwargs.pop("frames", None)
if frames is None:
frames = np.sort(self.profiles.keys()[:: kwargs.pop("step", 1)])
else:
frames = asiterable(frames)
kw["frames"] = frames
kw["yshift"] = kwargs.pop("yshift", 0.0)
kw["rmax"] = kwargs.pop("rmax", None)
kw["label"] = kwargs.pop("label", True)
if kw["label"] == "_nolegend_":
kw["label"] = False
elif kw["label"] is None:
kw["label"] = True
color = kwargs.pop("color", None)
if color is None:
cmap = kwargs.pop("cmap", matplotlib.cm.jet)
normalize = matplotlib.colors.normalize(vmin=np.min(frames), vmax=np.max(frames))
colors = cmap(normalize(frames))
else:
colors = cycle(asiterable(color))
kw["colors"] = colors
kw["linestyles"] = cycle(asiterable(kwargs.pop("linestyle", "-")))
return kw, kwargs
def process_selection(select):
"""Return a canonical selection dictionary.
Parameters
----------
select : str / tuple / dict
- `str` -> Any valid string selection
- `dict` -> ``{'mobile':sel1, 'reference':sel2}``
- `tuple` -> ``(sel1, sel2)``
Returns
-------
dict
selections for 'reference' and 'mobile'. Values are guarenteed to be
iterable (so that one can provide selections to retain order)
Notes
-----
The dictionary input for `select` can be generated by
:func:`fasta2select` based on a ClustalW_ or STAMP_ sequence alignment.
"""
if type(select) is str:
select = {'reference': select, 'mobile': select}
elif type(select) is tuple:
try:
select = {'mobile': select[0], 'reference': select[1]}
except IndexError:
raise IndexError("select must contain two selection strings "
"(reference, mobile)")
elif type(select) is dict:
# compatability hack to use new nomenclature
try:
select['mobile'] = select['target']
warnings.warn("use key 'mobile' instead of deprecated 'target'; "
"'target' will be removed in 0.8",
DeprecationWarning)
except KeyError:
pass
try:
select['mobile']
select['reference']
except KeyError:
raise KeyError("select dictionary must contain entries for keys "
"'mobile' and 'reference'.")
else:
raise TypeError("'select' must be either a string, 2-tuple, or dict")
select['mobile'] = asiterable(select['mobile'])
select['reference'] = asiterable(select['reference'])
return select
def process_selection(select):
"""Return a canonical selection dictionary.
Parameters
----------
select : str / tuple / dict
- `str` -> Any valid string selection
- `dict` -> ``{'mobile':sel1, 'reference':sel2}``
- `tuple` -> ``(sel1, sel2)``
Returns
-------
dict
selections for 'reference' and 'mobile'. Values are guarenteed to be
iterable (so that one can provide selections to retain order)
Notes
-----
The dictionary input for `select` can be generated by
:func:`fasta2select` based on a ClustalW_ or STAMP_ sequence alignment.
"""
if type(select) is str:
select = {'reference': select, 'mobile': select}
elif type(select) is tuple:
try:
select = {'mobile': select[0], 'reference': select[1]}
except IndexError:
raise IndexError("select must contain two selection strings "
"(reference, mobile)")
elif type(select) is dict:
# compatability hack to use new nomenclature
try:
select['mobile'] = select['target']
warnings.warn(
"use key 'mobile' instead of deprecated 'target'; "
"'target' will be removed in 0.8", DeprecationWarning)
except KeyError:
pass
try:
select['mobile']
select['reference']
except KeyError:
raise KeyError("select dictionary must contain entries for keys "
"'mobile' and 'reference'.")
else:
raise TypeError("'select' must be either a string, 2-tuple, or dict")
select['mobile'] = asiterable(select['mobile'])
select['reference'] = asiterable(select['reference'])
return select
def process_selection(select):
"""Return a canonical selection dictionary.
Parameters
----------
select : str or tuple or dict
- `str` -> Any valid string selection
- `dict` -> ``{'mobile':sel1, 'reference':sel2}``
- `tuple` -> ``(sel1, sel2)``
Returns
-------
dict
selections for 'reference' and 'mobile'. Values are guarenteed to be
iterable (so that one can provide selections to retain order)
Notes
-----
The dictionary input for `select` can be generated by
:func:`fasta2select` based on a ClustalW_ or STAMP_ sequence alignment.
"""
if isinstance(select, string_types):
select = {'reference': str(select), 'mobile': str(select)}
elif type(select) is tuple:
try:
select = {'mobile': select[0], 'reference': select[1]}
except IndexError:
raise_from(
IndexError("select must contain two selection strings "
"(reference, mobile)"),
None,
)
elif type(select) is dict:
# compatability hack to use new nomenclature
try:
select['mobile']
select['reference']
except KeyError:
raise_from(
KeyError("select dictionary must contain entries for keys "
"'mobile' and 'reference'."),
None,
)
else:
raise TypeError("'select' must be either a string, 2-tuple, or dict")
select['mobile'] = asiterable(select['mobile'])
select['reference'] = asiterable(select['reference'])
return select
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 __init__(cls, name, bases, classdict):
type.__init__(type, name, bases, classdict)
try:
fmt = asiterable(classdict['model'])
except KeyError:
pass
else:
for f in fmt:
f = f.upper()
_MODELS[f] = cls
try:
description = asiterable(classdict['describe'])
except KeyError:
pass
else:
for f, d in zip(fmt, description):
f = f.upper()
_DESCRIBE[f] = d
def _process_selection(select):
"""Return a canonical selection dictionary.
:Arguments:
*select*
- any valid selection string for
:meth:`~MDAnalysis.core.AtomGroup.AtomGroup.select_atoms` that produces identical
selections in *mobile* and *reference*; or
- dictionary ``{'mobile':sel1, 'reference':sel2}``.
The :func:`fasta2select` function returns such a
dictionary based on a ClustalW_ or STAMP_ sequence alignment.
- tuple ``(sel1, sel2)``
:Returns: dict with keys `reference` and `mobile`; the values are guaranteed to
be iterable (so that one can provide selections that retain order)
"""
if type(select) is str:
select = {'reference': select, 'mobile': select}
elif type(select) is tuple:
try:
select = {'mobile': select[0], 'reference': select[1]}
except IndexError:
raise IndexError("select must contain two selection strings "
"(reference, mobile)")
elif type(select) is dict:
# compatability hack to use new nomenclature
try:
select['mobile'] = select['target']
warnings.warn("use key 'mobile' instead of deprecated 'target'; "
"'target' will be removed in 0.8",
DeprecationWarning)
except KeyError:
pass
try:
select['mobile']
select['reference']
except KeyError:
raise KeyError("select dictionary must contain entries for keys "
"'mobile' and 'reference'.")
else:
raise TypeError("'select' must be either a string, 2-tuple, or dict")
select['mobile'] = asiterable(select['mobile'])
select['reference'] = asiterable(select['reference'])
return select
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)
