def __init__(self, **params):
self.polygons = OrderedDict()
self.balls = OrderedDict()
self.params = Params(params)
self.boundaries = OrderedDict()
self.names = []
self.add_molecule_ball()
def __init__(self, poly, name="protein", **params):
self.name = name
self.protein = Polygon(poly)
self.polygons = OrderedDict({name: self.protein})
self.balls = OrderedDict()
self.params = Params(params)
self.boundaries = OrderedDict()
# cs ... protein crosssections for partition of boundary
self.add_proteinpartition()
self.add_molecule_ball()
def init_params(self, params, **paramsets):
active = set()
for p in paramsets:
setattr(self, p, Params(self.default[p]))
dic = getattr(self, p)
if paramsets[p] is not None:
dic.update(paramsets[p])
for k in dic:
if k in params:
active.add(k)
dic[k] = params[k]
self.active_params = {p: params[p] for p in active}
self.inactive_params = {p: params[p] for p in params if not p in active}
def wrapper(X, cache=True, calc=True, overwrite=False,
nproc=self.nproc, name=self.name, **params):
if not cache:
return f(X, **params)
if calc:
# calculate remaining points (in parallel)
calculate_forcefield(name, X, f, params, self.default, nproc,
overwrite=overwrite)
# load requested data points
load_params = dict(self.default, **params)
try:
result = fields.get_fields(name, **load_params)
I = [result["x"].index(x) for x in X if x in result["x"]]
except KeyError:
print "KeyError, returning nothing."
result = {}
I = []
result = {key: [val[i] for i in I] for key, val in result.items()}
return Params(result)
def __init__(self, h=1., reconstruct=False, **params):
lazy_import()
self.params = Params(self.default, **params)
self.h = h
self.reconstruct = reconstruct