def test_describe_atom(self):
str1 = _describe_atom(self.traj.topology, 0)
str2 = _describe_atom(self.traj.topology, self.traj.n_atoms - 1)
assert len(str1.split()) >= 4
assert len(str2.split()) >= 4
assert str1.split()[-1] == '0'
assert str2.split()[-1] == '1'
def describe(self):
labels = [
"%s %s - %s" % (self.prefix_label, _describe_atom(
self.top, pair[0]), _describe_atom(self.top, pair[1]))
for pair in self.distance_indexes
]
return labels
def describe(self):
labels = []
for i in self.indexes:
labels.append("%s%s x" %
(self.prefix_label, _describe_atom(self.top, i)))
labels.append("%s%s y" %
(self.prefix_label, _describe_atom(self.top, i)))
labels.append("%s%s z" %
(self.prefix_label, _describe_atom(self.top, i)))
return labels
def describe(self):
labels = [
"%s %u--%u: [%s...%s]--[%s...%s]" %
(self.prefix_label, pair[0], pair[1],
_describe_atom(self.top, self.group_definitions[pair[0]][0]),
_describe_atom(self.top, self.group_definitions[pair[0]][-1]),
_describe_atom(self.top, self.group_definitions[pair[1]][0]),
_describe_atom(self.top, self.group_definitions[pair[1]][-1]))
for pair in self.group_pairs
]
return labels
def describe(self):
if self.cossin:
sin_cos = ("DIH: COS(%s - %s - %s - %s)",
"DIH: SIN(%s - %s - %s - %s)")
labels = [
s % (_describe_atom(
self.top, quad[0]), _describe_atom(
self.top, quad[1]), _describe_atom(self.top, quad[2]),
_describe_atom(self.top, quad[3]))
for quad in self.angle_indexes for s in sin_cos
]
else:
labels = [
"DIH: %s - %s - %s - %s " % (_describe_atom(
self.top, quad[0]), _describe_atom(
self.top, quad[1]), _describe_atom(self.top, quad[2]),
_describe_atom(self.top, quad[3]))
for quad in self.angle_indexes
]
return labels
def describe(self):
if self.cossin:
sin_cos = ("ANGLE: COS(%s - %s - %s)", "ANGLE: SIN(%s - %s - %s)")
labels = [
s % (_describe_atom(
self.top, triple[0]), _describe_atom(self.top, triple[1]),
_describe_atom(self.top, triple[2]))
for triple in self.angle_indexes for s in sin_cos
]
else:
labels = [
"ANGLE: %s - %s - %s " % (_describe_atom(
self.top, triple[0]), _describe_atom(self.top, triple[1]),
_describe_atom(self.top, triple[2]))
for triple in self.angle_indexes
]
return labels
