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