def __str__(self):
return "InternalRepresentation of {} with coordinates\n{}".format(
shortstr(self.molecule),
indented('\n'.join('[{}] {}: {}'.format(
i, shortstr(coord), str(coord.value_with_units)
) for i, coord in enumerate(self.coords)))
)
def __str__(self):
ret_val = "CartesianRepresentation of molecule {}, in {}:\n".format(
shortstr(self.molecule), self.units)
for i, (x, y, z) in enumerate(grouper(3, self)):
ret_val += indent(
'{:>9} {:12.8f} {:12.8f} {:12.8f}\n'.format(
'[{}-{}]'.format(3 * i, 3 * i + 2), x.value, y.value,
z.value), 2)
return ret_val
def validate(self):
bmat = self.b_matrix
evals = np.linalg.eigvalsh(bmat * bmat.T)
nvalid = len([e for e in evals if abs(e) > InternalRepresentation.zero_eigenvalue])
if nvalid != self.molecule.ninternals:
raise RepresentationError("Have {} nonredundant internal coordinates, but need {}.\nCoordnates are:\n{}".format(
nvalid,
self.molecule.ninternals,
indented('\n'.join('[' + str(i) + '] ' + shortstr(c) for i, c in enumerate(self.coords)))
))
def __str__(self):
ret_val = "CartesianRepresentation of molecule {}, in {}:\n".format(shortstr(self.molecule), self.units)
for i, (x, y, z) in enumerate(grouper(3, self)):
ret_val += indent(
"{:>9} {:12.8f} {:12.8f} {:12.8f}\n".format(
"[{}-{}]".format(3 * i, 3 * i + 2), x.value, y.value, z.value
),
2,
)
return ret_val
def validate(self):
bmat = self.b_matrix
evals = np.linalg.eigvalsh(bmat * bmat.T)
nvalid = len([
e for e in evals if abs(e) > InternalRepresentation.zero_eigenvalue
])
if nvalid != self.molecule.ninternals:
raise RepresentationError(
"Have {} nonredundant internal coordinates, but need {}.\nCoordnates are:\n{}"
.format(
nvalid, self.molecule.ninternals,
indented('\n'.join('[' + str(i) + '] ' + shortstr(c)
for i, c in enumerate(self.coords)))))
def __str__(self):
namestrs = []
valstrs = []
it = np.nditer(self, flags=['multi_index'])
for x in it:
namestrs.append(", ".join(shortstr(self.representation[i]) for i in it.multi_index))
valstrs.append("{: .8f}{}".format(float(x), (" " + str(self.units) if hasunits(self) else '')))
width=max(len(s) for s in namestrs) + 4
ret_val = self.__class__.__name__ + ":\n"
for name, val in zip(namestrs, valstrs):
ret_val += ("{:>"+str(width)+"}: {}\n").format(name, val)
ret_val += " for representation:\n{}".format(indent(str(self.representation)))
return ret_val
def __str__(self):
namestrs = []
valstrs = []
it = np.nditer(self, flags=['multi_index'])
for x in it:
namestrs.append(", ".join(
shortstr(self.representation[i]) for i in it.multi_index))
valstrs.append("{: .8f}{}".format(
float(x), (" " + str(self.units) if hasunits(self) else '')))
width = max(len(s) for s in namestrs) + 4
ret_val = self.__class__.__name__ + ":\n"
for name, val in zip(namestrs, valstrs):
ret_val += ("{:>" + str(width) + "}: {}\n").format(name, val)
ret_val += " for representation:\n{}".format(
indent(str(self.representation)))
return ret_val
def __str__(self):
return "InternalRepresentation of {} with coordinates\n{}".format(
shortstr(self.molecule),
indented('\n'.join('[{}] {}: {}'.format(
i, shortstr(coord), str(coord.value_with_units))
for i, coord in enumerate(self.coords))))