def _test_if_can_be_added(self, other):
cols = ['atom', 'b', 'a', 'd']
if not (np.alltrue(self.loc[:, cols] == other.loc[:, cols])
and np.alltrue(self.index == other.index)):
message = ("You can add only those zmatrices that have the same "
"index, use the same construction table, have the same "
"ordering... The only allowed difference is in the "
"columns ['bond', 'angle', 'dihedral']")
raise PhysicalMeaning(message)
def set_index(self,
keys,
drop=True,
append=False,
inplace=False,
verify_integrity=False):
"""Set the DataFrame index (row labels) using one or more existing
columns.
Wrapper around the :meth:`pandas.DataFrame.set_index` method.
"""
if drop is True:
try:
assert type(keys) is not str
dropped_cols = set(keys)
except (TypeError, AssertionError):
dropped_cols = set([keys])
if not self._required_cols <= (set(self.columns) - set(dropped_cols)):
raise PhysicalMeaning('You drop a column that is needed to '
'be a physical meaningful description '
'of a molecule.')
if inplace:
self._frame.set_index(keys,
drop=drop,
append=append,
inplace=inplace,
verify_integrity=verify_integrity)
else:
new = self._frame.set_index(keys,
drop=drop,
append=append,
inplace=inplace,
verify_integrity=verify_integrity)
return self.__class__(new,
_metadata=self._metadata,
metadata=self.metadata)
def __init__(self, frame, metadata=None, _metadata=None):
"""How to initialize a Zmat instance.
Args:
init (pd.DataFrame): A Dataframe with at least the columns
``['atom', 'b', 'bond', 'a', 'angle',
'd', 'dihedral']``.
Where ``'atom'`` is a string for the elementsymbol.
order_of_definition (list like): Specify in which order
the Zmatrix is defined. If ``None`` it just uses
``self.index``.
Returns:
Zmat: A new zmat instance.
"""
if not self._required_cols <= set(frame.columns):
raise PhysicalMeaning('There are columns missing for a '
'meaningful description of a molecule')
self._frame = frame.copy()
if metadata is None:
self.metadata = {}
else:
self.metadata = metadata.copy()
if _metadata is None:
self._metadata = {}
else:
self._metadata = copy.deepcopy(_metadata)
def fill_missing_keys_with_defaults(_metadata):
if 'last_valid_cartesian' not in _metadata:
_metadata['last_valid_cartesian'] = self.get_cartesian()
if 'has_dummies' not in _metadata:
_metadata['has_dummies'] = {}
fill_missing_keys_with_defaults(self._metadata)
def columns(self, value):
if not self._required_cols <= set(value):
raise PhysicalMeaning('There are columns missing for a '
'meaningful description of a molecule')
self._frame.columns = value