# -*- coding: utf-8 -*-
import chemcoord.constants as constants
import pandas as pd
class GenericCore(object):
def add_data(self, new_cols=None):
"""Adds a column with the requested data.
If you want to see for example the mass, the colormap used in
jmol and the block of the element, just use::
['mass', 'jmol_color', 'block']
The underlying ``pd.DataFrame`` can be accessed with
``constants.elements``.
To see all available keys use ``constants.elements.info()``.
The data comes from the module `mendeleev
<http://mendeleev.readthedocs.org/en/latest/>`_ written
by Lukasz Mentel.
Please note that I added three columns to the mendeleev data::
['atomic_radius_cc', 'atomic_radius_gv', 'gv_color',
'valency']
The ``atomic_radius_cc`` is used by default by this module
for determining bond lengths.
The three others are taken from the MOLCAS grid viewer written
by Valera Veryazov.
Args:
new_cols (str): You can pass also just one value.
E.g. ``'mass'`` is equivalent to ``['mass']``. If
``new_cols`` is ``None`` all available data
is returned.
inplace (bool):
Returns:
Cartesian:
"""
atoms = self['atom']
data = constants.elements
if pd.api.types.is_list_like(new_cols):
new_cols = set(new_cols)
elif new_cols is None:
new_cols = set(data.columns)
else:
new_cols = [new_cols]
new_frame = data.loc[atoms, set(new_cols) - set(self.columns)]
new_frame.index = self.index
return self.__class__(pd.concat([self._frame, new_frame], axis=1))
def get_total_mass(self):
"""Returns the total mass in g/mol.
Args:
None
Returns:
float:
"""
try:
mass = self.loc[:, 'mass'].sum()
except KeyError:
mass_molecule = self.add_data('mass')
mass = mass_molecule.loc[:, 'mass'].sum()
return mass
def has_same_sumformula(self, other):
"""Determines if ``other`` has the same sumformula
Args:
other (molecule):
Returns:
bool:
"""
same_atoms = True
for atom in set(self['atom']):
own_atom_number = len(self[self['atom'] == atom])
other_atom_number = len(other[other['atom'] == atom])
same_atoms = (own_atom_number == other_atom_number)
if not same_atoms:
break
return same_atoms
def get_electron_number(self, charge=0):
"""Return the number of electrons.
Args:
charge (int): Charge of the molecule.
Returns:
int:
"""
atomic_number = constants.elements['atomic_number'].to_dict()
return sum([atomic_number[atom] for atom in self['atom']]) - charge