_cartesian_class_io.py 文件源码

def to_cjson(self, buf=None, **kwargs):
        """Write a cjson file or return dictionary.

        The cjson format is specified
        `here <https://github.com/OpenChemistry/chemicaljson>`_.

        Args:
            buf (str): If it is a filepath, the data is written to
                filepath. If it is None, a dictionary with the cjson
                information is returned.
            kwargs: The keyword arguments are passed into the
                ``dump`` function of the
                `json library <https://docs.python.org/3/library/json.html>`_.

        Returns:
            dict:
        """
        cjson_dict = {'chemical json': 0}

        cjson_dict['atoms'] = {}

        atomic_number = constants.elements['atomic_number'].to_dict()
        cjson_dict['atoms'] = {'elements': {}}
        cjson_dict['atoms']['elements']['number'] = [
            int(atomic_number[x]) for x in self['atom']]

        cjson_dict['atoms']['coords'] = {}
        coords = self.loc[:, ['x', 'y', 'z']].values.reshape(len(self) * 3)
        cjson_dict['atoms']['coords']['3d'] = [float(x) for x in coords]

        bonds = []
        bond_dict = self.get_bonds()
        for i in bond_dict:
            for b in bond_dict[i]:
                bonds += [int(i), int(b)]
                bond_dict[b].remove(i)

        cjson_dict['bonds'] = {'connections': {}}
        cjson_dict['bonds']['connections']['index'] = bonds

        if buf is not None:
            with open(buf, mode='w') as f:
                f.write(json.dumps(cjson_dict, **kwargs))
        else:
            return cjson_dict