def write(self, fmt, filename, csv_filename = None, **kwargs):
        if fmt == 'mol2' and toolkit.backend == 'ob':
            if 'opt' in kwargs:
                kwargs['opt']['c'] = None
            else:
                kwargs['opt'] = {'c': None}
        output_mol_file = toolkit.Outputfile(fmt, filename, **kwargs)
        if csv_filename:
            f = open(csv_filename, 'w')
            csv_file = None
        for mol in self.fetch():
            if csv_filename:
                data = dict(mol.data)
                #filter some internal data
                blacklist_keys = ['OpenBabel Symmetry Classes', 'MOL Chiral Flag', 'PartialCharges', 'TORSDO', 'REMARK']
                for b in blacklist_keys:
                    if data.has_key(b):
                        del data[b]
                if len(data) > 0:
                    data['name'] = mol.title
                else:
                    print "There is no data to write in CSV file"
                    return False
                if csv_file is None:
                    csv_file = csv.DictWriter(f, data.keys(), **kwargs)
                    csv_file.writeheader()
                csv_file.writerow(data)
            # write ligand
            output_mol_file.write(mol)
        output_mol_file.close()
        if csv_filename:
            f.close()
#        if kwargs.has_key('keep_pipe') and kwargs['keep_pipe']:
        if isfile(filename):
            kwargs.pop('overwrite') # this argument is unsupported in readfile
            self._pipe = toolkit.readfile(fmt, filename, **kwargs)
Outputs molecules to a file
dataset/ETHPy150Open oddt/oddt/oddt/virtualscreening.py/virtualscreening.write