pymatgen.io.qchem.outputs module¶
Parsers for Qchem output files.
-
class
QCOutput
(filename: str)[source]¶ Bases:
monty.json.MSONable
Class to parse QChem output files.
- Parameters
filename (str) – Filename to parse
-
static
multiple_outputs_from_file
(cls, filename, keep_sub_files=True)[source]¶ Parses a QChem output file with multiple calculations # 1.) Seperates the output into sub-files
e.g. qcout -> qcout.0, qcout.1, qcout.2 … qcout.N a.) Find delimeter for multiple calcualtions b.) Make seperate output sub-files
2.) Creates seperate QCCalcs for each one from the sub-files
-
check_for_structure_changes
(mol1: pymatgen.core.structure.Molecule, mol2: pymatgen.core.structure.Molecule) → str[source]¶ Compares connectivity of two molecules (using MoleculeGraph w/ OpenBabelNN). This function will work with two molecules with different atom orderings,
but for proper treatment, atoms should be listed in the same order.
Possible outputs include: - no_change: the bonding in the two molecules is identical - unconnected_fragments: the MoleculeGraph of mol1 is connected, but the
MoleculeGraph is mol2 is not connected
fewer_bonds: the MoleculeGraph of mol1 has more bonds (edges) than the MoleculeGraph of mol2
more_bonds: the MoleculeGraph of mol2 has more bonds (edges) than the MoleculeGraph of mol1
bond_change: this case catches any other non-identical MoleculeGraphs
- Parameters
mol1 – Pymatgen Molecule object to be compared.
mol2 – Pymatgen Molecule object to be compared.
- Returns
One of [“unconnected_fragments”, “fewer_bonds”, “more_bonds”, “bond_change”, “no_change”]