pymatgen.io.qchem.outputs module

Parsers for Qchem output files.

class QCOutput(filename: str)

Bases: MSONable

Class to parse QChem output files.

Parameters:

filename (str) – Filename to parse

as_dict()

Returns:

MSONAble dict.

static multiple_outputs_from_file(cls, filename, keep_sub_files=True)

Parses a QChem output file with multiple calculations # 1.) Separates the output into sub-files

e.g. qcout -> qcout.0, qcout.1, qcout.2 … qcout.N a.) Find delimiter for multiple calculations b.) Make separate output sub-files

2.) Creates separate QCCalcs for each one from the sub-files

check_for_structure_changes(mol1: Molecule, mol2: Molecule) → str

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”]

get_percentage(line: str, orbital: str) → str

Retrieve the percent character of an orbital.

Parameters:

• line – Line containing orbital and percentage.

• orbital – Type of orbital (s, p, d, f).

Returns:

Percentage of character.

Raises:

n/a –

jump_to_header(lines: list[str], header: str) → list[str]

Given a list of lines, truncate the start of the list so that the first line of the new list contains the header.

Parameters:

• lines – List of lines.

• header – Substring to match.

Returns:

Truncated lines.

Raises:

RuntimeError –

nbo_parser(filename: str) → dict[str, list[pandas.core.frame.DataFrame]]

Parse all the important sections of NBO output.

Parameters:

filename – Path to QChem NBO output.

Returns:

Data frames of formatted output.

Raises:

RuntimeError –

parse_hybridization_character(lines: list[str]) → list[pandas.core.frame.DataFrame]

Parse the hybridization character section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frames of formatted output.

Raises:

RuntimeError –

parse_natural_populations(lines: list[str]) → list[pandas.core.frame.DataFrame]

Parse the natural populations section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frame of formatted output.

Raises:

RuntimeError –

parse_perturbation_energy(lines: list[str]) → list[pandas.core.frame.DataFrame]

Parse the perturbation energy section of NBO output.

Parameters:

lines – QChem output lines.

Returns:

Data frame of formatted output.

Raises:

RuntimeError –

z_int(string: str) → int

Convert string to integer. If string empty, return -1.

Parameters:

string – Input to be cast to int.

Returns:

Int representation.

Raises:

n/a –