utils.py

def _cclib_to_cjson_basis(basis):
    shell_type_map = {
        "s": 0,
        "p": 1,
        "d": 2,
        "f": 3,
        "g": 4,
        "h": 5,
        "i": 6,
        "k": 7,
        "l": 8,
        "m": 9,
        "n": 10,
        "o": 11,
    }
    coefficients = []
    exponents = []
    primitives_per_shell = []
    shell_to_atom_map = []
    shell_types = []
    for i_atom, atom_basis in enumerate(basis):
        for shell in atom_basis:
            l_label, primitives = shell
            n_primitives = len(primitives)
            shell_to_atom_map.append(i_atom)
            primitives_per_shell.append(n_primitives)
            shell_types.append(shell_type_map[l_label.lower()])
            for primitive in primitives:
                exponents.append(primitive[0])
                coefficients.append(primitive[1])
    cjson_basis = {
        "coefficients": coefficients,
        "exponents": exponents,
        "primitivesPerShell": primitives_per_shell,
        "shellToAtomMap": shell_to_atom_map,
        "shellTypes": shell_types,
    }
    return cjson_basis


def _cclib_to_cjson_mocoeffs(coeffs):
    cjson_coeffs = []
    # only take the orbitals at the end of the optimization
    for mo in coeffs[-1]:
        cjson_coeffs.extend(mo)
    return cjson_coeffs


def _cclib_to_cjson_vibdisps(vibdisps):
    cjson_vibdisps = []
    for vibdisp in vibdisps:
        cjson_vibdisps.append(list(vibdisp.flatten()))
    return cjson_vibdisps


def _cleanup_cclib_cjson(cjson):
    if "orbitals" in cjson["atoms"]:
        del cjson["atoms"]["orbitals"]
    if "properties" in cjson:
        del cjson["properties"]
    if "vibrations" in cjson:
        del cjson["vibrations"]
    if "optimization" in cjson:
        del cjson["optimization"]
    if "diagram" in cjson:
        del cjson["diagram"]
    if "inchi" in cjson:
        del cjson["inchi"]
    if "inchikey" in cjson:
        del cjson["inchikey"]
    if "smiles" in cjson:
        del cjson["smiles"]

    return cjson