qcorr_utils

check_isomerization(isom_data, file)

Inputs two molecules with the atoms in the same order and checks if any bond is too different between them.

Bonds are considered when the distance between two atoms is smaller than either the sum of their adjusted VDW radii or covalent radii (dist = n*R1 + n*R2, where n is a user defined parameter).

Bonds forming part of TSs are removed.

Parameters

isom_datadict

Contains data related to coordinates, atoms and connectivity for input and output files

filestring

Filename (with extension)

Returns

isomerizedbool

True if there is a clearly distorted bond within the geometries

detect_linear(errortype, atom_types, cclib_data)

Check whether a linear molecule contain the right number of frequencies

full_check(w_dir_main='/home/docs/checkouts/readthedocs.org/user_builds/aqme/checkouts/1.7.1/docs', destination_fullcheck='', files='*.json', log=None)

Checks that multiple calculations were done following the same protocols, including program and version, grid size, level of theory, dispersion and solvation model.

Parameters

w_dir_mainstr

Working directory

destination_fullcheckstr

Destination to create the file with the full check

fileslist of str

json files to compare (glob.glob('.json') and '.json are both valid inputs to include all the json files from a folder)

logaqme.utils.Logger

Logging instance where the status of the calculation will be written. If none provided it will default to aqme.utils.Logger('QCORR','fullcheck') and it will create the file QCORR_fullcheck.dat in the working directory.

gen_connectivity(isom_data, atom_types_conn, COORDINATES_conn)

Use VDW radii to infer a connectivity matrix

get_cclib_params(cclib_data, errortype)

Retrieve energy and rotational constant information from cclib dictionaries

get_json_data(self, file, cclib_data)

Get metadata and GoodVibes data for the json file (for older versions of cclib)