createFragments

Included in QATK.Surfaces

createFragments(configuration, template, fuzz_factor=1.1, filter_by_graphs=False, terminal_fragments=True)

Create fragments from a configuration based on a template configuration.

Parameters:

• configuration (MoleculeConfiguration | BulkConfiguration) – The configuration from which to create fragments.

• template (MoleculeConfiguration) – The template configuration to use for fragmenting the molecule.

• fuzz_factor (float) – A factor to adjust the bond length tolerance for matching atoms.

• filter_by_graphs (bool) – If True, filter out fragment pairs with identical main fragment graphs. Note that this does not take into account the point group symmetry of the fragments.

• terminal_fragments (bool) – If True, only return fragments that are terminal, i.e., cases where the template is not part of the central part of the configuration and does not split the configuration into multiple disconnected parts.

Returns:

A list of lists, where each sublist contains the main fragment and its corresponding sub fragment. The configuration type of the fragments is the same as the input configuration.

Return type:

list of lists