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topology #

Utilities for manipulating OpenFF topology objects.

Functions:

topology_to_components #

topology_to_components(
    topology: Topology,
) -> list[tuple[str, int]]

A helper method for condensing a topology down to a list of components and their counts.

Notes

If the topology is not contiguous then the returned list may contain multiple tuples with the same smiles but different counts.

Parameters:

  • topology (Topology) –

    The topology to condense.

Returns:

  • list[tuple[str, int]] –

    A list of the form components[i] = (smiles_i, count_i) where smiles_i is the SMILES representation of component i and count_i is the number of corresponding instances of that component to create.

Source code in absolv/utils/topology.py 
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def topology_to_components(topology: openff.toolkit.Topology) -> list[tuple[str, int]]:
    """A helper method for condensing a topology down to a list of components
    and their counts.

    Notes:
        If the topology is not contiguous then the returned list may contain multiple
        tuples with the same smiles but different counts.

    Args:
        topology: The topology to condense.

    Returns:
        A list of the form ``components[i] = (smiles_i, count_i)`` where
        ``smiles_i`` is the SMILES representation of component `i` and
        ``count_i`` is the number of corresponding instances of that component
        to create.
    """
    components = []

    current_smiles = None
    current_count = 0

    for molecule in topology.molecules:
        smiles = molecule.to_smiles()

        if smiles == current_smiles:
            current_count += 1
            continue

        if current_count > 0:
            components.append((current_smiles, current_count))

        current_smiles = smiles
        current_count = 1

    if current_count > 0:
        components.append((current_smiles, current_count))

    return components