Skip to content

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 
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
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

topology_to_atom_indices #

topology_to_atom_indices(
    topology: Topology,
) -> list[set[int]]

A helper method for extracting the sets of atom indices associated with each molecule in a topology.

Parameters:

  • topology (Topology) –

    The topology to extract the atom indices from.

Returns:

  • list[set[int]] –

    The set of atoms indices associated with each molecule in the topology.

Source code in absolv/utils/topology.py 
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
def topology_to_atom_indices(topology: openff.toolkit.Topology) -> list[set[int]]:
    """A helper method for extracting the sets of atom indices associated with each
    molecule in a topology.

    Args:
        topology: The topology to extract the atom indices from.

    Returns:
        The set of atoms indices associated with each molecule in the topology.
    """

    atom_indices: list[set[int]] = []
    current_atom_idx = 0

    for molecule in topology.molecules:
        atom_indices.append({i + current_atom_idx for i in range(molecule.n_atoms)})
        current_atom_idx += molecule.n_atoms

    return atom_indices