Skip to content

setup #

Setup systems ready for calculations.

Functions:

  • setup_system –

    Generate a set of molecule coordinate by using the PACKMOL package.

setup_system #

setup_system(
    components: list[tuple[str, int]],
    box_target_density: Quantity = 0.95 * _G_PER_ML,
    box_scale_factor: float = 1.1,
    box_padding: Quantity = 2.0 * openmm.unit.angstrom,
    tolerance: Quantity = 2.0 * openmm.unit.angstrom,
) -> tuple[Topology, Quantity]

Generate a set of molecule coordinate by using the PACKMOL package.

Parameters:

  • components (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.

  • box_target_density (Quantity, default: 0.95 * _G_PER_ML ) –

    Target mass density when approximating the box size for the final system with units compatible with g / mL.

  • box_scale_factor (float, default: 1.1 ) –

    The amount to scale the approximate box size by.

  • box_padding (Quantity, default: 2.0 * angstrom ) –

    The amount of extra padding to add to the box size to avoid PBC issues in units compatible with angstroms.

  • tolerance (Quantity, default: 2.0 * angstrom ) –

    The minimum spacing between molecules during packing in units compatible with angstroms.

Returns:

  • tuple[Topology, Quantity] –

    A topology containing the molecules the coordinates were generated for and a unit [A] wrapped numpy array of coordinates with shape=(n_atoms, 3).

Source code in absolv/setup.py 
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
def setup_system(
    components: list[tuple[str, int]],
    box_target_density: openmm.unit.Quantity = 0.95 * _G_PER_ML,
    box_scale_factor: float = 1.1,
    box_padding: openmm.unit.Quantity = 2.0 * openmm.unit.angstrom,
    tolerance: openmm.unit.Quantity = 2.0 * openmm.unit.angstrom,
) -> tuple[openff.toolkit.Topology, openmm.unit.Quantity]:
    """Generate a set of molecule coordinate by using the PACKMOL package.

    Args:
        components: 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.
        box_target_density: Target mass density when approximating the box size for the
            final system with units compatible with g / mL.
        box_scale_factor: The amount to scale the approximate box size by.
        box_padding: The amount of extra padding to add to the box size to avoid PBC
            issues in units compatible with angstroms.
        tolerance: The minimum spacing between molecules during packing in units
             compatible with angstroms.

    Returns:
        A topology containing the molecules the coordinates were generated for and
        a unit [A] wrapped numpy array of coordinates with shape=(n_atoms, 3).
    """

    packmol_path = shutil.which("packmol")

    if packmol_path is None:
        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), "packmol")

    box_size = (
        _approximate_box_size_by_density(components, box_target_density)
        * box_scale_factor
    )

    molecules = {}

    for smiles, _ in components:
        if smiles in molecules:
            continue

        molecule = openff.toolkit.Molecule.from_smiles(smiles)
        molecule.generate_conformers(n_conformers=1)
        molecule.name = f"component-{len(molecules)}.xyz"
        molecules[smiles] = molecule

    with openff.utilities.temporary_cd():
        for molecule in molecules.values():
            molecule.to_file(molecule.name, "xyz")

        input_file_contents = _generate_input_file(
            [(molecules[smiles].name, count) for smiles, count in components],
            box_size,
            tolerance,
        )

        with open("input.txt", "w") as file:
            file.write(input_file_contents)

        with open("input.txt") as file:
            subprocess.run(packmol_path, stdin=file, check=True, capture_output=True)

        with open("output.xyz") as file:
            output_lines = file.read().splitlines(False)

    coordinates = (
        numpy.array(
            [
                [float(coordinate) for coordinate in coordinate_line.split()[1:]]
                for coordinate_line in output_lines[2:]
                if len(coordinate_line) > 0
            ]
        )
        * openmm.unit.angstrom
    )

    topology = openff.toolkit.Topology.from_molecules(
        [molecules[smiles] for smiles, count in components for _ in range(count)]
    )
    topology.box_vectors = numpy.eye(3) * (box_size + box_padding)

    return topology, coordinates