Skip to content

system #

Utilities for preparing and modifying OpenMM systems.

Functions:

  • load_ligand –

    Load a ligand from its coordinate and parameter definition.

  • load_ligands –

    Load the first, and optionally second, ligand from their coordinates and

  • load_receptor –

    Loads a receptor from its coordinates and optionally parameters.

  • apply_hmr –

    Apply hydrogen mass repartitioning to a system.

load_ligand #

load_ligand(
    coord_path: Path,
    param_path: Path,
    residue_name: str | None = None,
) -> AmberParm

Load a ligand from its coordinate and parameter definition.

Parameters:

  • coord_path (Path) –

    The path to the ligand coordinate file (.rst7 / .mol2)

  • param_path (Path) –

    The path to the ligand parameter file (.parm7)

  • residue_name (str | None, default: None ) –

    The (optional) residue name to assign to the ligand.

Returns:

Source code in femto/md/system.py 
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
def load_ligand(
    coord_path: pathlib.Path, param_path: pathlib.Path, residue_name: str | None = None
) -> parmed.amber.AmberParm:
    """Load a ligand from its coordinate and parameter definition.

    Args:
        coord_path: The path to the ligand coordinate file (.rst7 / .mol2)
        param_path: The path to the ligand parameter file (.parm7)
        residue_name: The (optional) residue name to assign to the ligand.

    Returns:
        The loaded ligand
    """

    ligand = parmed.amber.AmberParm(str(param_path), str(coord_path))

    for residue in ligand.residues:
        residue.name = residue_name

    ligand.parm_data["RESIDUE_LABEL"] = [residue_name]

    return ligand

load_ligands #

load_ligands(
    ligand_1_coords: Path,
    ligand_1_params: Path,
    ligand_2_coords: Path | None,
    ligand_2_params: Path | None,
) -> tuple[AmberParm, AmberParm | None]

Load the first, and optionally second, ligand from their coordinates and parameters.

Parameters:

  • ligand_1_coords (Path) –

    The coordinates of the first ligand.

  • ligand_1_params (Path) –

    The parameters of the first ligand.

  • ligand_2_coords (Path | None) –

    The (optional) coordinates of the second ligand.

  • ligand_2_params (Path | None) –

    The (optional) parameters of the second ligand.

Returns:

Source code in femto/md/system.py 
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
def load_ligands(
    ligand_1_coords: pathlib.Path,
    ligand_1_params: pathlib.Path,
    ligand_2_coords: pathlib.Path | None,
    ligand_2_params: pathlib.Path | None,
) -> tuple[parmed.amber.AmberParm, parmed.amber.AmberParm | None]:
    """Load the first, and optionally second, ligand from their coordinates and
    parameters.

    Args:
        ligand_1_coords: The coordinates of the first ligand.
        ligand_1_params: The parameters of the first ligand.
        ligand_2_coords: The (optional) coordinates of the second ligand.
        ligand_2_params: The (optional) parameters of the second ligand.

    Returns:
        The loaded ligands.
    """

    assert (ligand_2_params is None and ligand_2_coords is None) or (
        ligand_2_params is not None and ligand_2_coords is not None
    ), "both or neither of ligand_2_coords and ligand_2_params must be provided"

    ligand_1 = load_ligand(ligand_1_coords, ligand_1_params, LIGAND_1_RESIDUE_NAME)

    if ligand_2_coords is None:
        return ligand_1, None

    ligand_2 = load_ligand(ligand_2_coords, ligand_2_params, LIGAND_2_RESIDUE_NAME)

    return ligand_1, ligand_2

load_receptor #

load_receptor(
    coord_path: Path,
    param_path: Path | None,
    tleap_sources: list[str] | None = None,
) -> AmberParm

Loads a receptor from its coordinates and optionally parameters.

If no parameters are provided, the receptor will be parameterized using tLeap.

Parameters:

  • coord_path (Path) –

    The coordinates of the receptor.

  • param_path (Path | None) –

    The parameters of the receptor.

  • tleap_sources (list[str] | None, default: None ) –

    The tLeap sources to use to parameterize the receptor. See femto.md.config.DEFAULT_TLEAP_SOURCES for the defaults.

Returns:

Source code in femto/md/system.py 
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
def load_receptor(
    coord_path: pathlib.Path,
    param_path: pathlib.Path | None,
    tleap_sources: list[str] | None = None,
) -> parmed.amber.AmberParm:
    """Loads a receptor from its coordinates and optionally parameters.

    If no parameters are provided, the receptor will be parameterized using tLeap.

    Args:
        coord_path: The coordinates of the receptor.
        param_path: The parameters of the receptor.
        tleap_sources: The tLeap sources to use to parameterize the receptor.
            See ``femto.md.config.DEFAULT_TLEAP_SOURCES`` for the defaults.

    Returns:
        The loaded receptor.
    """
    tleap_sources = (
        femto.md.config.DEFAULT_TLEAP_SOURCES
        if tleap_sources is None
        else tleap_sources
    )

    if param_path is not None:
        return parmed.amber.AmberParm(str(param_path), str(coord_path))

    receptor = parmed.load_file(str(coord_path), structure=True)

    _LOGGER.info(
        f"no receptor parameters provided, the receptor will parameterize using "
        f"tLeap: {tleap_sources}"
    )
    return femto.md.utils.amber.parameterize_structure(receptor, tleap_sources)

apply_hmr #

apply_hmr(
    system: System,
    topology: Structure,
    hydrogen_mass: Quantity = 1.5 * openmm.unit.amu,
)

Apply hydrogen mass repartitioning to a system.

Parameters:

  • system (System) –

    The system to modify in-place.

  • topology (Structure) –

    The topology of the system.

  • hydrogen_mass (Quantity, default: 1.5 * amu ) –

    The mass to use ofr hydrogen atoms.

Source code in femto/md/system.py 
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
def apply_hmr(
    system: openmm.System,
    topology: parmed.Structure,
    hydrogen_mass: openmm.unit.Quantity = 1.5 * openmm.unit.amu,
):
    """Apply hydrogen mass repartitioning to a system.

    Args:
        system: The system to modify in-place.
        topology: The topology of the system.
        hydrogen_mass: The mass to use ofr hydrogen atoms.
    """

    for bond in topology.bonds:
        atom_1, atom_2 = bond.atom1, bond.atom2

        if atom_1.atomic_number == 1:
            (atom_1, atom_2) = (atom_2, atom_1)

        if atom_2.atomic_number != 1:
            continue
        if atom_1.atomic_number == 1:
            continue

        elements = sorted(a.atomic_number for a in atom_2.residue.atoms)

        if elements == [1, 1, 8]:
            continue

        mass_delta = hydrogen_mass - system.getParticleMass(atom_2.idx)

        system.setParticleMass(atom_2.idx, hydrogen_mass)
        system.setParticleMass(
            atom_1.idx, system.getParticleMass(atom_1.idx) - mass_delta
        )