Source code for sire.morph._hmr

__all__ = ["repartition_hydrogen_masses"]

[docs] def repartition_hydrogen_masses( mols, mass_factor=1.5, ignore_water: bool = False, ignore_non_water: bool = False, include_end_states: bool = True, map=None, ): """ Increase the mass of hydrogen atoms to hmass times * amu, and subtract the mass increase from the heavy atom the hydrogen is bonded to. (based heavily on the repartitionMasses function in Sire.Tools.OpenMMMD) Parameters ---------- mol : sire.mol.Molecule or list of molecules, or System The molecule(s) whose hydrogen masses should be repartitioned mass_factor : float The factor to multiply the mass of hydrogen atoms by. Using the default of 1.5 is known to be a good value to use to achieve a 4 fs timestep with the (default) LangevinMiddle integrator ignore_water : bool Whether or not to ignore water molecules (default False) ignore_non_water : bool Whether or not to ignore non-water molecules (default False) include_end_states : bool Whether or not to repartition the masses of the end states of perturbable molecules (default True) (i.e. this will automatically repartition `mass0` and `mass1` in addition to `mass`) map : dict The property map used to identify molecular properties Returns ------- sire.mol.Molecule, list of molecules or System The repartitioned molecule(s) """ try: from ..legacy.IO import ( repartitionHydrogenMass as _repartition_hydrogen_mass, ) except Exception: from ..legacy.IO import ( repartition_hydrogen_mass as _repartition_hydrogen_mass, ) if ignore_water and ignore_non_water: # ignoring everything ;-) return mols from ..base import create_map map = create_map(map) # convert the flag into the integer defined in the BioSimSpace function if ignore_water: water = 0 elif ignore_non_water: water = 2 else: water = 1 mols = mols.clone() for mol in mols.molecules(): mol = _repartition_hydrogen_mass(mol, mass_factor, water, map) if include_end_states: mass0 = f"{map['mass'].source()}0" mass1 = f"{map['mass'].source()}1" if mol.has_property(mass0): map0 = map.clone() map0.set("mass", mass0) mol = _repartition_hydrogen_mass(mol, mass_factor, water, map0) if mol.has_property(mass1): map1 = map.clone() map1.set("mass", mass1) mol = _repartition_hydrogen_mass(mol, mass_factor, water, map1) mols.update(mol) return mols