def __init__(self, resname):
super().__init__(_SireMol.ResName(resname))
def _rename_water_molecule(molecule):
"""Internal function to rename residues/atoms in a water molecule to match
the naming conventions used by GROMACS.
Parameters
----------
molecule : Sire.Mol.Molecule
A Sire Molecule object.
Returns
-------
molecule : Sire.Mol.Molecule
The updated Sire Molecule object.
"""
# Make the molecule editable.
molecule = molecule.edit()
# In GROMACS, all water molecules must be given the residue label "SOL".
# We extract all of the waters from the system and relabel the
# residues as appropriate.
#
# We need to work out what to do if existing water molecules don't contain
# all of the required atoms, e.g. if we have crystal water oxygen sites
# from a PDB file, or if the system is to be solvated with a 4- or 5-point
# water model (where we need to add virtual sites).
# Update the molecule with the new residue name.
molecule = molecule.residue(_SireMol.ResIdx(0)) \
.rename(_SireMol.ResName("SOL")) \
.molecule()
# Index for the hydrogen atoms.
hydrogen_idx = 1
# Gromacs water models use HW1/HW2 for hydrogen atoms at OW for water.
for atom in molecule.atoms():
try:
# Hydrogen.
if atom.property("element") == _SireMol.Element("H"):
molecule = molecule.atom(atom.number()) \
.rename(_SireMol.AtomName("HW%d" % hydrogen_idx)) \
.molecule()
hydrogen_idx += 1
# Oxygen.
elif atom.property("element") == _SireMol.Element("O"):
molecule = molecule.atom(atom.number()) \
.rename(_SireMol.AtomName("OW")) \
.molecule()
# Otherwise, try to infer the element from the atom name.
except:
# Strip all digits from the name.
name = "".join([x for x in atom.name().value() if not x.isdigit()])
# Remove any whitespace.
name = name.replace(" ", "")
# Try to infer the element.
element = _SireMol.Element.biologicalElement(name)
# Hydrogen.
if element == _SireMol.Element("H"):
molecule = molecule.atom(atom.number()) \
.rename(_SireMol.AtomName("HW%d" % hydrogen_idx)) \
.molecule()
hydrogen_idx += 1
# Oxygen.
elif element == _SireMol.Element("O"):
molecule = molecule.atom(atom.number()) \
.rename(_SireMol.AtomName("OW")) \
.molecule()
# Commit and return the updated molecule.
return molecule.commit()
def rescaleSystemParams(system,
scale,
includelist=None,
excludelist=None,
neutralise=True):
"""
Rescales charge, Lennard-Jones and dihedral parameters for REST(2).
Parameters
----------
system : BioSimSpace.System
Input system to be rescaled.
scale : float
Multiplication factor for the charge, Lennard-Jones and dihedral parameters. 0 < scale < 1.
includelist : [str]
Molecule names to be included in the rescaling. Default: None.
excludelist : [str]
Molecule names to be excluded in the rescaling. Default: ["WAT"].
neutralise : bool
Whether to rescale a minimum number of Na+ or Cl- ions so that the rescaled part of the system is neutralised.
Returns
-------
system_new : BioSimSpace.System
The rescaled system.
"""
if excludelist is None and includelist is None:
excludelist = ["WAT"]
elif excludelist is not None and includelist is not None:
raise ValueError("Only one of includelist and excludelist can be set")
if neutralise:
if excludelist is not None:
total_charge = round(
sum([
mol.charge().magnitude() for mol in system.getMolecules()
if mol._sire_object.name().value() not in excludelist
]))
elif includelist is not None:
total_charge = round(
sum([
mol.charge().magnitude() for mol in system.getMolecules()
if mol._sire_object.name().value() in includelist
]))
mols_mod = []
for mol in system.getMolecules():
if neutralise and mol._sire_object.name().value().lower(
) == "na" and total_charge < 0:
total_charge += 1
elif neutralise and mol._sire_object.name().value().lower(
) == "cl" and total_charge > 0:
total_charge -= 1
elif excludelist is not None:
if mol._sire_object.name().value() in excludelist:
mols_mod += [mol]
continue
elif includelist is not None:
if mol._sire_object.name().value() not in includelist:
mols_mod += [mol]
continue
mol_edit = mol._sire_object.edit()
if scale != 1:
for prop in [
"dihedral", "dihedral0", "dihedral1", "improper",
"improper0", "improper1"
]:
try:
potentials = mol_edit.property(prop).potentials()
prop_new = _SireMM.FourAtomFunctions(mol_edit.info())
for potential in potentials:
prop_new.set(potential.atom0(), potential.atom1(),
potential.atom2(), potential.atom3(),
potential.function() * scale)
mol_edit = mol_edit.setProperty(prop, prop_new).molecule()
except:
continue
for atom in mol_edit.atoms():
idx = atom.index()
for prop in ["atomtype", "atomtype0", "atomtype1"]:
try:
atomtype_new = atom.property(prop) + "_"
mol_edit = mol_edit.atom(idx).setProperty(
prop, atomtype_new).molecule()
except:
continue
if scale != 1:
for prop in ["LJ", "LJ0", "LJ1"]:
try:
LJ = atom.property(prop)
LJ = LJ.fromSigmaAndEpsilon(LJ.sigma(),
LJ.epsilon() * scale)
mol_edit = mol_edit.atom(idx).setProperty(
prop, LJ).molecule()
except:
continue
for prop in ["charge", "charge0", "charge1"]:
try:
charge = atom.property(prop)
charge = charge * scale
mol_edit = mol_edit.atom(idx).setProperty(
prop, charge).molecule()
except:
continue
if mol._sire_object.name().value().lower() in ["na", "cl"]:
resname = mol_edit.residue().name()
resname_new = _SireMol.ResName(resname.value() + "_")
mol_edit = mol_edit.residue(resname).rename(resname_new)
mol._sire_object = mol_edit.commit()
mols_mod += [mol]
system_new = _BSS._SireWrappers._system.System(mols_mod)
box = system._sire_object.property("space")
system_new._sire_object.setProperty("space", box)
return system_new