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 _restrain_backbone(system):
"""Restrain protein backbone atoms.
Parameters
----------
system : Sire.System.System
A Sire molecular system.
"""
# Copy the original system.
s = system
# A list of amino acid name abbreviations.
# Since we only want to restrain atoms in protein backbones, we compare
# molecule residue names against this list in order to determine whether
# the molecule is a protein.
amino_acids = ["ALA", "CYS", "ASP", "GLU", "PHE", "GLY", "HIS", "ILE",
"LYS", "LEU", "MET", "ASN", "PRO", "GLN", "ARG", "SER", "THR", "SEC",
"VAL", "TRP", "TYR"]
# Loop over all molecules by number.
for n in s.molNums():
# Extract the molecule and make it editable.
m = s.molecule(n).edit()
# Initialise a list of protein residues.
protein_residues = []
# Compare each residue name against the amino acid list.
for res in m.residues():
# This residue is an amino acid.
if res.name().value().upper() in amino_acids:
protein_residues.append(res.index())
# Loop over all of the protein residues.
for residx in protein_residues:
# Loop over all of the atoms in the residue.
for atom in m.residue(residx).atoms():
# Try to compare the atom element property against the list of
# backbone atoms and set the "restrained" property if a match
# is found.
try:
element = atom.property("element")
if element == _SireMol.Element("CA") or \
element == _SireMol.Element("N") or \
element == _SireMol.Element("C") or \
element == _SireMol.Element("O"):
m = m.atom(atom.index()).setProperty("restrained", 1.0).molecule()
except:
pass
# Update the system.
s.update(m.commit())
# Return the new system.
return s
