def setup_yank_calculation(receptor_file_name,
ligand_file_name,
setup_directory_name,
solvate=False):
# Cleanup setup directory
if os.path.exists(setup_directory_name):
shutil.rmtree(setup_directory_name)
os.makedirs(setup_directory_name)
# Read ligand and receptor molecule
ifs_mol2 = oechem.oemolistream()
ifs_mol2.open(ligand_file_name)
ligand_oemol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs_mol2, ligand_oemol)
ifs_mol2.close()
ifs_mol2 = oechem.oemolistream()
ifs_mol2.open(receptor_file_name)
receptor_oemol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs_mol2, receptor_oemol)
ifs_mol2.close()
# Push ligand close to receptor
pull_close(receptor_oemol, ligand_oemol, MIN_DISTANCE, MAX_DISTANCE)
# Add residue name 'MOL'
residue = oechem.OEResidue()
residue.SetName('MOL')
for atom in ligand_oemol.GetAtoms():
oechem.OEAtomSetResidue(atom, residue)
# Parametrize ligand
with working_directory(setup_directory_name):
# Save translated ligand
ofs = oechem.oemolostream()
ofs.open('ligand.mol2')
oechem.OEWriteMolecule(ofs, ligand_oemol)
ofs.close()
# Parametrize ligand
print "Parameterizing ligand with GAFF..."
run_command(
'antechamber -fi mol2 -i ligand.mol2 -fo mol2 -o ligand.gaff.mol2')
run_command(
'parmchk -i ligand.gaff.mol2 -o ligand.gaff.frcmod -f mol2')
# Copy receptor so that leap will know the PDB file name
shutil.copyfile(receptor_file_name, 'receptor.pdb')
# Create AMBER prmtop/inpcrd files.
print "Creating AMBER prmtop/inpcrd files..."
cmd = 'tleap -f {!s} > setup.leap.out'
if solvate:
run_command(cmd.format(LEAP_IN_EXPLICIT))
else:
run_command(cmd.format(LEAP_IN_IMPLICIT))
def PrintResidues(mol):
"""list alternate location code and occupancy by group and residue"""
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
print("%s - %d alternate location groups:" %
(mol.GetTitle(), alf.GetGroupCount()))
for grp in alf.GetGroups():
print("%d) %d alternate locations" %
(grp.GetGroupID() + 1, grp.GetLocationCount()),
end=" ")
prev = oechem.OEResidue()
prevCodes = ""
sumOcc = []
atNum = []
for atom in alf.GetAltAtoms(grp):
res = oechem.OEAtomGetResidue(atom)
if not oechem.OESameResidue(res, prev):
for i, code in enumerate(prevCodes):
print("%c(%.0f%c) " %
(code, (sumOcc[i] * 100.0) / atNum[i], "%"),
end=" ")
print()
prevCodes = ""
sumOcc = []
atNum = []
print("\t%s%d%c chain '%c': " %
(res.GetName(), res.GetResidueNumber(),
res.GetInsertCode(), res.GetChainID()),
end=" ")
prev = res
code = res.GetAlternateLocation()
whichCode = prevCodes.find(code)
if whichCode < 0:
prevCodes += code
sumOcc.append(res.GetOccupancy())
atNum.append(1)
else:
sumOcc[whichCode] += res.GetOccupancy()
atNum[whichCode] += 1
for i, code in enumerate(prevCodes):
print("%c(%.0f%c) " % (code, (sumOcc[i] * 100.0) / atNum[i], "%"),
end=" ")
print()
def CalcResCounts(mol):
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
resCt = 0
hetCt = 0
prevRes = oechem.OEResidue()
for atom in mol.GetAtoms():
thisRes = oechem.OEAtomGetResidue(atom)
if not oechem.OESameResidue(prevRes, thisRes):
resCt += 1
if thisRes.IsHetAtom():
hetCt += 1
prevRes = thisRes
print("Molecule: %s" % mol.GetTitle())
print("Residues: %d (%d hets)" % (resCt, hetCt))
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# in our example, we will select the first histidine
selectedResidue = oechem.OEResidue()
for atom in mol.GetAtoms():
res = oechem.OEAtomGetResidue(atom)
if oechem.OEGetResidueIndex(res) == oechem.OEResidueIndex_HIS:
selectedResidue = res
break
# @ <SNIPPET-PLACE-HYDROGENS-PRED>
# given predicate IsSameResidue, residue selectedResidue and molecule mol...
opt = oechem.OEPlaceHydrogensOptions()
opt.SetNoFlipPredicate(IsSameResidue(selectedResidue))
if oechem.OEPlaceHydrogens(mol, opt):
# selectedResidue will not be flipped...
# @ </SNIPPET-PLACE-HYDROGENS-PRED>
print("success")
ims.close()
def openmmTop_to_oemol(topology, positions, verbose=False):
"""
This function converts an OpenMM topology in an OEMol
Parameters:
-----------
topology : OpenMM Topology
The OpenMM topology
positions : OpenMM Quantity
The molecule atom positions associated with the
topology
Return:
-------
oe_mol : OEMol
The generated OEMol molecule
"""
# Create an empty OEMol
oe_mol = oechem.OEMol()
# Mapping dictionary between openmm atoms and oe atoms
openmm_atom_to_oe_atom = {}
# Python set used to identify atoms that are not in protein residues
keep = set(proteinResidues).union(dnaResidues).union(rnaResidues)
for chain in topology.chains():
for res in chain.residues():
# Create an OEResidue
oe_res = oechem.OEResidue()
# Set OEResidue name
oe_res.SetName(res.name)
# If the atom is not a protein atom then set its heteroatom
# flag to True
if res.name not in keep:
oe_res.SetFragmentNumber(chain.index + 1)
oe_res.SetHetAtom(True)
# Set OEResidue Chain ID
oe_res.SetChainID(chain.id)
# res_idx = int(res.id) - chain.index * len(chain._residues)
# Set OEResidue number
oe_res.SetResidueNumber(int(res.id))
for openmm_at in res.atoms():
# Create an OEAtom based on the atomic number
oe_atom = oe_mol.NewAtom(openmm_at.element._atomic_number)
# Set atom name
oe_atom.SetName(openmm_at.name)
# Set Symbol
oe_atom.SetType(openmm_at.element.symbol)
# Set Atom index
oe_res.SetSerialNumber(openmm_at.index + 1)
# Commit the changes
oechem.OEAtomSetResidue(oe_atom, oe_res)
# Update the dictionary OpenMM to OE
openmm_atom_to_oe_atom[openmm_at] = oe_atom
if topology.getNumAtoms() != oe_mol.NumAtoms():
raise ValueError(
"OpenMM topology and OEMol number of atoms mismatching: "
"OpenMM = {} vs OEMol = {}".format(topology.getNumAtoms(),
oe_mol.NumAtoms()))
# Count the number of bonds in the openmm topology
omm_bond_count = 0
# Create the bonds
for omm_bond in topology.bonds():
omm_bond_count += 1
at0 = omm_bond[0]
at1 = omm_bond[1]
oe_bond_order = omm_bond.order
# If bond order info are not present set the bond order temporary to one
if not omm_bond.order:
oe_bond_order = 1
# OE atoms
oe_atom0 = openmm_atom_to_oe_atom[at0]
oe_atom1 = openmm_atom_to_oe_atom[at1]
# Create the bond
oe_bond = oe_mol.NewBond(oe_atom0, oe_atom1, oe_bond_order)
if omm_bond.type:
if omm_bond.type == 'Aromatic':
oe_atom0.SetAromatic(True)
oe_atom1.SetAromatic(True)
oe_bond.SetAromatic(True)
oe_bond.SetType("Aromatic")
elif omm_bond.type in ["Single", "Double", "Triple", "Amide"]:
oe_bond.SetType(omm_bond.type)
else:
oe_bond.SetType("")
if omm_bond_count != oe_mol.NumBonds():
raise ValueError(
"OpenMM topology and OEMol number of bonds mismatching: "
"OpenMM = {} vs OEMol = {}".format(omm_bond_count,
oe_mol.NumBonds()))
# Set the OEMol positions
pos = positions.in_units_of(unit.angstrom) / unit.angstrom
pos = list(itertools.chain.from_iterable(pos))
oe_mol.SetCoords(pos)
oechem.OESetDimensionFromCoords(oe_mol)
return oe_mol