def main(args):
if len(args) != 2:
oechem.OEThrow.Usage("%s <input>" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
oechem.OEAddExplicitHydrogens(mol)
mmff = oeff.OEMMFF()
if not mmff.PrepMol(mol) or not mmff.Setup(mol):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" %
mol.GetTitle())
continue
# print out interactions
vecCoords = oechem.OEDoubleArray(3 * mol.GetMaxAtomIdx())
mol.GetCoords(vecCoords)
oechem.OEThrow.Info("Molecule: %s" % mol.GetTitle())
for intc in mmff.GetInteractions(mol, vecCoords):
vecGrads = oechem.OEDoubleArray(intc.NumValues())
oechem.OEThrow.Info("Interaction: %s Value: %d" %
(intc.GetName(), intc.GetValues(vecGrads)))
for atom in intc.GetAtoms():
oechem.OEThrow.Info("Atom index: %d" % atom.GetIdx())
return 0
def main(args):
if len(args) != 2:
oechem.OEThrow.Usage("%s <input>" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
oechem.OEAddExplicitHydrogens(mol)
mmff = oeff.OEMMFF()
if not mmff.PrepMol(mol) or not mmff.Setup(mol):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" %
mol.GetTitle())
continue
vecCoords = oechem.OEDoubleArray(3 * mol.GetMaxAtomIdx())
mol.GetCoords(vecCoords)
for fcomp in mmff.GetFComponents(vecCoords):
oechem.OEThrow.Info(
"Molecule: %s Component: %s Energy: %d kcal/mol" %
(mol.GetTitle(), fcomp.name, fcomp.value))
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
ofs = oechem.oemolostream()
if not ofs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[2])
mmff = oeff.OEMMFF()
# Setup adaptor. The first (false) means not to pass ownership of mmff,
# and the second (false) means not to exclude interactions related
# to the subset which would be fixed for calculations.
adaptor = oeff.OETorAdaptor(mmff, False, False)
# Use a simple predicate for the subset of torsions to optimize
adaptor.Set(oechem.OEIsRotor())
mol = oechem.OEMol()
while oechem.OEReadMolecule(ifs, mol):
oechem.OEAddExplicitHydrogens(mol)
# Use a simple atoms predicate for the subset, followed by setup
if (not mmff.PrepMol(mol)) or (not adaptor.Setup(mol)):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" % mol.GetTitle())
oechem.OEWriteMolecule(ofs, mol)
continue
vecCoords = oechem.OEDoubleArray(3*mol.GetMaxAtomIdx())
for conf in mol.GetConfs():
oechem.OEThrow.Info("Molecule: %s Conformer: %d" % (mol.GetTitle(), conf.GetIdx()+1))
conf.GetCoords(vecCoords)
# Get adaptor variables set corresponding to the coordinates
vecX = oechem.OEDoubleArray(adaptor.NumVar())
adaptor.GetVar(vecX, vecCoords)
# Calculate energy using adaptor
energy = adaptor(vecX)
oechem.OEThrow.Info("Initial energy: %d kcal/mol" % energy)
# Optimize the adaptor
optimizer = oeff.OEBFGSOpt()
energy = optimizer(adaptor, vecX, vecX)
oechem.OEThrow.Info("Optimized energy: %d kcal/mol" % energy)
# Get optimized coordinates corresponding to the adaptor optimized variables
adaptor.AdaptVar(vecCoords, vecX)
conf.SetCoords(vecCoords)
oechem.OEWriteMolecule(ofs, mol)
return 0
def mmff_energy(mol):
"""
Compute MMFF energy
"""
from openeye import oechem, oeff
mol = oechem.OEGraphMol(mol)
mmff = oeff.OEMMFF()
if not mmff.PrepMol(mol) or not mmff.Setup(mol):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" % mol.GetTitle())
return None
vecCoords = oechem.OEDoubleArray(3*mol.GetMaxAtomIdx())
mol.GetCoords(vecCoords)
energy = mmff(vecCoords)
return energy
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % args[0])
ifs = oechem.oemolistream()
if not ifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
ofs = oechem.oemolostream()
if not ofs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[2])
mol = oechem.OEMol()
while oechem.OEReadMolecule(ifs, mol):
oechem.OEAddExplicitHydrogens(mol)
mmff = oeff.OEMMFF()
if not mmff.PrepMol(mol) or not mmff.Setup(mol):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" %
mol.GetTitle())
oechem.OEWriteMolecule(ofs, mol)
continue
vecCoords = oechem.OEDoubleArray(3 * mol.GetMaxAtomIdx())
for conf in mol.GetConfs():
oechem.OEThrow.Info("Molecule: %s Conformer: %d" %
(mol.GetTitle(), conf.GetIdx() + 1))
conf.GetCoords(vecCoords)
energy = mmff(vecCoords)
oechem.OEThrow.Info("Initial energy: %d kcal/mol" % energy)
optimizer = oeff.OEBFGSOpt()
energy = optimizer(mmff, vecCoords, vecCoords)
oechem.OEThrow.Info("Optimized energy: %d kcal/mol" % energy)
conf.SetCoords(vecCoords)
oechem.OEWriteMolecule(ofs, mol)
return 0
def main(args):
if len(args) != 5:
oechem.OEThrow.Usage("%s <protein> <ligand> <bound-ligand> <output>" %
args[0])
ips = oechem.oemolistream()
if not ips.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading protein" % args[1])
ils = oechem.oemolistream()
if not ils.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading ligand" % args[2])
ibs = oechem.oemolistream()
if not ibs.open(args[3]):
oechem.OEThrow.Fatal("Unable to open %s for reading bound ligand" %
args[3])
ofs = oechem.oemolostream()
if not ofs.open(args[4]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[4])
# Load the protein molecule and Prepare with MMFF
protein = oechem.OEGraphMol()
oechem.OEReadMolecule(ips, protein)
oechem.OEAddExplicitHydrogens(protein)
mmff2 = oeff.OEMMFF()
mmff = oeff.OEGenericFF(mmff2)
mmff.PrepMol(protein)
# Get bounds for protein ligand interaction
bounds = oechem.OEDoubleArray(6)
boundsMol = oechem.OEGraphMol()
oechem.OEReadMolecule(ibs, boundsMol)
GetBoundsFromMol(bounds, boundsMol, 5.0)
# Create intermolecular interaction functions and add to MMFF
params = oeff.OEMMFFParams()
interVdw = oeff.OEMMFFInterVdwNN(protein, params, bounds)
interCoul = oeff.OEMMFFInterCoulomb(protein, bounds, 1.0, 1.0, 0.5)
mmff.Add(interVdw)
mmff.Add(interCoul)
mol = oechem.OEMol()
while oechem.OEReadMolecule(ils, mol):
oechem.OEAddExplicitHydrogens(mol)
if (not mmff.PrepMol(mol)) or (not mmff.Setup(mol)):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" %
mol.GetTitle())
oechem.OEWriteMolecule(ofs, mol)
continue
vecCoords = oechem.OEDoubleArray(3 * mol.GetMaxAtomIdx())
for conf in mol.GetConfs():
oechem.OEThrow.Info("Molecule: %s Conformer: %d" %
(mol.GetTitle(), conf.GetIdx() + 1))
conf.GetCoords(vecCoords)
# Calculate energy
energy = mmff(vecCoords)
oechem.OEThrow.Info("Initial energy: %d kcal/mol" % energy)
# Optimize the ligand
optimizer = oeff.OEBFGSOpt()
energy = optimizer(mmff, vecCoords, vecCoords)
oechem.OEThrow.Info("Optimized energy: %d kcal/mol" % energy)
conf.SetCoords(vecCoords)
oechem.OEWriteMolecule(ofs, mol)
return 0