def main(args):
if len(args) != 2:
oechem.OEThrow.Usage("%s <initial guess>" % args[0])
x = oechem.OEDoubleArray(1)
try:
x[0] = float(args[1])
except ValueError:
oechem.OEThrow.Usage("%s <initial guess (expecting a number)>" %
args[0])
func = Function()
# Calculate function value at given x
value = func(x)
oechem.OEThrow.Info("Function value at x = %d is %d" % (x[0], value))
# Optimize function using BFGS Optimizer and checkpoint
xOpt = oechem.OEDoubleArray(1)
optimizer = oeff.OEBFGSOpt()
value = optimizer(func, ChkPt(), x, xOpt)
oechem.OEThrow.Info(
"Function has a minimia at x = %d and the minimum value is %d" %
(xOpt[0], value))
return 0
def minimize(self, mol):
oechem.OEAddExplicitHydrogens(mol)
if (not self.mmff.PrepMol(mol)) or (not self.mmff.Setup(mol)):
oechem.OEThrow.Warning("Unable to process molecule: title = '%s'" %
mol.GetTitle())
return None
adaptor = oeff.OEQuatAdaptor(self.mmff, False, False)
if not adaptor.Setup(mol):
oechem.OEThrow.Warning(
"Unable to process subset for molecule: title = '%s'" %
mol.GetTitle())
return None
vecCoords = oechem.OEDoubleArray(3 * mol.GetMaxAtomIdx())
mol.GetCoords(vecCoords)
vecX = oechem.OEDoubleArray(adaptor.NumVar())
adaptor.GetVar(vecX, vecCoords)
initial_energy = adaptor(vecX)
optimizer = oeff.OEBFGSOpt()
final_energy = optimizer(adaptor, vecX, vecX)
adaptor.AdaptVar(vecCoords, vecX)
mol.SetCoords(vecCoords)
return initial_energy, final_energy
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 __call__(self, x, h=None, g=None):
if isinstance(x, oechem.OEDoubleArray):
if g is not None:
g[0] = 2.0 * x[0] - 7.0 # gradient
h[0] = 2.0 # hessien
return True
elif h is not None:
h[0] = 2.0 * x[0] - 7.0 # gradient
return x[0] * x[0] - 7 * x[0] + 63
else:
return x[0] * x[0] - 7 * x[0] + 63
else:
x1 = oechem.OEDoubleArray(x, self.NumVar(), False)
if g is not None:
g1 = oechem.OEDoubleArray(g, self.NumVar(), False)
g1[0] = 2.0 * x1[0] - 7.0
h1 = oechem.OEDoubleArray(h, self.NumVar(), False)
h1[0] = 2.0
return True
elif h is not None:
h1 = oechem.OEDoubleArray(h, self.NumVar(), False)
h1[0] = 2.0 * x1[0] - 7.0
return x1[0] * x1[0] - 7 * x1[0] + 63
else:
return x1[0] * x1[0] - 7 * x1[0] + 63
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 main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData, argv)
if not itf.GetBool("-verbose"):
oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Warning)
rfname = itf.GetString("-ref")
ifname = itf.GetString("-in")
automorph = itf.GetBool("-automorph")
heavy = itf.GetBool("-heavyonly")
overlay = itf.GetBool("-overlay")
ifs = oechem.oemolistream()
if not ifs.open(rfname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % rfname)
rmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, rmol):
oechem.OEThrow.Fatal("Unable to read reference molecule")
ifs = oechem.oemolistream()
if not ifs.open(ifname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % ifname)
ofs = oechem.oemolostream()
if itf.HasString("-out"):
ofname = itf.GetString("-out")
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open %s for writing" % ofname)
if not overlay:
oechem.OEThrow.Warning(
"Output is the same as input when overlay is false")
for mol in ifs.GetOEMols():
oechem.OEThrow.Info(mol.GetTitle())
rmsds = oechem.OEDoubleArray(mol.GetMaxConfIdx())
rmtx = oechem.OEDoubleArray(9 * mol.GetMaxConfIdx())
tmtx = oechem.OEDoubleArray(3 * mol.GetMaxConfIdx())
# perform RMSD for all confomers
oechem.OERMSD(rmol, mol, rmsds, automorph, heavy, overlay, rmtx, tmtx)
for conf in mol.GetConfs():
cidx = conf.GetIdx()
oechem.OEThrow.Info("Conformer %i : rmsd = %f" %
(cidx, rmsds[cidx]))
if itf.GetBool("-overlay"):
oechem.OERotate(conf, rmtx[cidx * 9:cidx * 9 + 9])
oechem.OETranslate(conf, tmtx[cidx * 3:cidx * 3 + 3])
if itf.HasString("-out"):
oechem.OEWriteMolecule(ofs, mol)
return 0
def OERMSD_Array(refcrds, fitcrds, size):
oechem.OERMSD(refcrds, fitcrds, size)
overlay = True
oechem.OERMSD(refcrds, fitcrds, size, overlay)
rotmat = oechem.OEDoubleArray(9)
oechem.OERMSD(refcrds, fitcrds, size, overlay, rotmat)
transvec = oechem.OEDoubleArray(3)
oechem.OERMSD(refcrds, fitcrds, size, overlay, rotmat, transvec)
def __call__(self, coord, grad=None):
energy = 0.0
if isinstance(coord, oechem.OEDoubleArray):
if grad is not None:
for i in range(0, self.natoms):
grad[3 * i] += 2.0 * coord[3 * i] # x gradient
grad[3 * i + 1] += 2.0 * coord[3 * i + 1] # y gradient
grad[3 * i + 2] += 2.0 * coord[3 * i + 2] # z gradient
energy += coord[3 * i] * coord[3 *
i] # x distance from zero
energy += coord[3 * i +
1] * coord[3 * i +
1] # y distance from zero
energy += coord[3 * i +
2] * coord[3 * i +
2] # z distance from zero
else:
for i in range(0, self.natoms):
energy += coord[3 * i] * coord[3 *
i] # x distance from zero
energy += coord[3 * i +
1] * coord[3 * i +
1] # y distance from zero
energy += coord[3 * i +
2] * coord[3 * i +
2] # z distance from zero
else:
coord1 = oechem.OEDoubleArray(coord, self.NumVar(), False)
if grad is not None:
grad1 = oechem.OEDoubleArray(grad, self.NumVar(), False)
for i in range(0, self.natoms):
grad1[3 * i] += 2.0 * coord1[3 * i] # x gradient
grad1[3 * i + 1] += 2.0 * coord1[3 * i + 1] # y gradient
grad1[3 * i + 2] += 2.0 * coord1[3 * i + 2] # z gradient
energy += coord1[3 * i] * coord1[3 *
i] # x distance from zero
energy += coord1[3 * i +
1] * coord1[3 * i +
1] # y distance from zero
energy += coord1[3 * i +
2] * coord1[3 * i +
2] # z distance from zero
else:
for i in range(0, self.natoms):
energy += coord1[3 * i] * coord1[3 *
i] # x distance from zero
energy += coord1[3 * i +
1] * coord1[3 * i +
1] # y distance from zero
energy += coord1[3 * i +
2] * coord1[3 * i +
2] # z distance from zero
return energy
def CliqueAlign(refmol, fitmol, ofs):
cs = oechem.OECliqueSearch(refmol, oechem.OEExprOpts_DefaultAtoms,
oechem.OEExprOpts_DefaultBonds)
cs.SetSaveRange(5)
cs.SetMinAtoms(6)
for mi in cs.Match(fitmol):
rmat = oechem.OEDoubleArray(9)
trans = oechem.OEDoubleArray(3)
overlay = True
oechem.OERMSD(cs.GetPattern(), fitmol, mi, overlay, rmat, trans)
oechem.OERotate(fitmol, rmat)
oechem.OETranslate(fitmol, trans)
oechem.OEWriteMolecule(ofs, fitmol)
def OERMSD_Part_MolBase(ref, fit):
match = oechem.OEMatch()
for aRef, aFit in zip(ref.GetAtoms(), fit.GetAtoms()):
match.AddPair(aRef, aFit)
oechem.OERMSD(ref, fit, match)
overlay = True
oechem.OERMSD(ref, fit, match, overlay)
rotmat = oechem.OEDoubleArray(9)
oechem.OERMSD(ref, fit, match, overlay, rotmat)
transvec = oechem.OEDoubleArray(3)
oechem.OERMSD(ref, fit, match, overlay, rotmat, transvec)
def SmartsAlign(refmol, fitmol, ss, ofs):
unique = True
for match1 in ss.Match(refmol, unique):
for match2 in ss.Match(fitmol, unique):
match = oechem.OEMatch()
for mp1, mp2 in zip(match1.GetAtoms(), match2.GetAtoms()):
match.AddPair(mp1.target, mp2.target)
overlay = True
rmat = oechem.OEDoubleArray(9)
trans = oechem.OEDoubleArray(3)
oechem.OERMSD(refmol, fitmol, match, overlay, rmat, trans)
oechem.OERotate(fitmol, rmat)
oechem.OETranslate(fitmol, trans)
oechem.OEWriteConstMolecule(ofs, fitmol)
def __call__(self, x, g=None):
if isinstance(x, oechem.OEDoubleArray):
if g is not None:
g[0] = 2.0 * x[0] - 7.0
return x[0] * x[0] - 7 * x[0] + 63
else:
return x[0] * x[0] - 7 * x[0] + 63
else:
x1 = oechem.OEDoubleArray(x, self.NumVar(), False)
if g is not None:
g1 = oechem.OEDoubleArray(g, self.NumVar(), False)
g1[0] = 2.0 * x1[0] - 7.0
return x1[0] * x1[0] - 7 * x1[0] + 63
else:
return x1[0] * x1[0] - 7 * x1[0] + 63
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 GetBoundsFromMol(bounds, mol, pad):
set = False
c = oechem.OEDoubleArray(3)
for atom in mol.GetAtoms():
mol.GetCoords(atom, c)
if not set:
bounds[0] = bounds[3] = c[0]
bounds[1] = bounds[4] = c[1]
bounds[2] = bounds[5] = c[2]
set = True
else:
if (c[0] < bounds[0]):
bounds[0] = c[0]
if (c[1] < bounds[1]):
bounds[1] = c[1]
if (c[2] < bounds[2]):
bounds[2] = c[2]
if (c[0] > bounds[3]):
bounds[3] = c[0]
if (c[1] > bounds[4]):
bounds[4] = c[1]
if (c[2] > bounds[5]):
bounds[5] = c[2]
bounds[0] -= pad
bounds[1] -= pad
bounds[2] -= pad
bounds[3] += pad
bounds[4] += pad
bounds[5] += pad
def OERMSD_Full_MolBase(ref, fit):
oechem.OERMSD(ref, fit)
automorf = True
oechem.OERMSD(ref, fit, automorf)
heavyOnly = True
oechem.OERMSD(ref, fit, automorf, heavyOnly)
overlay = False
oechem.OERMSD(ref, fit, automorf, heavyOnly, overlay)
rotmat = oechem.OEDoubleArray(9)
oechem.OERMSD(ref, fit, automorf, heavyOnly, overlay, rotmat)
transvec = oechem.OEDoubleArray(3)
oechem.OERMSD(ref, fit, automorf, heavyOnly, overlay, rotmat, transvec)
def OERMSD_Part_MCMolBase(ref, fit):
match = oechem.OEMatch()
for aRef, aFit in zip(ref.GetAtoms(), fit.GetAtoms()):
match.AddPair(aRef, aFit)
nConfs = fit.GetMaxConfIdx()
vecRmsd = oechem.OEDoubleArray(nConfs)
oechem.OERMSD(ref, fit, vecRmsd, match)
overlay = True
oechem.OERMSD(ref, fit, vecRmsd, match, overlay)
rotmat = oechem.OEDoubleArray(9*nConfs)
oechem.OERMSD(ref, fit, vecRmsd, match, overlay, rotmat)
transvec = oechem.OEDoubleArray(3*nConfs)
oechem.OERMSD(ref, fit, vecRmsd, match, overlay, rotmat, transvec)
def normalize_coordinates(mol, dih):
"""Reset the coordinates of an OEGraphMol object with respect to a dihedral.
The first three atoms of the dihedral will be set to the following
coordinates:
|Atom| Position |
|----|----------|
| 0 | (0,0,0) |
| 1 | (x1,0,0) |
| 2 | (x2,y2,0)|
This defines the coordinate system required to determine the coordinates of
all the other atoms in the fragment.
Arguments:
mol: An OEGraphMol object.
dih: An OEAtomBondSet with atoms belonging to mol.
Returns:
success: A bool indicating whether the transformation was successful.
"""
dih_atoms = [atom for atom in dih.GetAtoms()]
# Translate the fragment until the first atom of the dihedral is at the origin
origin = mol.GetCoords()[dih_atoms[0].GetIdx()]
shift = oechem.OEDoubleArray([-x for x in origin])
oechem.OETranslate(mol, shift)
# Get coordinates of atoms 2 and 3 in the dihedral
u = np.array(mol.GetCoords()[dih_atoms[1].GetIdx()])
v = np.array(mol.GetCoords()[dih_atoms[2].GetIdx()])
# Get three orthogonal unit vectors
u_hat = u / np.linalg.norm(u)
v_hat = v - (
(np.dot(u, v) * u) / np.dot(u, u)) # Gram-Schmidt Orthogonalization
v_hat = v_hat / np.linalg.norm(v_hat)
w_hat = np.cross(u_hat, v_hat)
# Assemble unit vectors into rotation matrix
R = np.stack((u_hat, v_hat, w_hat), axis=0)
rotation_matrix = oechem.OEDoubleArray(R.flatten())
oechem.OERotate(mol, rotation_matrix)
def OERMSD_Full_MCMolBase(ref, fit):
nConfs = fit.GetMaxConfIdx()
vecRmsd = oechem.OEDoubleArray(nConfs)
oechem.OERMSD(ref, fit, vecRmsd)
automorf = True
oechem.OERMSD(ref, fit, vecRmsd, automorf)
heavyOnly = True
oechem.OERMSD(ref, fit, vecRmsd, automorf, heavyOnly)
overlay = True
oechem.OERMSD(ref, fit, vecRmsd, automorf, heavyOnly, overlay)
rotmat = oechem.OEDoubleArray(9*nConfs)
oechem.OERMSD(ref, fit, vecRmsd, automorf, heavyOnly, overlay, rotmat)
transvec = oechem.OEDoubleArray(3*nConfs)
oechem.OERMSD(ref, fit, vecRmsd, automorf, heavyOnly, overlay, rotmat, transvec)
def MCSAlign(refmol, fitmol, ofs):
atomexpr = oechem.OEExprOpts_AtomicNumber | oechem.OEExprOpts_Aromaticity
bondexpr = 0
mcss = oechem.OEMCSSearch(oechem.OEMCSType_Exhaustive)
mcss.Init(refmol, atomexpr, bondexpr)
mcss.SetMCSFunc(oechem.OEMCSMaxBondsCompleteCycles())
rmat = oechem.OEDoubleArray(9)
trans = oechem.OEDoubleArray(3)
unique = True
overlay = True
for match in mcss.Match(fitmol, unique):
rms = oechem.OERMSD(mcss.GetPattern(), fitmol, match, overlay, rmat, trans)
if rms < 0.0:
oechem.OEThrow.Warning("RMS overlay failure")
continue
oechem.OERotate(fitmol, rmat)
oechem.OETranslate(fitmol, trans)
oechem.OEWriteMolecule(ofs, fitmol)
def __call__(self, iteration, nvar, fval, var, state):
# Intermediate information during optimization
var1 = oechem.OEDoubleArray(var, 1, False)
oechem.OEThrow.Info("iteration: %d x: %d value: %d state: %d" %
(iteration, var1[0], fval, state))
# To demonstrate how to force quitting optimization from checkpoint
# this returns false when iteration is 5
if iteration >= 5:
return False
else:
return True
def main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <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])
ofs = oechem.oemolostream()
if not ofs.open(args[3]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[3])
# Load the protein molecule and Prepare with MMFF
protein = oechem.OEGraphMol()
oechem.OEReadMolecule(ips, protein)
oechem.OEAddExplicitHydrogens(protein)
mmff = oeff.OEMMFFAmber(protein)
mmff.PrepMol(protein)
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
def SeqAlign(ref, fit, ofs):
sa = oechem.OEGetAlignment(ref, fit)
print()
print("Alignment of %s to %s" % (fit.GetTitle(), ref.GetTitle()))
print()
print(" Method: %s" % oechem.OEGetAlignmentMethodName(sa.GetMethod()))
print(" Gap : %d" % sa.GetGap())
print(" Extend: %d" % sa.GetExtend())
print(" Score : %d" % sa.GetScore())
print()
oss = oechem.oeosstream()
oechem.OEWriteAlignment(oss, sa)
print(oss.str().decode("UTF-8"))
onlyCAlpha = True
overlay = True
rot = oechem.OEDoubleArray(9)
trans = oechem.OEDoubleArray(3)
rmsd = oechem.OERMSD(ref, fit, sa, onlyCAlpha, overlay, rot, trans)
print(" RMSD = %.1f" % rmsd)
oechem.OERotate(fit, rot)
oechem.OETranslate(fit, trans)
oechem.OEWriteMolecule(ofs, fit)
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 GetTorsionEnvAtoms(self, elem, bgnAtom, endAtom, envMol):
elemEnvList = []
for envAtom in oechem.OEGetSubtree(bgnAtom, endAtom):
if elem == 'pc' and envAtom.GetFormalCharge() >= 1:
elemEnvList.append(envAtom)
elif elem == 'nc' and envAtom.GetFormalCharge() <= -1:
elemEnvList.append(envAtom)
elif envAtom.GetAtomicNum() == elem:
elemEnvList.append(envAtom)
coordsList = []
for elemEnvAtom in elemEnvList:
coords = oechem.OEDoubleArray(3)
if envMol.GetCoords(elemEnvAtom, coords):
coordsList.append(coords)
return elemEnvList, coordsList
def GetEnvAtomCoords(self, elem, refAtom, envMol, envAtoms):
elemEnvList = []
for envAtom in envAtoms:
if envAtom == refAtom:
continue
if elem == 'pc' and envAtom.GetFormalCharge() >= 1:
elemEnvList.append(envAtom)
elif elem == 'nc' and envAtom.GetFormalCharge() <= -1:
elemEnvList.append(envAtom)
elif envAtom.GetAtomicNum() == elem:
elemEnvList.append(envAtom)
coordsList = []
for elemEnvAtom in elemEnvList:
coords = oechem.OEDoubleArray(3)
if envMol.GetCoords(elemEnvAtom, coords):
coordsList.append(coords)
return coordsList
def GetTorsionCenterAsOEMol(self, mol):
refCoords = oechem.OEDoubleArray(3)
try:
torsion_atoms = get_torsion_oeatom_list(mol)
bgnCoords = mol.GetCoords(torsion_atoms[1])
endCoords = mol.GetCoords(torsion_atoms[2])
refCoords[0] = (bgnCoords[0] + endCoords[0]) / 2.0
refCoords[1] = (bgnCoords[1] + endCoords[1]) / 2.0
refCoords[2] = (bgnCoords[2] + endCoords[2]) / 2.0
except Exception as e:
print(e)
return None
refMol = oechem.OEMol()
refAtom = refMol.NewAtom(oechem.OEElemNo_C)
refMol.SetCoords(refAtom, refCoords)
refMol.Sweep()
return refMol
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()
oechem.OEReadMolecule(ifs, mol)
vecCoords = oechem.OEDoubleArray(3 * mol.GetMaxAtomIdx())
mol.GetCoords(vecCoords)
hermonic = Harmonic()
hermonic.Setup(mol)
optimizer = oeff.OEBFGSOpt()
energy = optimizer(hermonic, vecCoords, vecCoords)
oechem.OEThrow.Info("Optimized energy: %d" % energy)
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])
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) != 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[3])
# Load the protein molecule and Prepare with MMFF
smir = oeff.OESmirnoff()
optimizer = oeff.OENewtonOpt()
mol = oechem.OEMol()
while oechem.OEReadMolecule(ifs, mol):
if ((not smir.PrepMol(mol)) or (not smir.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 = smir(vecCoords)
oechem.OEThrow.Info("Initial energy: %d kcal/mol" % energy)
energy = optimizer(smir, 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) != 4:
oechem.OEThrow.Usage("%s <protein> <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])
ofs = oechem.oemolostream()
if not ofs.open(args[3]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % args[3])
# Load the protein molecule and Prepare with MMFF
protein = oechem.OEGraphMol()
oechem.OEReadMolecule(ips, protein)
oechem.OEAddExplicitHydrogens(protein)
mmff = oeff.OEMMFFAmber(protein)
mmff.PrepMol(protein)
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
# 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.OEQuatAdaptor(mmff, False, False)
if not adaptor.Setup(mol):
oechem.OEThrow.Warning("Unable to process subset for 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 ligand
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
