def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("calc_et.py <reffile> <fitfile>")
refmol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
oechem.OEReadMolecule(ifs, refmol)
oechem.OEAssignBondiVdWRadii(refmol)
oechem.OEMMFFAtomTypes(refmol)
oechem.OEMMFF94PartialCharges(refmol)
et = oezap.OEET()
et.SetRefMol(refmol)
oechem.OEThrow.Info("dielectric: %.4f" % et.GetDielectric())
oechem.OEThrow.Info("inner mask: %.4f" % et.GetInnerMask())
oechem.OEThrow.Info("outer mask: %.4f" % et.GetOuterMask())
oechem.OEThrow.Info("salt conc : %.4f" % et.GetSaltConcentration())
oechem.OEThrow.Info("join : %d" % et.GetJoin())
if not ifs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[2])
fitmol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, fitmol):
oechem.OEAssignBondiVdWRadii(fitmol)
oechem.OEMMFFAtomTypes(fitmol)
oechem.OEMMFF94PartialCharges(fitmol)
oechem.OEThrow.Info("Title: %s, ET %4.2f" %
(fitmol.GetTitle(), et.Tanimoto(fitmol)))
return 0
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
epsin = 1.0
zap = oezap.OEZap()
zap.SetInnerDielectric(epsin)
zap.SetGridSpacing(0.5)
area = oezap.OEArea()
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
oechem.OEThrow.Info("%-20s %6s\n" % ("Title", "Vacuum->Water(kcal)"))
while oechem.OEReadMolecule(ifs, mol):
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap.SetMolecule(mol)
solv = zap.CalcSolvationEnergy()
aval = area.GetArea(mol)
oechem.OEThrow.Info("%-20s %6.2f" % (mol.GetTitle(),
KCalsPerKT*solv+KCalsPerSqAngstrom*aval))
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface()
if not SetupInterface(argv, itf):
return 1
zap = oezap.OEZap()
zap.SetInnerDielectric(itf.GetFloat("-epsin"))
zap.SetOuterDielectric(itf.GetFloat("-epsout"))
zap.SetGridSpacing(itf.GetFloat("-grid_spacing"))
zap.SetBoundarySpacing(itf.GetFloat("-buffer"))
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(itf.GetString("-in")):
oechem.OEThrow.Fatal("Unable to open %s for reading" %
itf.GetString("-in"))
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap.SetMolecule(mol)
grid = oegrid.OEScalarGrid()
if zap.CalcPotentialGrid(grid):
if itf.GetBool("-mask"):
oegrid.OEMaskGridByMolecule(grid, mol)
oegrid.OEWriteGrid(itf.GetString("-out"), grid)
return 0
def SetPartialCharge(mol, tagname):
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
tag = oechem.OEGetTag(tagname)
for atom in mol.GetAtoms():
atom.SetData(tag, atom.GetPartialCharge())
def Draw2DSurfacePartialCharge(image, mol):
oedepict.OEPrepareDepiction(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
coloranion = oechem.OEColorStop(-1.0, oechem.OEColor(oechem.OEDarkRed))
colorcation = oechem.OEColorStop(+1.0, oechem.OEColor(oechem.OEDarkBlue))
colorg = oechem.OELinearColorGradient(coloranion, colorcation)
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEColor(oechem.OEWhite)))
arcfxn = AtomPartialChargeArcFxn(colorg)
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(image, disp)
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
epsin = 1.0
zap = oezap.OEZap()
zap.SetInnerDielectric(epsin)
zap.SetGridSpacing(0.5)
area = oezap.OEArea()
PrintHeader()
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
while oechem.OEReadMolecule(ifs, mol):
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap.SetMolecule(mol)
solv = zap.CalcSolvationEnergy()
aval = area.GetArea(mol)
coul = oezap.OECoulombicSelfEnergy(mol, epsin)
PrintLine(mol.GetTitle(), solv, aval, coul)
return 0
def SetPartialCharge(mol, tagname, minvalue, maxvalue):
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
tag = oechem.OEGetTag(tagname)
for atom in mol.GetAtoms():
charge = atom.GetPartialCharge()
atom.SetData(tag, charge)
minvalue = min(minvalue, charge)
maxvalue = max(maxvalue, charge)
return minvalue, maxvalue
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <protein> <ligand>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
protein = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, protein)
if not ifs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[2])
ligand = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, ligand)
oechem.OEAssignBondiVdWRadii(protein)
oechem.OEMMFFAtomTypes(protein)
oechem.OEMMFF94PartialCharges(protein)
oechem.OEAssignBondiVdWRadii(ligand)
oechem.OEMMFFAtomTypes(ligand)
oechem.OEMMFF94PartialCharges(ligand)
cmplx = oechem.OEGraphMol(protein)
oechem.OEAddMols(cmplx, ligand)
epsin = 1.0
spacing = 0.5
zap = oezap.OEZap()
zap.SetInnerDielectric(epsin)
zap.SetGridSpacing(spacing)
PrintHeader(protein.GetTitle(), ligand.GetTitle())
CalcBindingEnergy(zap, protein, ligand, cmplx)
zap.SetFocusTarget(ligand)
CalcBindingEnergy(zap, protein, ligand, cmplx)
return 0
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <protein> <ligands>" % argv[0])
protein = oechem.OEMol()
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
oechem.OEReadMolecule(ifs, protein)
oechem.OEAssignBondiVdWRadii(protein)
oechem.OEMMFFAtomTypes(protein)
oechem.OEMMFF94PartialCharges(protein)
print("protein: " + protein.GetTitle())
epsin = 1.0
bind = oezap.OEBind()
bind.GetZap().SetInnerDielectric(epsin)
bind.SetProtein(protein)
results = oezap.OEBindResults()
if not ifs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[2])
ifs.SetConfTest(oechem.OEIsomericConfTest())
ligand = oechem.OEMol()
while oechem.OEReadMolecule(ifs, ligand):
oechem.OEAssignBondiVdWRadii(ligand)
oechem.OEMMFFAtomTypes(ligand)
oechem.OEMMFF94PartialCharges(ligand)
print("ligand: %s has %d conformers" %
(ligand.GetTitle(), ligand.NumConfs()))
for conf in ligand.GetConfs():
bind.Bind(conf, results)
print(" conf# %d be = %f" %
(conf.GetIdx(), results.GetBindingEnergy()))
return 0
def assignELF10charges(molecule, max_confs=800, strictStereo=True):
"""
This function computes atomic partial charges for an OEMol by
using the ELF10 method
Parameters:
-----------
molecule : OEMol object
The molecule that needs to be charged
max_confs : integer
The max number of conformers used to calculate the atomic partial charges
strictStereo : bool
a flag used to check if atoms need to have assigned stereo chemistry or not
Return:
-------
mol_copy : OEMol
a copy of the original molecule with assigned atomic partial charges
"""
mol_copy = molecule.CreateCopy()
# The passed molecule could have already conformers. If the conformer number
# does not exceed the max_conf threshold then max_confs conformations will
# be generated
if not mol_copy.GetMaxConfIdx() > 200:
# Generate up to max_confs conformers
mol_copy = generate_conformers(mol_copy,
max_confs=max_confs,
strictStereo=strictStereo)
# Assign MMFF Atom types
if not oechem.OEMMFFAtomTypes(mol_copy):
raise RuntimeError("MMFF atom type assignment returned errors")
# ELF10 charges
status = oequacpac.OEAssignCharges(mol_copy,
oequacpac.OEAM1BCCELF10Charges())
if not status:
raise RuntimeError("OEAssignCharges returned error code %d" % status)
return mol_copy
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
epsin = 1.0
zap = oezap.OEZap()
zap.SetInnerDielectric(epsin)
zap.SetMolecule(mol)
grid = oegrid.OEScalarGrid()
if zap.CalcPotentialGrid(grid):
oegrid.OEWriteGrid("zap.grd", grid)
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
epsin = 1.0
zap = oezap.OEZap()
zap.SetInnerDielectric(epsin)
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
while oechem.OEReadMolecule(ifs, mol):
PrintHeader(mol.GetTitle())
forces = oechem.OEFloatArray(mol.GetMaxAtomIdx() * 3)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap.SetMolecule(mol)
zap.CalcForces(forces)
PrintForces(mol, forces)
return 0
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
zap = oezap.OEZap()
zap.SetInnerDielectric(1.0)
zap.SetGridSpacing(0.5)
zap.SetMolecule(mol)
# calculate standard 2-dielectric grid
grid1 = oegrid.OEScalarGrid()
zap.CalcPotentialGrid(grid1)
# calculate grid with single dielectric
grid2 = oegrid.OEScalarGrid()
zap.SetOuterDielectric(zap.GetInnerDielectric())
zap.CalcPotentialGrid(grid2)
# take the difference
oegrid.OESubtractScalarGrid(grid1, grid2)
# mask out everything outside the molecule
oegrid.OEMaskGridByMolecule(grid1, mol,
oegrid.OEGridMaskType_GaussianMinus)
oegrid.OEWriteGrid("zap_diff.grd", grid1)
from openeye import oezap
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % sys.argv[0])
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading", sys.argv[1])
if not oechem.OEIs3DFormat(ifs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
# @ <SNIPPET-GetArea-Molecule>
area = oezap.OEArea()
a = area.GetArea(mol)
print("Molecule area =", a)
# @ </SNIPPET-GetArea-Molecule>
# @ <SNIPPET-GetArea-Atoms>
atomArea = oechem.OEFloatArray(mol.GetMaxAtomIdx())
area = oezap.OEArea()
area.GetArea(mol, atomArea)
for atom in mol.GetAtoms():
idx = atom.GetIdx()