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(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <protein> <ligand>" % args[0])
pifs = oechem.oemolistream()
if not pifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading protein." %
args[1])
prot = oechem.OEGraphMol()
if not oechem.OEReadMolecule(pifs, prot):
oechem.OEThrow.Fatal("Unable to read protein")
oechem.OEAddExplicitHydrogens(prot)
oechem.OEAssignBondiVdWRadii(prot)
lifs = oechem.oemolistream()
if not lifs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading ligand." % args[2])
lig = oechem.OEGraphMol()
if not oechem.OEReadMolecule(lifs, lig):
oechem.OEThrow.Fatal("Unable to read ligand")
oechem.OEAddExplicitHydrogens(lig)
oechem.OEAssignBondiVdWRadii(lig)
comp = oechem.OEGraphMol(prot)
oechem.OEAddMols(comp, lig)
compSurf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(compSurf, comp)
protSurf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(protSurf, prot)
ligSurf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(ligSurf, lig)
compVol = oespicoli.OESurfaceVolume(compSurf)
protVol = oespicoli.OESurfaceVolume(protSurf)
ligVol = oespicoli.OESurfaceVolume(ligSurf)
oespicoli.OEWriteSurface("comp.oesrf", compSurf)
oespicoli.OEWriteSurface("prot.oesrf", protSurf)
oespicoli.OEWriteSurface("lig.oesrf", ligSurf)
oechem.OEThrow.Info(
"%s-%s: dV(C-P) = %.1f V(L) = %.1f V(C) = %.1f V(P) = %.1f" %
(prot.GetTitle(), lig.GetTitle(), compVol - protVol, ligVol, compVol,
protVol))
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 main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <ligand> <surface>" % args[0])
pfs = oechem.oemolistream(args[1])
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(pfs, prot)
oechem.OEAssignBondiVdWRadii(prot)
lfs = oechem.oemolistream(args[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(lfs, lig)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, prot)
# Iterate through all the protein surface vertices
for i in range(surf.GetNumVertices()):
vert = surf.GetVertex(i)
# Check the distance to each atom
for atom in lig.GetAtoms():
dist2 = GetDist2(lig.GetCoords(atom), vert)
if dist2 < MAX_DIST * MAX_DIST:
surf.SetVertexCliqueElement(i, 1)
# Crop to the binding site and output
oespicoli.OESurfaceCropToClique(surf, 1)
oespicoli.OEWriteSurface(args[3], surf)
return 0
def main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <ligand> <surface>" % args[0])
pfs = oechem.oemolistream(args[1])
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(pfs, prot)
oechem.OEAssignBondiVdWRadii(prot)
lfs = oechem.oemolistream(args[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(lfs, lig)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, prot)
oespicoli.OESurfaceToMoleculeDistance(surf, lig)
# Mark the vertices to keep
for i in range(surf.GetNumVertices()):
if surf.GetDistanceElement(i) < MAX_DIST:
surf.SetVertexCliqueElement(i, 1)
# Crop to the binding site and output
oespicoli.OESurfaceCropToClique(surf, 1)
oespicoli.OEWriteSurface(args[3], surf)
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__]):
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 main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <ref> <fit>" % args[0])
refifs = oechem.oemolistream()
if not refifs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
refmol = oechem.OEGraphMol()
oechem.OEReadMolecule(refifs, refmol)
oechem.OEAssignBondiVdWRadii(refmol)
fitifs = oechem.oemolistream()
if not fitifs.open(args[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[2])
fitmol = oechem.OEGraphMol()
oechem.OEReadMolecule(fitifs, fitmol)
oechem.OEAssignBondiVdWRadii(fitmol)
# Map the reference molecule onto a grid
grd = oegrid.OEScalarGrid()
oegrid.OEMakeMolecularGaussianGrid(grd, refmol, 0.5)
# Get the total volume of the reference molecule
refsrf = oespicoli.OESurface()
oespicoli.OEMakeSurfaceFromGrid(refsrf, grd, 1.0)
totalv = oespicoli.OESurfaceVolume(refsrf)
# Mask out the fit molecule
oegrid.OEMaskGridByMolecule(grd, fitmol)
# Find how much of the reference volume is remaining
fitsrf = oespicoli.OESurface()
oespicoli.OEMakeSurfaceFromGrid(fitsrf, grd, 1.0)
remaining = oespicoli.OESurfaceVolume(fitsrf)
print("Percent overlap: %f" % ((1 - remaining / totalv) * 100))
return 0
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 ImportMolecule(filename):
ifs = oechem.oemolistream()
if not ifs.open(filename):
oechem.OEThrow.Fatal("Unable to open %s for reading" % filename)
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OESuppressHydrogens(mol)
return mol
def main(args):
if len(args) != 4:
oechem.OEThrow.Usage("%s <protein> <ligand> <surface>" % args[0])
prtfs = oechem.oemolistream(args[1])
prt = oechem.OEGraphMol()
oechem.OEReadMolecule(prtfs, prt)
oechem.OESuppressHydrogens(prt)
oechem.OEAssignBondiVdWRadii(prt)
ligfs = oechem.oemolistream(args[2])
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(ligfs, lig)
oechem.OESuppressHydrogens(lig)
oechem.OEAssignBondiVdWRadii(lig)
grid = oegrid.OEScalarGrid()
oespicoli.OEMakeVoidVolume(prt, lig, grid, 0.5)
surf = oespicoli.OESurface()
oespicoli.OEMakeSurfaceFromGrid(surf, grid, 0.5)
oespicoli.OEWriteSurface(args[3], surf)
return 0
def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % argv[0])
ifs = oechem.oemolistream(argv[1])
for mol in ifs.GetOEMols():
oechem.OEAssignBondiVdWRadii(mol)
area, polararea = AverageSurfaceArea(mol)
print(mol.GetTitle())
print("molecule has %d conformers" % mol.NumConfs())
print("Average total surface area: %f" % area)
print("Average polar area : %f" % polararea)
print("Average %% polar : %f" % ((polararea/area) * 100))
print()
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <protein> <surface>" % 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)
oechem.OEPerceiveResidues(mol)
oechem.OEAssignBondiVdWRadii(mol)
# Generate the molecular surface
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol, 0.5)
# Mark all the vertices associated with hydrophobic atoms
for i in range(surf.GetNumVertices()):
atom = mol.GetAtom(oechem.OEHasAtomIdx(surf.GetAtomsElement(i)))
if (AtomInHydrophobicResidue(atom)):
surf.SetVertexCliqueElement(i, 1)
# Crop to only those triangles
oespicoli.OESurfaceCropToClique(surf, 1)
# nlqs is the number of different connected components
nclqs = oespicoli.OEMakeConnectedSurfaceCliques(surf)
# Find the largest component
maxclq = 0
maxarea = 0.0
for i in range(nclqs):
area = oespicoli.OESurfaceCliqueArea(surf, i+1)
print("clique: %d area: %f" % (i+1, area))
if (area > maxarea):
maxclq = i+1
maxarea = area
# Crop to it
oespicoli.OESurfaceCropToClique(surf, maxclq)
oespicoli.OEWriteSurface(args[2], surf)
return 0
def main(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <protein> <surface>" % args[0])
prtfs = oechem.oemolistream()
if not prtfs.open(args[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % args[1])
prt = oechem.OEGraphMol()
oechem.OEReadMolecule(prtfs, prt)
oechem.OEAssignBondiVdWRadii(prt)
surf = oespicoli.OESurface()
oespicoli.OEMakeCavitySurfaces(prt, surf)
oespicoli.OEInvertSurface(surf)
oespicoli.OEWriteSurface(args[2], surf)
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)
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(args):
if len(args) != 3:
oechem.OEThrow.Usage("%s <molecules> <oebfile>" % 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])
for mol in ifs.GetOEGraphMols():
oechem.OEAssignBondiVdWRadii(mol)
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol, 0.5)
ColorSurface(surf, mol)
mol.SetData("psasurf", surf)
oechem.OEWriteMolecule(ofs, mol)
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)
import sys
from openeye import oechem
from openeye import oespicoli
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <input>" % sys.argv[0])
ims = oechem.oemolistream()
if not ims.open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s" % sys.argv[1])
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read a molecule")
oechem.OEAssignBondiVdWRadii(mol)
# @ <SNIPPET-SetData>
surf = oespicoli.OESurface()
oespicoli.OEMakeMolecularSurface(surf, mol)
mol.SetData("surface", surf)
ofs = oechem.oemolostream("foo.oeb")
oechem.OEWriteMolecule(ofs, mol)
# @ </SNIPPET-SetData>
ofs.close()
# @ <SNIPPET-GetData>
ifs = oechem.oemolistream("foo.oeb")
oechem.OEReadMolecule(ifs, mol)
