def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <input> <output>" % argv[0])
# input - preserve rotor-offset-compression
ifs = oechem.oemolistream()
ihand = ifs.GetBinaryIOHandler()
ihand.Clear()
oechem.OEInitHandler(ihand, oechem.OEBRotCompressOpts(),
oechem.OEBRotCompressOpts())
ifname = argv[1]
if not ifs.open(ifname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
# output
ofname = argv[2]
oformt = oechem.OEGetFileType(oechem.OEGetFileExtension(ofname))
if oformt != oechem.OEFormat_OEB:
oechem.OEThrow.Fatal("Output file format much be OEB")
ofs = oechem.oemolostream()
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open %s for writing" % ofname)
iss = oechem.oeisstream(COLOR_FORCE_FIELD)
cff = oeshape.OEColorForceField()
if not cff.Init(iss):
oechem.OEThrow.Fatal("Unable to initialize OEColorForceField")
dots = oechem.OEDots(10000, 200, "molecules")
for mol in ifs.GetOEMols():
oefastrocs.OEPrepareFastROCSMol(mol, cff)
oechem.OEWriteMolecule(ofs, mol)
dots.Update()
dots.Total()
ofs.close()
print("Indexing %s" % ofname)
if not oechem.OECreateMolDatabaseIdx(ofname):
oechem.OEThrow.Fatal("Failed to index %s" % argv[2])
return 0
def GetShapeDatabaseArgs(itf):
shapeOnly = itf.GetBool("-shapeOnly")
if shapeOnly and itf.GetParameter("-chemff").GetHasValue():
oechem.OEThrow.Fatal(
"Unable to specify -shapeOnly and -chemff at the same time!")
chemff = itf.GetString("-chemff")
if not chemff.endswith(".cff"):
return (GetDatabaseType(shapeOnly), OECOLOR_FORCEFIELDS[chemff])
# given a .cff file, use that to construct a OEColorForceField
assert not shapeOnly
cff = oeshape.OEColorForceField()
if not cff.Init(chemff):
oechem.OEThrow.Fatal("Unable to read color force field from '%s'" %
chemff)
return (cff, )
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <reffile> <overlayfile>" % argv[0])
reffs = oechem.oemolistream(argv[1])
fitfs = oechem.oemolistream(argv[2])
refmol = oechem.OEGraphMol()
oechem.OEReadMolecule(reffs, refmol)
# Modify ImplicitMillsDean color force field by
# adding user defined color interactions
cff = oeshape.OEColorForceField()
cff.Init(oeshape.OEColorFFType_ImplicitMillsDean)
cff.ClearInteractions()
donorType = cff.GetType("donor")
accepType = cff.GetType("acceptor")
cff.AddInteraction(donorType, donorType, "gaussian", -1.0, 1.0)
cff.AddInteraction(accepType, accepType, "gaussian", -1.0, 1.0)
# Prepare reference molecule for calculation
# With default options this will add required color atoms
# Set the modified color force field for addignment
prep = oeshape.OEOverlapPrep()
prep.SetColorForceField(cff)
prep.Prep(refmol)
# Get appropriate function to calculate exact color
# Set appropriate options to use the user defined color
options = oeshape.OEColorOptions()
options.SetColorForceField(cff)
colorFunc = oeshape.OEExactColorFunc(options)
colorFunc.SetupRef(refmol)
res = oeshape.OEOverlapResults()
for fitmol in fitfs.GetOEGraphMols():
prep.Prep(fitmol)
colorFunc.Overlap(fitmol, res)
print("Fit Title: %s Color Tanimoto: %.2f" %
(fitmol.GetTitle(), res.GetColorTanimoto()))
from openeye import oegrapheme
from openeye import oeshape
###############################################################
# USED TO GENERATE CODE SNIPPETS FOR THE GRAPHEME DOCUMENTATION
###############################################################
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <mol file>" % sys.argv[0])
ifs = oechem.oemolistream(sys.argv[1])
refmol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, refmol)
# @ <SNIPPET-RENDER-SHAPE-QUERY>
opts = oegrapheme.OEShapeQueryDisplayOptions()
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
arcpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_On,
2.0)
opts.SetSurfaceArcFxn(oegrapheme.OEDefaultArcFxn(arcpen))
cff = oeshape.OEColorForceField()
cff.Init(oeshape.OEColorFFType_ImplicitMillsDean)
disp = oegrapheme.OEShapeQueryDisplay(refmol, cff, opts)
image = oedepict.OEImage(420.0, 280.0)
oegrapheme.OERenderShapeQuery(image, disp)
# @ </SNIPPET-RENDER-SHAPE-QUERY>
oedepict.OEWriteImage("RenderShapeQuery.png", image)
oedepict.OEWriteImage("RenderShapeQuery.pdf", image)