def main(argv=[__name__]):
if len(argv) != 4:
oechem.OEThrow.Usage("%s <database> <prefix> <n_servers>" % argv[0])
# input - preserve rotor-offset-compression
ifs = oechem.oemolistream()
oechem.OEPreserveRotCompress(ifs)
ifname = argv[1]
if not ifs.open(ifname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
# output
prefix = argv[2]
ext = oechem.OEGetFileExtension(prefix)
extstrt = len(prefix)
if ext:
extstrt = -(len(ext) + 1)
else:
ext = oechem.OEGetFileExtension(ifname)
base = prefix[:extstrt]
fmt = base + "_%i." + ext
nservers = int(argv[3])
outstrms = []
for i in range(1, nservers + 1):
ofs = oechem.oemolostream()
if not ofs.open(fmt % i):
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])
outstrms.append(ofs)
dots = oechem.OEDots(10000, 200, "molecules")
for mol in ifs.GetOEMols():
oefastrocs.OEPrepareFastROCSMol(mol)
nhvyatoms = oechem.OECount(mol, oechem.OEIsHeavy())
ofs = outstrms[nhvyatoms % nservers]
oechem.OEWriteMolecule(ofs, mol)
dots.Update()
dots.Total()
for strm in outstrms:
fname = strm.GetFileName()
strm.close()
oechem.OEThrow.Info("Indexing %s" % fname)
if not oechem.OECreateMolDatabaseIdx(fname):
oechem.OEThrow.Fatal("Failed to index %s" % fname)
return 0
def main(argv=[__name__]):
if len(argv) != 5:
oechem.OEThrow.Usage("%s <queryfile> <fitfile> <outfile> <nhits>" %
argv[0])
if oechem.OEGetFileExtension(sys.argv[1]) != "sq":
oechem.OEThrow.Fatal("Requires a shape query .sq input file format")
fitfs = oechem.oemolistream(sys.argv[2])
outfs = oechem.oemolostream(sys.argv[3])
nhits = int(sys.argv[4])
query = oeshape.OEShapeQuery()
oeshape.OEReadShapeQuery(sys.argv[1], query)
# Setup OEROCS with specified number of best hits
options = oeshape.OEROCSOptions()
options.SetNumBestHits(nhits)
rocs = oeshape.OEROCS(options)
rocs.SetDatabase(fitfs)
for res in rocs.Overlay(query):
outmol = res.GetOverlayConf()
oechem.OEWriteMolecule(outfs, outmol)
print("title: %s tanimoto combo = %.2f" %
(outmol.GetTitle(), res.GetTanimotoCombo()))
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
ifs.SetConfTest(oechem.OEAbsoluteConfTest()) # VTL
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if ext != "pdf":
oechem.OEThrow.Fatal("Output must be PDF format.")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(),
oedepict.OEScale_AutoScale)
for mol in ifs.GetOEMols(): # VTL ignore confs; dont use GetOEGraphMols
print(mol.GetTitle()) # VTL
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(cell, disp)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, 12,
oedepict.OEAlignment_Center, oechem.OEBlack)
for pagenum, footer in enumerate(report.GetFooters()):
text = "Page %d of %d" % (pagenum + 1, report.NumPages())
oedepict.OEDrawTextToCenter(footer, text, font)
oedepict.OEWriteReport(ofs, ext, report)
return 0
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <molfile> <queryfile>" % sys.argv[0])
molfs = oechem.oemolistream(sys.argv[1])
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(molfs, mol)
if oechem.OEGetFileExtension(sys.argv[2]) != "sq":
oechem.OEThrow.Fatal(
"Only can write shape query to .sq output file format")
# Use OEOverlapPrep to remove hydrogens and add
# color atoms to the molecule
prep = oeshape.OEOverlapPrep()
prep.Prep(mol)
# Get the color atoms, create gaussians and add them
# to the shape query
query = oeshape.OEShapeQuery()
for atom in oeshape.OEGetColorAtoms(mol):
coords = oechem.OEFloatArray(3)
mol.GetCoords(atom, coords)
gauss = oegrid.OEGaussian(1.0, 1.0, coords,
oeshape.OEGetColorType(atom))
query.AddColorGaussian(gauss)
# Remove color atoms from the molecule and add to the query
oeshape.OERemoveColorAtoms(mol)
query.SetMolecule(mol)
oeshape.OEWriteShapeQuery(sys.argv[2], query)
print("shape query created")
def SetupInterface(argv, itf):
oechem.OEConfigure(itf, InterfaceData)
if oechem.OECheckHelp(itf, argv):
return False
if not oechem.OEParseCommandLine(itf, argv):
return False
infile = itf.GetString("-in")
if not oechem.OEIsReadable(
oechem.OEGetFileType(oechem.OEGetFileExtension(infile))):
oechem.OEThrow.Warning("%s is not a readable input file" % infile)
return False
outfile = itf.GetString("-out")
if not oegrid.OEIsWriteableGrid(
oegrid.OEGetGridFileType(oechem.OEGetFileExtension(outfile))):
oechem.OEThrow.Warning("%s is not a writable grid file" % outfile)
return False
return True
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 400.0)
oedepict.OEConfigureImageHeight(itf, 400.0)
oedepict.OEConfigureImageGridParams(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
rows = oedepict.OEGetImageGridNumRows(itf)
cols = oedepict.OEGetImageGridNumColumns(itf)
grid = oedepict.OEImageGrid(image, rows, cols)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
celliter = grid.GetCells()
for iname in itf.GetStringList("-in"):
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Warning("Cannot open %s input file!" % iname)
continue
for mol in ifs.GetOEGraphMols():
if not celliter.IsValid():
break
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(celliter.Target(), disp)
celliter.Next()
oedepict.OEWriteImage(ofs, ext, image)
return 0
def repo_new(self, oid, filename, hitsize, remote_addr):
ext = oechem.OEGetFileExtension(filename)
basename = filename[:-len(ext) - 1]
reportable = 0 if ext == 'sq' else 1
timestamp1 = time.time()
self('INSERT into repo (oid, basename, ext, hitsize, reportable, timestamp1, ip) '
'VALUES (?,?,?,?,?,?,?)', \
(oid, basename, ext, hitsize, reportable, timestamp1, remote_addr),
commit=True)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oegraphsim.OEConfigureFingerPrint(
itf, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
if not oechem.OEParseCommandLine(itf, argv):
return 1
ifname = itf.GetString("-in")
ffname = itf.GetString("-fpdb")
if oechem.OEGetFileExtension(ffname) != "fpbin":
oechem.OEThrow.Fatal(
"Fingerprint database file should have '.fpbin' file extension!")
idxfname = oechem.OEGetMolDatabaseIdxFileName(ifname)
if not os.path.exists(idxfname):
if not oechem.OECreateMolDatabaseIdx(ifname):
oechem.OEThrow.Warning("Unable to create %s molecule index file" %
idxfname)
oechem.OEThrow.Info("Using %s index molecule file" % idxfname)
moldb = oechem.OEMolDatabase()
if not moldb.Open(ifname):
oechem.OEThrow.Fatal("Cannot open molecule database file!")
nrmols = moldb.GetMaxMolIdx()
fptype = oegraphsim.OESetupFingerPrint(itf)
oechem.OEThrow.Info("Using fingerprint type %s" % fptype.GetFPTypeString())
opts = oegraphsim.OECreateFastFPDatabaseOptions(fptype)
opts.SetTracer(oechem.OEDots(100000, 1000, "fingerprints"))
oechem.OEThrow.Info("Generating fingerprints with %d threads" %
opts.GetNumProcessors())
timer = oechem.OEWallTimer()
if not oegraphsim.OECreateFastFPDatabaseFile(ffname, ifname, opts):
oechem.OEThrow.Fatal("Cannot create fingerprint database file!")
oechem.OEThrow.Info("%5.2f secs to generate %d fingerprints" %
(timer.Elapsed(), nrmols))
return 0
def upload(self, file, hitsize, remote_addr):
oid = uuid.uuid4().hex
filename = secure_filename(file.filename)
ext = oechem.OEGetFileExtension(filename)
os.makedirs(f'instance/{oid}', exist_ok=True)
opath = f'instance/{oid}/query.{ext}'
file.save(opath)
if ext != 'sq' and not misc.check_mol(opath):
os.unlink(opath)
return
st = state.State()
print('hitsize:', hitsize) #@@
st.repo_new(oid, filename, hitsize, remote_addr)
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 main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
if ifs.GetFormat() != oechem.OEFormat_MDL:
oechem.OEThrow.Fatal("Input file is not an MDL query file")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMDLQueryFile(ifs, mol):
oechem.OEThrow.Fatal("Cannot read mdl query input file!")
clearcoords, suppressH = False, False
oedepict.OEPrepareDepiction(mol, clearcoords, suppressH)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def __init__(self, ipf, keepAlts=F, verbose=T):
self.ipf = ipf
self.keepAlts = keepAlts
self.verbose = verbose
flavor = oechem.OEIFlavor_PDB_Default
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, flavor)
if not ims.open(self.ipf):
oechem.OEThrow.Fatal("Unable to open %s for reading." % self.ipf)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % self.ipf)
iftp = oechem.OEGetFileType(oechem.OEGetFileExtension(self.ipf))
if (iftp == oechem.OEFormat_PDB) and not self.keepAlts:
oechem.OEThrow.Verbose(
"Default processing of alt locations (keep just 'A' and ' ').")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Unable to read %s." % self.ipf)
ims.close()
if (inmol.NumAtoms() == 0):
oechem.OEThrow.Fatal("Input molecule %s contains no atoms." %
self.ipf)
if inmol.GetTitle() == "":
inmol.SetTitle(ipf[:-4])
oechem.OEThrow.Verbose("Processing %s." % inmol.GetTitle())
if not oechem.OEHasResidues(inmol):
oechem.OEPerceiveResidues(inmol, oechem.OEPreserveResInfo_All)
self.inmol = inmol
self.mol = inmol.CreateCopy()
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 900.0)
oedepict.OEConfigureImageHeight(itf, 600.0)
oedepict.OEConfigure2DMolDisplayOptions(
itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
oechem.OEConfigureSplitMolComplexOptions(
itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
# Separate ligand and protein
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
ligand = oechem.OEGraphMol()
protein = oechem.OEGraphMol()
water = oechem.OEGraphMol()
other = oechem.OEGraphMol()
pfilter = sopts.GetProteinFilter()
wfilter = sopts.GetWaterFilter()
sopts.SetProteinFilter(oechem.OEOrRoleSet(pfilter, wfilter))
sopts.SetWaterFilter(
oechem.OEMolComplexFilterFactory(
oechem.OEMolComplexFilterCategory_Nothing))
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Perceive interactions
asite = oechem.OEInteractionHintContainer(protein, ligand)
if not asite.IsValid():
oechem.OEThrow.Fatal("Cannot initialize active site!")
asite.SetTitle(ligand.GetTitle())
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)
# Depict active site with interactions
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
cframe = oedepict.OEImageFrame(image, width * 0.80, height,
oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, width * 0.20, height,
oedepict.OE2DPoint(width * 0.80, 0.0))
opts = oegrapheme.OE2DActiveSiteDisplayOptions(cframe.GetWidth(),
cframe.GetHeight())
oedepict.OESetup2DMolDisplayOptions(opts, itf)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(cframe, adisp)
lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(10, 1)
oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts)
oedepict.OEWriteImage(oname, image)
return 0
def main(argv=[__name__]):
if len(argv) < 3:
oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])
return 0
# check system
if not oefastrocs.OEFastROCSIsGPUReady():
oechem.OEThrow.Info("No supported GPU available!")
return 0
# read in database
dbname = argv[1]
print("Opening database file %s ..." % dbname)
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
# customize search options
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetInitialOrientation(
oefastrocs.OEFastROCSOrientation_UserInertialStarts)
opts.SetLimit(5)
for qfname in argv[2:]:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)
ext = oechem.OEGetFileExtension(qfname)
base = qfname[:-(len(ext) + 1)]
# write out everthing to a similary named file
ofs = oechem.oemolostream()
ofname = base + "_user_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
oechem.OEWriteMolecule(ofs, query)
startsCoords = oechem.OEFloatVector()
atomIdx = 1
xyz = query.GetCoords()[atomIdx]
for x in xyz:
startsCoords.append(x)
if not len(startsCoords) % 3 == 0:
oechem.OEThrow.Fatal(
"Something went wrong whilst reading in user-starts coordinates"
)
opts.SetUserStarts(oechem.OEFloatVector(startsCoords),
int(len(startsCoords) / 3))
opts.SetMaxOverlays(opts.GetNumInertialStarts() *
opts.GetNumUserStarts())
if opts.GetInitialOrientation(
) == oefastrocs.OEFastROCSOrientation_UserInertialStarts:
numStarts = opts.GetNumUserStarts()
print("This example will use %u starts" % numStarts)
print("Searching for %s" % qfname)
for score in dbase.GetSortedScores(query, opts):
print("Score for mol %u(conf %u) %f shape %f color" %
(score.GetMolIdx(), score.GetConfIdx(),
score.GetShapeTanimoto(), score.GetColorTanimoto()))
dbmol = oechem.OEMol()
molidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, molidx):
print("Unable to retrieve molecule '%u' from the database" %
molidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
print("Wrote results to %s" % ofname)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
oedepict.OEConfigureHighlightParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
smarts = itf.GetString("-smarts")
ss = oechem.OESubSearch()
if not ss.Init(smarts):
oechem.OEThrow.Fatal("Cannot parse smarts: %s" % smarts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetMargins(10.0)
disp = oedepict.OE2DMolDisplay(mol, dopts)
hstyle = oedepict.OEGetHighlightStyle(itf)
hcolor = oedepict.OEGetHighlightColor(itf)
oechem.OEPrepareSearch(mol, ss)
unique = True
for match in ss.Match(mol, unique):
oedepict.OEAddHighlighting(disp, hcolor, hstyle, match)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 900.0)
oedepict.OEConfigureImageHeight(itf, 600.0)
oedepict.OEConfigure2DMolDisplayOptions(
itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
oechem.OEConfigureSplitMolComplexOptions(
itf, oechem.OESplitMolComplexSetup_LigName
| oechem.OESplitMolComplexSetup_CovLig)
if not oechem.OEParseCommandLine(itf, argv):
return 1
if itf.HasString("-complex") and (itf.HasString("-protein")
or itf.HasString("-ligand")):
oechem.OEThrow.Warning("Only complex in %s file fill be used!" %
itf.GetString("-complex"))
if not (itf.HasString("-complex")) ^ (itf.HasString("-protein")
and itf.HasString("-ligand")):
oechem.OEThrow.Fatal(
"Please specify either complex or ligand and protein input files!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
# initialize protein and ligand
protein = oechem.OEGraphMol()
ligand = oechem.OEGraphMol()
if not get_protein_and_ligands(protein, ligand, itf):
oechem.OEThrow.Fatal("Cannot initialize protein and/or ligand!")
# depict active site with interactions
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
interactive_legend = False
magnify_residue = 1.0
if ext == 'svg':
interactive_legend = itf.GetBool("-interactive-legend")
magnify_residue = itf.GetFloat("-magnify-residue")
cwidth, cheight = width, height
if not interactive_legend:
cwidth = cwidth * 0.8
opts = oegrapheme.OE2DActiveSiteDisplayOptions(cwidth, cheight)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetRenderInteractiveLegend(interactive_legend)
opts.SetSVGMagnifyResidueInHover(magnify_residue)
if interactive_legend:
depict_complex(image, protein, ligand, opts)
else:
main_frame = oedepict.OEImageFrame(
image, width * 0.80, height, oedepict.OE2DPoint(width * 0.2, 0.0))
legend_frame = oedepict.OEImageFrame(
image, width * 0.20, height, oedepict.OE2DPoint(width * 0.0, 0.0))
depict_complex(main_frame, protein, ligand, opts, legend_frame)
if ext == 'svg' and (interactive_legend or magnify_residue > 1.0):
iconscale = 0.5
oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight,
iconscale)
oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteImage(oname, image)
return 0
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from openeye import oechem
import sys
if len(sys.argv) != 4:
oechem.OEThrow.Usage("%s <input> <output> <title>" % sys.argv[0])
moldb = oechem.OEMolDatabase()
if not moldb.Open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s" % sys.argv[1])
if moldb.GetFormat() != oechem.OEGetFileType(
oechem.OEGetFileExtension(sys.argv[2])):
oechem.OEThrow.Fatal(
"Output format does not match input format: %s != %s" %
(oechem.OEGetFileExtension(
sys.argv[1]), oechem.OEGetFileExtension(sys.argv[2])))
ofs = oechem.oemolostream()
if not ofs.open(sys.argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % sys.argv[2])
title = sys.argv[3]
for idx in range(moldb.GetMaxMolIdx()):
if moldb.GetTitle(idx) == title:
moldb.WriteMolecule(ofs, idx)
# @ </SNIPPET>
def is_allowed_file(name):
d = read_config()
return oechem.OEGetFileExtension(name) in d['ALLOWED_EXTENSIONS']
def render_atom_mapping(filename, molecule1, molecule2, new_to_old_atom_map, width=1200, height=600):
"""
Render the atom mapping to a PDF file.
Parameters
----------
filename : str
The PDF filename to write to.
molecule1 : openeye.oechem.OEMol
Initial molecule
molecule2 : openeye.oechem.OEMol
Final molecule
new_to_old_atom_map : dict of int
new_to_old_atom_map[molecule2_atom_index] is the corresponding molecule1 atom index
width : int, optional, default=1200
Width in pixels
height : int, optional, default=1200
Height in pixels
"""
from openeye import oechem, oedepict
# Make copies of the input molecules
molecule1, molecule2 = oechem.OEGraphMol(molecule1), oechem.OEGraphMol(molecule2)
oechem.OEGenerate2DCoordinates(molecule1)
oechem.OEGenerate2DCoordinates(molecule2)
# Add both to an OEGraphMol reaction
rmol = oechem.OEGraphMol()
rmol.SetRxn(True)
def add_molecule(mol):
# Add atoms
new_atoms = list()
old_to_new_atoms = dict()
for old_atom in mol.GetAtoms():
new_atom = rmol.NewAtom(old_atom.GetAtomicNum())
new_atoms.append(new_atom)
old_to_new_atoms[old_atom] = new_atom
# Add bonds
for old_bond in mol.GetBonds():
rmol.NewBond(old_to_new_atoms[old_bond.GetBgn()], old_to_new_atoms[old_bond.GetEnd()], old_bond.GetOrder())
return new_atoms, old_to_new_atoms
[new_atoms_1, old_to_new_atoms_1] = add_molecule(molecule1)
[new_atoms_2, old_to_new_atoms_2] = add_molecule(molecule2)
# Label reactant and product
for atom in new_atoms_1:
atom.SetRxnRole(oechem.OERxnRole_Reactant)
for atom in new_atoms_2:
atom.SetRxnRole(oechem.OERxnRole_Product)
core1 = oechem.OEAtomBondSet()
core2 = oechem.OEAtomBondSet()
# add all atoms to the set
core1.AddAtoms(new_atoms_1)
core2.AddAtoms(new_atoms_2)
# Label mapped atoms
core_change = oechem.OEAtomBondSet()
index =1
for (index2, index1) in new_to_old_atom_map.items():
new_atoms_1[index1].SetMapIdx(index)
new_atoms_2[index2].SetMapIdx(index)
# now remove the atoms that are core, so only uniques are highlighted
core1.RemoveAtom(new_atoms_1[index1])
core2.RemoveAtom(new_atoms_2[index2])
if new_atoms_1[index1].GetAtomicNum() != new_atoms_2[index2].GetAtomicNum():
# this means the element type is changing
core_change.AddAtom(new_atoms_1[index1])
core_change.AddAtom(new_atoms_2[index2])
index += 1
# Set up image options
itf = oechem.OEInterface()
oedepict.OEConfigureImageOptions(itf)
ext = oechem.OEGetFileExtension(filename)
if not oedepict.OEIsRegisteredImageFile(ext):
raise Exception('Unknown image type for filename %s' % filename)
ofs = oechem.oeofstream()
if not ofs.open(filename):
raise Exception('Cannot open output file %s' % filename)
# Setup depiction options
oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetBondWidthScaling(True)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx())
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
# Depict reaction with component highlights
oechem.OEGenerate2DCoordinates(rmol)
rdisp = oedepict.OE2DMolDisplay(rmol, opts)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPink),oedepict.OEHighlightStyle_Stick, core1)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPurple),oedepict.OEHighlightStyle_Stick, core2)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEGreen),oedepict.OEHighlightStyle_Stick, core_change)
oedepict.OERenderMolecule(ofs, ext, rdisp)
ofs.close()
def main(argv=[__name__]):
"""
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
return 1
oname = itf.GetString("-out")
iname = itf.GetString("-in")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
## INPUT PARAMETERS
#########################################################
#########################################################
mm = 'tyk2/og_pdbs'
qml = 'tyk2/forward_snapshots'
phase = 'solvent'
which_ligand = 'old'
dir_name = iname
ligand_pdbs_mm = glob.glob(f"{mm}/{dir_name}/{which_ligand}*{phase}.pdb")
print(len(ligand_pdbs_mm))
ligand_pdbs_qml = glob.glob(f"{qml}/{dir_name}/{which_ligand}*{phase}.pdb")
print(len(ligand_pdbs_qml))
#d = np.load('full_data_dict.npy', allow_pickle=True)
from_ligand, to_ligand = iname.replace('from', '').replace('to', '').replace('lig', '')
print(from_ligand)
print(to_ligand)
#key1 = (1, 8)
#key2 = ('solvent', which_ligand)
#########################################################
#########################################################
#d = d.flatten()[0]
#work = d[key1][key2]
#print(work)
for i, (mm_pdb_path, ani_pdb_path) in enumerate(zip(ligand_pdbs_mm, ligand_pdbs_qml)):
print(mm_pdb_path, ani_pdb_path)
if i == 0:
MM_mol = createOEMolFromSDF(mm_pdb_path, 0)
ANI_mol = createOEMolFromSDF(ani_pdb_path, 0)
else:
# there absolutely must be a better/faster way of doing this because this is ugly and slow
MM_mol.NewConf(createOEMolFromSDF(mm_pdb_path, 0))
ANI_mol.NewConf(createOEMolFromSDF(ani_pdb_path, 0))
"""
ofs = oechem.oeofstream()
oname = f"tor_out"
ext = oechem.OEGetFileExtension(oname)
mm_pdb_path = f"og_lig0_solvent.pdb"
ani_pdb_path = f"forward_lig0.solvent.pdb"
MM_mol = createOEMolFromSDF(mm_pdb_path, 0)
ANI_mol = createOEMolFromSDF(ani_pdb_path, 0)
mol = MM_mol
mol2 = ANI_mol
for m in [mol, mol2]:
oechem.OESuppressHydrogens(m)
oechem.OECanonicalOrderAtoms(m)
oechem.OECanonicalOrderBonds(m)
m.Sweep()
refmol = None
stag = "dihedral_histogram"
itag = oechem.OEGetTag(stag)
nrbins = 20
print(mol.NumConfs())
print(mol2.NumConfs())
get_dihedrals(mol, itag)
set_dihedral_histograms(mol, itag, nrbins)
get_dihedrals(mol2, itag)
#set_weighted_dihedral_histograms(mol2, itag, work, nrbins)
set_dihedral_histograms(mol2, itag, nrbins)
width, height = 800, 400
image = oedepict.OEImage(width, height)
moffset = oedepict.OE2DPoint(0, 0)
mframe = oedepict.OEImageFrame(image, width * 0.70, height, moffset)
doffset = oedepict.OE2DPoint(mframe.GetWidth(), height * 0.30)
dframe = oedepict.OEImageFrame(image, width * 0.30, height * 0.5, doffset)
flexibility = True
colorg = get_color_gradient(nrbins, flexibility)
opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(),
mframe.GetHeight(),
oedepict.OEScale_AutoScale)
depict_dihedrals(mframe, dframe, mol, mol2, refmol, opts, itag, nrbins,
colorg)
if flexibility:
lopts = oedepict.OELegendLayoutOptions(
oedepict.OELegendLayoutStyle_HorizontalTopLeft,
oedepict.OELegendColorStyle_LightBlue,
oedepict.OELegendInteractiveStyle_Hover)
lopts.SetButtonWidthScale(1.2)
lopts.SetButtonHeightScale(1.2)
lopts.SetMargin(oedepict.OEMargin_Right, 40.0)
lopts.SetMargin(oedepict.OEMargin_Bottom, 80.0)
legend = oedepict.OELegendLayout(image, "Legend", lopts)
legend_area = legend.GetLegendArea()
draw_color_gradient(legend_area, colorg)
oedepict.OEDrawLegendLayout(legend)
iconscale = 0.5
oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight,
iconscale)
oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteImage(ofs, ext, image)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 600.0)
oedepict.OEConfigureImageHeight(itf, 600.0)
oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
oechem.OEConfigureSplitMolComplexOptions(itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
# Separate ligand and protein
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
ligand = oechem.OEGraphMol()
protein = oechem.OEGraphMol()
water = oechem.OEGraphMol()
other = oechem.OEGraphMol()
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Calculate average BFactor of the whole complex
avgbfactor = GetAverageBFactor(complexmol)
# Calculate minimum and maximum BFactor of the ligand and its environment
minbfactor, maxbfactor = GetMinAndMaxBFactor(ligand, protein)
# Attach to each ligand atom the average BFactor of the nearby protein atoms
stag = "avg residue BFfactor"
itag = oechem.OEGetTag(stag)
SetAverageBFactorOfNearbyProteinAtoms(ligand, protein, itag)
oechem.OEThrow.Info("Average BFactor of the complex = %+.3f" % avgbfactor)
oechem.OEThrow.Info("Minimum BFactor of the ligand and its environment = %+.3f" % minbfactor)
oechem.OEThrow.Info("Maximum BFactor of the ligand and its environment = %+.3f" % maxbfactor)
# Create image
imagewidth, imageheight = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
image = oedepict.OEImage(imagewidth, imageheight)
mframe = oedepict.OEImageFrame(image, imagewidth,
imageheight * 0.90, oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.10,
oedepict.OE2DPoint(0.0, imageheight * 0.90))
opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(), mframe.GetHeight(),
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
# Create BFactor color gradient
colorg = oechem.OELinearColorGradient()
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEDarkBlue))
colorg.AddStop(oechem.OEColorStop(10.0, oechem.OELightBlue))
colorg.AddStop(oechem.OEColorStop(25.0, oechem.OEYellowTint))
colorg.AddStop(oechem.OEColorStop(50.0, oechem.OERed))
colorg.AddStop(oechem.OEColorStop(100.0, oechem.OEDarkRose))
# Prepare ligand for depiction
oegrapheme.OEPrepareDepictionFrom3D(ligand)
arcfxn = BFactorArcFxn(colorg, itag)
for atom in ligand.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(ligand, atom, arcfxn)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(ligand, opts))
# Render ligand and visualize BFactor
disp = oedepict.OE2DMolDisplay(ligand, opts)
colorbfactor = ColorLigandAtomByBFactor(colorg)
oegrapheme.OEAddGlyph(disp, colorbfactor, oechem.OEIsTrueAtom())
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(mframe, disp)
# Draw color gradient
opts = oegrapheme.OEColorGradientDisplayOptions()
opts.SetColorStopPrecision(1)
opts.AddMarkedValue(avgbfactor)
opts.SetBoxRange(minbfactor, maxbfactor)
oegrapheme.OEDrawColorGradient(lframe, colorg, opts)
oedepict.OEWriteImage(oname, image)
return 0
def main(argv=[__name__]):
if len(argv) < 3:
oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])
dbname = argv[1]
# read in database
ifs = oechem.oemolistream()
if not ifs.open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
print("Opening database file %s ..." % dbname)
timer = oechem.OEWallTimer()
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(ifs):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
dots.Total()
print("%s seconds to load database" % timer.Elapsed())
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetSimFunc(oefastrocs.OEShapeSimFuncType_Tversky)
numHits = moldb.NumMols()
opts.SetLimit(numHits)
for qfname in argv[2:]:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[1])
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % argv[1])
ext = oechem.OEGetFileExtension(qfname)
base = qfname[:-(len(ext) + 1)]
# write out everthing to a similary named file
ofs = oechem.oemolostream()
ofname = base + "_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
print("Searching for %s" % qfname)
for score in dbase.GetSortedScores(query, opts):
dbmol = oechem.OEMol()
molidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, molidx):
print("Unable to retrieve molecule '%u' from the database" %
molidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "ShapeTversky",
"%.4f" % score.GetShapeTversky())
oechem.OESetSDData(mol, "ColorTversky",
"%.4f" % score.GetColorTversky())
oechem.OESetSDData(mol, "TverskyCombo",
"%.4f" % score.GetTverskyCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
print("Wrote results to %s" % ofname)
return 0
def main(argv=[__name__]):
if len(argv) < 3:
oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])
return 0
# check system
if not oefastrocs.OEFastROCSIsGPUReady():
oechem.OEThrow.Info("No supported GPU available!")
return 0
# read in database
dbname = argv[1]
print("Opening database file %s ..." % dbname)
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
# customize search options
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetLimit(5)
for qfname in argv[2:]:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)
ext = oechem.OEGetFileExtension(qfname)
base = qfname[:-(len(ext) + 1)]
# write out everthing to a similary named file
ofs = oechem.oemolostream()
ofname = base + "_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
oechem.OEWriteMolecule(ofs, query)
print("Searching for %s" % qfname)
for score in dbase.GetSortedScores(query, opts):
print("Score for mol %u(conf %u) %f shape %f color" %
(score.GetMolIdx(), score.GetConfIdx(),
score.GetShapeTanimoto(), score.GetColorTanimoto()))
dbmol = oechem.OEMol()
molidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, molidx):
print("Unable to retrieve molecule '%u' from the database" %
molidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
print("Wrote results to %s" % ofname)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
oedepict.OEConfigureHighlightParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
qname = itf.GetString("-query")
tname = itf.GetString("-target")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredMultiPageImageFile(ext):
oechem.OEThrow.Fatal("Unknown multipage image type!")
qfile = oechem.oemolistream()
if not qfile.open(qname):
oechem.OEThrow.Fatal("Cannot open mdl query file!")
if qfile.GetFormat() != oechem.OEFormat_MDL and qfile.GetFormat(
) != oechem.OEFormat_SDF:
oechem.OEThrow.Fatal("Query file has to be an MDL file!")
ifs = oechem.oemolistream()
if not ifs.open(tname):
oechem.OEThrow.Fatal("Cannot open target input file!")
depictquery = oechem.OEGraphMol()
if not oechem.OEReadMDLQueryFile(qfile, depictquery):
oechem.OEThrow.Fatal("Cannot read query molecule!")
oedepict.OEPrepareDepiction(depictquery)
queryopts = oechem.OEMDLQueryOpts_Default | oechem.OEMDLQueryOpts_SuppressExplicitH
qmol = oechem.OEQMol()
oechem.OEBuildMDLQueryExpressions(qmol, depictquery, queryopts)
ss = oechem.OESubSearch()
if not ss.Init(qmol):
oechem.OEThrow.Fatal("Cannot initialize substructure search!")
hstyle = oedepict.OEGetHighlightStyle(itf)
hcolor = oedepict.OEGetHighlightColor(itf)
align = itf.GetBool("-align")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetHeaderHeight(140.0)
report = oedepict.OEReport(ropts)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
dopts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
unique = True
for mol in ifs.GetOEGraphMols():
oechem.OEPrepareSearch(mol, ss)
miter = ss.Match(mol, unique)
if not miter.IsValid():
continue # no match
alignres = oedepict.OEAlignmentResult(miter.Target())
if align:
alignres = oedepict.OEPrepareAlignedDepiction(mol, ss)
else:
oedepict.OEPrepareDepiction(mol)
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, dopts)
if alignres.IsValid():
oedepict.OEAddHighlighting(disp, hcolor, hstyle, alignres)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawBorder(cell, oedepict.OELightGreyPen)
# render query structure in each header
headwidth, headheight = report.GetHeaderWidth(), report.GetHeaderHeight()
dopts.SetDimensions(headwidth, headheight, oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(depictquery, dopts)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, oedepict.OELightGreyPen)
oedepict.OEWriteReport(oname, report)
return 0
def main(argv=[__name__]):
parser = argparse.ArgumentParser()
# positional arguments retaining backward compatibility
parser.add_argument(
'database',
help='File containing the database molecules to be search \
(format not restricted to *.oeb).')
parser.add_argument(
'query',
default=[],
nargs='+',
help='File containing the query molecule(s) to be search \
(format not restricted to *.oeb).')
parser.add_argument(
'--nHits',
dest='nHits',
type=int,
default=100,
help='Number of hits to return (default = number of database mols).')
parser.add_argument('--cutoff',
dest='cutoff',
type=float,
default=argparse.SUPPRESS,
help='Specify a cutoff criteria for scores.')
parser.add_argument(
'--tversky',
dest='tversky',
action='store_true',
default=argparse.SUPPRESS,
help='Switch to Tversky similarity scoring (default = Tanimoto).')
args = parser.parse_args()
dbname = args.database
if not oefastrocs.OEFastROCSIsGPUReady():
oechem.OEThrow.Info("No supported GPU available!")
return 0
# set options
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetLimit(args.nHits)
print("Number of hits set to %u" % opts.GetLimit())
if hasattr(args, 'cutoff') is not False:
opts.SetCutoff(args.cutoff)
print("Cutoff set to %f" % args.cutoff)
if hasattr(args, 'tversky') is not False:
opts.SetSimFunc(args.tversky)
print("Tversky similarity scoring set.")
# read in database
ifs = oechem.oemolistream()
if not ifs.open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
print("\nOpening database file %s ..." % dbname)
timer = oechem.OEWallTimer()
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(ifs):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
dots.Total()
print("%f seconds to load database\n" % timer.Elapsed())
for qfname in args.query:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)
mcmol = oechem.OEMol()
if not oechem.OEReadMolecule(qfs, mcmol):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)
qfs.rewind()
ext = oechem.OEGetFileExtension(qfname)
qmolidx = 0
while oechem.OEReadMolecule(qfs, mcmol):
# write out to file name based on molecule title
ofs = oechem.oemolostream()
moltitle = mcmol.GetTitle()
if len(moltitle) == 0:
moltitle = str(qmolidx)
ofname = moltitle + "_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
print("Searching for %s of %s (%s conformers)" %
(moltitle, qfname, mcmol.NumConfs()))
qconfidx = 0
for conf in mcmol.GetConfs():
for score in dbase.GetSortedScores(conf, opts):
dbmol = oechem.OEMol()
dbmolidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, dbmolidx):
print(
"Unable to retrieve molecule '%u' from the database"
% dbmolidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "QueryConfidx", "%s" % qconfidx)
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
qconfidx += 1
print("%s conformers processed" % qconfidx)
print("Wrote results to %s\n" % ofname)
qmolidx += 1
return 0
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oedepict
import sys
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <imagefile>" % sys.argv[0])
# @ <SNIPPET-OEIsRegisteredImageFile>
filename = sys.argv[1]
ext = oechem.OEGetFileExtension(filename)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
# @ </SNIPPET-OEIsRegisteredImageFile>
