def main(argv=(__name__)):
"""
the protein should have charges and radii but the ligand need not
"""
itf = oechem.OEInterface()
if not oechem.OEConfigure(itf, InterfaceData):
oechem.OEThrow.Fatal("Problem configuring OEInterface!")
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to parse command line")
ligFile = itf.GetString("-l")
ims = oechem.oemolistream()
if not ims.open(ligFile):
oechem.OEThrow.Fatal("Unable to open %s for reading" % ligFile)
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(ims, lig)
contextFile = itf.GetString("-p")
ims = oechem.oemolistream()
if not ims.open(contextFile):
oechem.OEThrow.Fatal("Unable to open %s for reading" % contextFile)
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(ims, prot)
highRes = itf.GetBool("-high_res")
GetSzmapEnergies(lig, prot, highRes)
def main(argv=[__name__]):
# import configuration file
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
# add configuration for image size and display options
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ifname = itf.GetString("-in")
ofname = itf.GetString("-out")
ifs = oechem.oemolistream(ifname)
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oedepict.OEPrepareDepiction(mol)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
# set up display options from command line parameters
oedepict.OESetup2DMolDisplayOptions(opts, itf)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(ofname, disp)
def main(argv=(__name__)):
"""
the protein should have charges and radii but the ligand need not
"""
itf = oechem.OEInterface()
if not oechem.OEConfigure(itf, InterfaceData):
oechem.OEThrow.Fatal("Problem configuring OEInterface!")
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to parse command line")
ligFile = itf.GetString("-l")
ims = oechem.oemolistream()
if not ims.open(ligFile):
oechem.OEThrow.Fatal("Unable to open %s for reading" % ligFile)
lig = oechem.OEGraphMol()
oechem.OEReadMolecule(ims, lig)
contextFile = itf.GetString("-p")
ims = oechem.oemolistream()
if not ims.open(contextFile):
oechem.OEThrow.Fatal("Unable to open %s for reading" % contextFile)
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(ims, prot)
outputFile = itf.GetString("-o")
oms = oechem.oemolostream()
if not oms.open(outputFile):
oechem.OEThrow.Fatal("Unable to open %s for writing" % outputFile)
GenerateSzmapProbes(oms, itf.GetDouble("-prob"), lig, prot)
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 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 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)
defopts = oegraphsim.OEFPDatabaseOptions(10,
oegraphsim.OESimMeasure_Tanimoto)
oegraphsim.OEConfigureFPDatabaseOptions(itf, defopts)
oegraphsim.OEConfigureFPDatabaseMemoryType(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 0
qfname = itf.GetString("-query")
mfname = itf.GetString("-molfname")
ffname = itf.GetString("-fpdbfname")
ofname = itf.GetString("-out")
# initialize databases
timer = oechem.OEWallTimer()
timer.Start()
ifs = oechem.oemolistream()
if not ifs.open(qfname):
oechem.OEThrow.Fatal("Cannot open input file!")
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, query):
oechem.OEThrow.Fatal("Cannot read query molecule!")
moldb = oechem.OEMolDatabase()
if not moldb.Open(mfname):
oechem.OEThrow.Fatal("Cannot open molecule database!")
memtype = oegraphsim.OEGetFPDatabaseMemoryType(itf)
fpdb = oegraphsim.OEFastFPDatabase(ffname, memtype)
if not fpdb.IsValid():
oechem.OEThrow.Fatal("Cannot open fingerprint database!")
nrfps = fpdb.NumFingerPrints()
memtypestr = fpdb.GetMemoryTypeString()
ofs = oechem.oemolostream()
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Cannot open output file!")
if not oegraphsim.OEAreCompatibleDatabases(moldb, fpdb):
oechem.OEThrow.Fatal("Databases are not compatible!")
oechem.OEThrow.Info("%5.2f sec to initialize databases" % timer.Elapsed())
fptype = fpdb.GetFPTypeBase()
oechem.OEThrow.Info("Using fingerprint type %s" % fptype.GetFPTypeString())
opts = oegraphsim.OEFPDatabaseOptions()
oegraphsim.OESetupFPDatabaseOptions(opts, itf)
# search fingerprint database
timer.Start()
scores = fpdb.GetSortedScores(query, opts)
oechem.OEThrow.Info("%5.2f sec to search %d fingerprints %s" %
(timer.Elapsed(), nrfps, memtypestr))
timer.Start()
nrhits = 0
hit = oechem.OEGraphMol()
for si in scores:
if moldb.GetMolecule(hit, si.GetIdx()):
nrhits += 1
oechem.OESetSDData(hit, "Similarity score", "%.2f" % si.GetScore())
oechem.OEWriteMolecule(ofs, hit)
oechem.OEThrow.Info("%5.2f sec to write %d hits" %
(timer.Elapsed(), nrhits))
return 0
!END
!PARAMETER -i
!TYPE int
!BRIEF An integer parameter
!END
!PARAMETER -f
!TYPE float
!BRIEF A float parameter
!END
!PARAMETER -str
!TYPE string
!BRIEF A string parameter
!END
"""
# @ <SNIPPET-OEINTERFACE-CONVENIENCE>
itf = oechem.OEInterface()
if not oechem.OEConfigure(itf, InterfaceData):
oechem.OEThrow.Fatal("Problem configuring OEInterface!")
if not oechem.OEParseCommandLine(itf, sys.argv):
oechem.OEThrow.Fatal("Unable to parse command line")
# @ </SNIPPET-OEINTERFACE-CONVENIENCE>
print("-b =", itf.GetBool("-b"))
print("-i =", itf.GetInt("-i"))
print("-f =", itf.GetFloat("-f"))
print("-str =", itf.GetString("-str"))
# @ </SNIPPET>
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__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, Interface)
OEAddParameterColors(itf, "-atom_contribution_positive_color")
OEAddParameterColors(itf, "-atom_contribution_negative_color")
OEAddParameterColors(itf, "-classification_colors")
if not oechem.OEParseCommandLine(itf, argv):
return 1
# Figure out output file name
outFile = OEGetFilename(itf, "-molecule_file")
reportFile = OEGetFilename(itf, "-report_file")
failTrainFile = OEGetFilename(itf, "-training_fail_file")
failKrigeFile = OEGetFilename(itf, "-prediction_fail_file")
settingsFile = OEGetFilename(itf, "-settings_file")
# Write the settings file and splash to screen
oechem.OEWriteSettings(itf, oechem.oeout, False)
ofs = oechem.oeofstream(settingsFile)
oechem.OEWriteSettings(itf, ofs, True)
ofs.close()
# Setup report options
rOpts = oestats.OEKrigeReportOptions()
if itf.HasString("-report_title"):
rOpts.SetTitle(itf.GetString("-report_title"))
if itf.HasString("-response_name"):
rOpts.SetResponseName(itf.GetString("-response_name"))
responseName = itf.GetString("-response_name")
else:
rOpts.SetResponseName(itf.GetString("-response_tag"))
responseName = itf.GetString("-response_tag")
if itf.HasString("-atom_contribution_negative_color"):
color = OETextToColor(
itf.GetString("-atom_contribution_negative_color"))
rOpts.SetContributionNegativeColor(color)
if itf.HasString("-atom_contribution_positive_color"):
color = OETextToColor(
itf.GetString("-atom_contribution_positive_color"))
rOpts.SetContributionPositiveColor(color)
iExtra = 0
while itf.HasString("-report_tagged_data", iExtra):
rOpts.PushSDProperty(itf.GetString("-report_tagged_data", iExtra))
iExtra += 1
iClass = 0
while itf.HasDouble("-classification_boundries", iClass):
boundry = itf.GetDouble("-classification_boundries", iClass)
if itf.GetBool("-krige_log"):
boundry = log10(boundry)
rOpts.PushClassificationBoundry(boundry)
iClass += 1
iClass = 0
while itf.HasString("-classification_colors", iClass):
color = OETextToColor(itf.GetString("-classification_colors", iClass))
rOpts.PushClassificationColor(color)
iClass += 1
if itf.GetBool("-hide_krige_details"):
rOpts.SetShowKrigeDetails(False)
else:
rOpts.SetShowKrigeDetails(True)
rOpts.SetUnlog(itf.GetBool("-krige_log"))
rOpts.SetShowConfidence(itf.GetBool("-show_response_confidence"))
rOpts.SetResponseSignificantFigures(
itf.GetUnsignedInt("-report_significant_figures"))
if itf.HasString("-atom_contribution_positive_label"):
rOpts.SetContributionPositiveLabel(
itf.GetString("-atom_contribution_positive_label"))
if itf.HasString("-atom_contribution_negative_label"):
rOpts.SetContributionNegativeLabel(
itf.GetString("-atom_contribution_negative_label"))
if itf.HasDouble("-atom_contribution_baseline_response"):
baseline = itf.GetDouble("-atom_contribution_baseline_response")
if itf.GetBool("-krige_log"):
baseline = log10(baseline)
rOpts.SetContributionBaseline(baseline)
# Figure out the trend properties for universal kriging if we have them
universalProps = oechem.OEMolPropertyList()
iProp = 0
while itf.HasString("-universal_prop", iProp):
propStr = itf.GetString("-universal_prop", iProp)
if propStr == "mw":
universalProps.Add(oestats.OEMolecularWeightPropertyFxn())
rOpts.PushProperty(oestats.OEMolecularWeightPropertyFxn(),
"Molecular Weight")
else:
oechem.OEThrow.Error(
"Unknow property (%s) passed to -universal_prop" % propStr)
iProp += 1
# Setup the object for getting the response from the training molecules
responseFxn = oechem.OEMolTaggedPropertyFxn(itf.GetString("-response_tag"))
if itf.GetBool("-krige_log"):
responseFxn = oestats.OEMolLog10PropertyFxn(responseFxn)
# Construct the krige
if itf.HasUnsignedInt("-local_krige"):
opts = oestats.OELocalKrigeOptions()
opts.SetNumLocal(itf.GetUnsignedInt("-local_krige"))
else:
opts = oestats.OEGlobalKrigeOptions()
# Set if the distance function is stereo aware
distOpts = oestats.OEDefaultKrigeDistanceOptions()
distOpts.SetStereoAware(not itf.GetBool("-ignore_stereo"))
krige = oestats.OEMolKrige(distOpts, universalProps, opts)
# Add the training molecules to the Krige
print("Reading in training molecules")
sw = oechem.OEStopwatch()
failStr = None
numTrain = 0
numTrainFail = 0
numTrainUnmeasured = 0
numTrainMeasured = 0
for trainFile in itf.GetStringList("-train"):
imstr = oechem.oemolistream(trainFile)
for mol in imstr.GetOEMols():
success = False
# measured = True
if responseFxn.Has(mol):
response = responseFxn.Get(mol)
if OEIsUnmeasured(itf, response):
numTrainUnmeasured += 1
# measured = False
success = krige.AddUnmeasuredTraining(mol, response)
else:
numTrainMeasured += 1
success = krige.AddTraining(mol, response)
numTrain += 1
if not success:
numTrainFail += 1
if failStr is None:
failStr = oechem.oemolostream(failTrainFile)
oechem.OEWriteMolecule(failStr, mol)
if sw.Elapsed() > 10.0:
sw.Start()
if numTrainFail != 0:
print("So far added %d training molecules, and of those \
%d unmeasured are unmeasured. "
"%d input molecules are missing response data or \
universal krige properties." %
(numTrain, numTrainUnmeasured, numTrainFail))
else:
print("So far added %d training molecules, and of those \
%d unmeasured are unmeasured." %
(numTrain, numTrainUnmeasured))
imstr.close()
if failStr is not None:
failStr.close()
print("Training failed molecules written to %s" % failTrainFile)
if numTrainFail != 0:
print(
"Added %d training molecules, and of those %d unmeasured are unmeasured. "
"%d input molecules are missing response data or universal krige properties."
% (numTrain, numTrainUnmeasured, numTrainFail))
else:
print(
"Added %d training molecules, and of those %d unmeasured are unmeasured."
% (numTrain, numTrainUnmeasured))
# Train the Krige on the molecules we added
print("Training krige model")
if krige.Train():
print("Training successful")
else:
print("Training failed, aborting")
return
# Krige for MW of the test molecules, and compare to actual MW
krigeTag = "Krige(%s)" % responseName
upperTag = "Krige(%s) 95%% confidence upper" % responseName
lowerTag = "Krige(%s) 95%% confidence lower" % responseName
print("Predicting %s of input molecules" % responseName)
numKrige = 0
numKrigeFail = 0
outstr = oechem.oemolostream(outFile)
multi = oedepict.OEMultiPageImageFile(oedepict.OEPageOrientation_Landscape,
oedepict.OEPageSize_US_Letter)
failStr = None
sw.Start()
for molFile in itf.GetStringList("-in"):
imstr = oechem.oemolistream(molFile)
for mol in imstr.GetOEMols():
result = krige.GetResult(mol)
success = True
if result.Valid():
response = result.GetResponse()
conf95 = 1.96 * sqrt(result.GetVariance())
upper95 = response + conf95
lower95 = response - conf95
if itf.GetBool("-krige_log"):
response = pow(10.0, response)
upper95 = pow(10.0, upper95)
lower95 = pow(10.0, lower95)
oechem.OESetSDData(mol, krigeTag, str(response))
oechem.OESetSDData(mol, upperTag, str(upper95))
oechem.OESetSDData(mol, lowerTag, str(lower95))
if not itf.GetBool("-no_report"):
oestats.OEKrigeRenderReport(multi.NewPage(), result, mol,
rOpts)
oechem.OEWriteMolecule(outstr, mol)
else:
success = False
numKrige += 1
if not success:
numKrigeFail += 1
failStr = oechem.oemolostream(failKrigeFile)
oechem.OEWriteMolecule(failStr, mol)
if sw.Elapsed() > 10.0:
print("Kriging predicted %d molecules (%d failures) so far" %
(numKrige, numKrigeFail))
sw.Start()
imstr.close()
outstr.close()
if failStr is not None:
failStr.close()
print("Kriging predicted %d molecules (%d failures)" %
(numKrige, numKrigeFail))
if not itf.GetBool("-no_report"):
print("Writing report to %s" % reportFile)
oedepict.OEWriteMultiPageImage(reportFile, multi)
print("Finished")
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
defopts = oegraphsim.OEFPDatabaseOptions(10,
oegraphsim.OESimMeasure_Tanimoto)
oegraphsim.OEConfigureFPDatabaseOptions(itf, defopts)
oegraphsim.OEConfigureFingerPrint(
itf, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
if not oechem.OEParseCommandLine(itf, argv):
return 0
qfname = itf.GetString("-query")
mfname = itf.GetString("-molfname")
ofname = itf.GetString("-out")
# initialize databases
timer = oechem.OEWallTimer()
timer.Start()
ifs = oechem.oemolistream()
if not ifs.open(qfname):
oechem.OEThrow.Fatal("Cannot open input file!")
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, query):
oechem.OEThrow.Fatal("Cannot read query molecule!")
moldb = oechem.OEMolDatabase()
if not moldb.Open(mfname):
oechem.OEThrow.Fatal("Cannot open molecule database!")
ofs = oechem.oemolostream()
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Cannot open output file!")
fptype = oegraphsim.OESetupFingerPrint(itf)
oechem.OEThrow.Info("Using fingerprint type %s" % fptype.GetFPTypeString())
fpdb = oegraphsim.OEFPDatabase(fptype)
emptyfp = oegraphsim.OEFingerPrint()
emptyfp.SetFPTypeBase(fptype)
nrmols = moldb.GetMaxMolIdx()
mol = oechem.OEGraphMol()
for idx in range(0, nrmols):
if moldb.GetMolecule(mol, idx):
fpdb.AddFP(mol)
else:
fpdb.AddFP(emptyfp)
nrfps = fpdb.NumFingerPrints()
oechem.OEThrow.Info("%5.2f sec to initialize databases" % timer.Elapsed())
opts = oegraphsim.OEFPDatabaseOptions()
oegraphsim.OESetupFPDatabaseOptions(opts, itf)
# search fingerprint database
timer.Start()
scores = fpdb.GetSortedScores(query, opts)
oechem.OEThrow.Info("%5.2f sec to search %d fingerprints" %
(timer.Elapsed(), nrfps))
timer.Start()
hit = oechem.OEGraphMol()
for si in scores:
if moldb.GetMolecule(hit, si.GetIdx()):
oechem.OEWriteMolecule(ofs, hit)
oechem.OEThrow.Info("%5.2f sec to write %d hits" %
(timer.Elapsed(), opts.GetLimit()))
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__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oechem.OEConfigureSplitMolComplexOptions(
itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Unable to open %s for reading" % iname)
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 oechem.OEIsValidActiveSite(asite):
oechem.OEThrow.Fatal("Cannot initialize active site!")
oechem.OEPerceiveInteractionHints(asite)
print("Number of interactions:", asite.NumInteractions())
for itype in oechem.OEGetActiveSiteInteractionHintTypes():
numinters = asite.NumInteractions(
oechem.OEHasInteractionHintType(itype))
if numinters == 0:
continue
print("%d %s :" % (numinters, itype.GetName()))
inters = [
s for s in asite.GetInteractions(
oechem.OEHasInteractionHintType(itype))
]
print("\n".join(sorted(GetInteractionString(s) for s in inters)))
print("\nResidue interactions:")
for res in oechem.OEGetResidues(
asite.GetMolecule(oechem.OEProteinInteractionHintComponent())):
PrintResidueInteractions(asite, res)
print("\nLigand atom interactions:")
for atom in asite.GetMolecule(
oechem.OELigandInteractionHintComponent()).GetAtoms():
PrintLigandAtomInteractions(asite, atom)
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