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__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-i")
oname = itf.GetString("-o")
ims = oechem.oemolistream()
if not ims.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oms = oechem.oemolostream()
if not oms.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Cannot read input file!")
allSites = itf.GetBool("-a")
splitCovalent = itf.GetBool("-c")
separateResidues = itf.GetBool("-s")
combineFilters = itf.GetBool("-pw")
if combineFilters:
SplitMolComplexCombineFilters(oms, inmol)
elif allSites:
SplitMolComplexAllSites(oms, inmol, splitCovalent)
else:
SplitMolComplex(oms, inmol, splitCovalent, separateResidues)
oms.close()
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
return 1
imstr = oechem.oemolistream(itf.GetString("-in"))
omstr = oechem.oemolostream(itf.GetString("-out"))
receptors = []
for receptor_filename in itf.GetStringList("-receptors"):
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, receptor_filename):
oechem.OEThrow.Fatal("Unable to read receptor from %s" %
receptor_filename)
receptors.append(receptor)
poser = oedocking.OEPosit()
for receptor in receptors:
poser.AddReceptor(receptor)
for mcmol in imstr.GetOEMols():
print("posing", mcmol.GetTitle())
result = oedocking.OESinglePoseResult()
ret_code = poser.Dock(result, mcmol)
if ret_code == oedocking.OEDockingReturnCode_Success:
posedMol = result.GetPose()
oechem.OESetSDData(posedMol, poser.GetName(),
str(result.GetProbability()))
oechem.OESetSDData(posedMol, "Receptor Index",
str(result.GetReceptorIndex()))
oechem.OEWriteMolecule(omstr, posedMol)
else:
errMsg = oedocking.OEDockingReturnCodeGetName(ret_code)
oechem.OEThrow.Warning("%s: %s" % (mcmol.GetTitle(), errMsg))
return 0
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(InterfaceData)
oemolprop.OEConfigureFilterParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ftype = oemolprop.OEGetFilterType(itf)
filt = oemolprop.OEFilter(ftype)
ver = itf.GetInt("-verbose")
oechem.OEThrow.SetLevel(ver)
ostr = oechem.oeosstream()
pwnd = False
filt.SetTable(ostr, pwnd)
headers = ostr.str().split(b'\t')
ostr.clear() # remove the header row from the stream
for mol in ifs.GetOEGraphMols():
filt(mol)
fields = ostr.str().decode("UTF-8").split('\t')
ostr.clear() # remove this row from the stream
tmpdct = dict(zip(headers, fields))
print(mol.GetTitle(), tmpdct[b"Lipinski violations"])
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__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
MMPAnalyzeProbe(itf)
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__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ifs = oechem.oemolistream()
inputFile = itf.GetString("-in")
if not ifs.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading" % inputFile)
ofs = oechem.oemolostream()
outFile = itf.GetString("-out")
if not ofs.open(outFile):
oechem.OEThrow.Fatal("Unable to open %s for writing" % outFile)
chargeName = itf.GetString("-method")
mol = oechem.OEMol()
while oechem.OEReadMolecule(ifs, mol):
if not AssignChargesByName(mol, chargeName):
oechem.OEThrow.Warning("Unable to assign %s charges to mol %s" %
(chargeName, mol.GetTitle()))
oechem.OEWriteMolecule(ofs, mol)
ifs.close()
ofs.close()
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oemedchem.OEConfigureMCSFragDatabaseOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
MCSFragIndex(itf)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oemedchem.OEConfigureMatchedPairIndexOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
SerializeInput(itf)
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(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
# @ <SNIPPET-ALTLOCFACT-FLAVOR>
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
# @ </SNIPPET-ALTLOCFACT-FLAVOR>
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# @ <SNIPPET-ALTLOCFACT-PRIMARY>
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# @ </SNIPPET-ALTLOCFACT-PRIMARY>
# @ <SNIPPET-PLACE-HYDROGENS-BASIC>
if oechem.OEPlaceHydrogens(mol):
# ...
# @ </SNIPPET-PLACE-HYDROGENS-BASIC>
print("success")
# @ <SNIPPET-PLACE-HYDROGENS-OPTIONS>
opt = oechem.OEPlaceHydrogensOptions()
opt.SetStandardizeBondLen(False)
# @ </SNIPPET-PLACE-HYDROGENS-OPTIONS>
# @ <SNIPPET-PLACE-HYDROGENS-DETAILS>
# given molecule mol and OEPlaceHydrogensOptions opt...
details = oechem.OEPlaceHydrogensDetails()
if oechem.OEPlaceHydrogens(mol, details, opt):
print(details.Describe())
# @ </SNIPPET-PLACE-HYDROGENS-DETAILS>
ims.close()
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 main(argv=[__name__]):
# @ <SNIPPET-OECONFIGURECOLOR>
itf = oechem.OEInterface()
oedepict.OEConfigureColor(itf, "mycolor", "c",
"Example of using OEConfigureColor", "blue")
# @ </SNIPPET-OECONFIGURECOLOR>
if oechem.OECheckHelp(itf, argv):
return True
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
color = oechem.OEGetColor(itf, "mycolor")
print(str(color))
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
# @ <SNIPPET-RESCORE-POSES-CONFIGURE>
oedocking.OEScoreTypeConfigure(itf, "-score")
# @ </SNIPPET-RESCORE-POSES-CONFIGURE>
if not oechem.OEParseCommandLine(itf, argv):
return 1
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, itf.GetString("-receptor")):
oechem.OEThrow.Fatal("Unable to read receptor")
imstr = oechem.oemolistream()
if not imstr.open(itf.GetString("-in")):
oechem.OEThrow.Fatal("Unable to open input file of ligands")
omstr = oechem.oemolostream()
if not omstr.open(itf.GetString("-out")):
oechem.OEThrow.Fatal("Unable to open out file for rescored ligands")
# @ <SNIPPET-RESCORE-POSES-GET-VALUE>
scoreType = oedocking.OEScoreTypeGetValue(itf, "-score")
# @ </SNIPPET-RESCORE-POSES-GET-VALUE>
# @ <SNIPPET-RESCORE-POSES-SETUP-SCORE>
score = oedocking.OEScore(scoreType)
# @ </SNIPPET-RESCORE-POSES-SETUP-SCORE>
# @ <SNIPPET-RESCORE-POSES-INITIALIZE>
score.Initialize(receptor)
# @ </SNIPPET-RESCORE-POSES-INITIALIZE>
for ligand in imstr.GetOEMols():
if itf.GetBool("-optimize"):
# @ <SNIPPET-RESCORE-POSES-OPTIMIZE>
score.SystematicSolidBodyOptimize(ligand)
# @ </SNIPPET-RESCORE-POSES-OPTIMIZE>
# @ <SNIPPET-RESCORE-POSES-ANNOTATE>
score.AnnotatePose(ligand)
# @ </SNIPPET-RESCORE-POSES-ANNOTATE>
sdtag = score.GetName()
# @ <SNIPPET-RESCORE-POSES-ASSIGN-SCORE>
oedocking.OESetSDScore(ligand, score, sdtag)
# @ </SNIPPET-RESCORE-POSES-ASSIGN-SCORE>
# @ <SNIPPET-RESCORE-POSES-SCORE-SORTING>
oechem.OESortConfsBySDTag(ligand, sdtag,
score.GetHighScoresAreBetter())
# @ </SNIPPET-RESCORE-POSES-SCORE-SORTING>
oechem.OEWriteMolecule(omstr, ligand)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# in our example, we will select the first histidine
selectedResidue = oechem.OEResidue()
for atom in mol.GetAtoms():
res = oechem.OEAtomGetResidue(atom)
if oechem.OEGetResidueIndex(res) == oechem.OEResidueIndex_HIS:
selectedResidue = res
break
# @ <SNIPPET-PLACE-HYDROGENS-PRED>
# given predicate IsSameResidue, residue selectedResidue and molecule mol...
opt = oechem.OEPlaceHydrogensOptions()
opt.SetNoFlipPredicate(IsSameResidue(selectedResidue))
if oechem.OEPlaceHydrogens(mol, opt):
# selectedResidue will not be flipped...
# @ </SNIPPET-PLACE-HYDROGENS-PRED>
print("success")
ims.close()
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
# @ <SNIPPET-DOCK-MOLECULES-CONFIGURE>
oedocking.OEDockMethodConfigure(itf, "-method")
oedocking.OESearchResolutionConfigure(itf, "-resolution")
# @ </SNIPPET-DOCK-MOLECULES-CONFIGURE>
if not oechem.OEParseCommandLine(itf, argv):
return 1
imstr = oechem.oemolistream(itf.GetString("-in"))
omstr = oechem.oemolostream(itf.GetString("-out"))
receptor = oechem.OEGraphMol()
if not oedocking.OEReadReceptorFile(receptor, itf.GetString("-receptor")):
oechem.OEThrow.Fatal("Unable to read receptor")
# @ <SNIPPET-DOCK-MOLECULES-GET-VALUE>
dockMethod = oedocking.OEDockMethodGetValue(itf, "-method")
dockResolution = oedocking.OESearchResolutionGetValue(itf, "-resolution")
# @ </SNIPPET-DOCK-MOLECULES-GET-VALUE>
# @ <SNIPPET-DOCK-MOLECULES-SETUP>
dock = oedocking.OEDock(dockMethod, dockResolution)
# @ </SNIPPET-DOCK-MOLECULES-SETUP>
# @ <SNIPPET-DOCK-MOLECULES-INITIALIZE>
dock.Initialize(receptor)
# @ </SNIPPET-DOCK-MOLECULES-INITIALIZE>
for mcmol in imstr.GetOEMols():
print("docking", mcmol.GetTitle())
dockedMol = oechem.OEGraphMol()
# @ <SNIPPET-DOCK-MOLECULES-DOCK>
retCode = dock.DockMultiConformerMolecule(dockedMol, mcmol)
if (retCode != oedocking.OEDockingReturnCode_Success):
oechem.OEThrow.Fatal("Docking Failed with error code " + oedocking.OEDockingReturnCodeGetName(retCode))
# @ </SNIPPET-DOCK-MOLECULES-DOCK>
sdtag = oedocking.OEDockMethodGetName(dockMethod)
# @ <SNIPPET-DOCK-MOLECULES-ASSIGN-SCORE>
oedocking.OESetSDScore(dockedMol, dock, sdtag)
# @ </SNIPPET-DOCK-MOLECULES-ASSIGN-SCORE>
# @ <SNIPPET-DOCK-MOLECULES-ANNOTATE>
dock.AnnotatePose(dockedMol)
# @ </SNIPPET-DOCK-MOLECULES-ANNOTATE>
oechem.OEWriteMolecule(omstr, dockedMol)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
rname = itf.GetString("-ref")
fname = itf.GetString("-fit")
oname = itf.GetString("-out")
rifs = oechem.oemolistream()
if not rifs.open(rname):
oechem.OEThrow.Fatal("Cannot open reference molecule file!")
refmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(rifs, refmol):
oechem.OEThrow.Fatal("Cannot read reference molecule!")
fifs = oechem.oemolistream()
if not fifs.open(fname):
oechem.OEThrow.Fatal("Cannot open align molecule file!")
ofs = oechem.oemolostream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if not oechem.OEIs2DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output format for 2D coordinates")
oedepict.OEPrepareDepiction(refmol)
mcss = oechem.OEMCSSearch(oechem.OEMCSType_Approximate)
atomexpr = oechem.OEExprOpts_DefaultAtoms
bondexpr = oechem.OEExprOpts_DefaultBonds
mcss.Init(refmol, atomexpr, bondexpr)
mcss.SetMCSFunc(oechem.OEMCSMaxBondsCompleteCycles())
oechem.OEWriteConstMolecule(ofs, refmol)
for fitmol in fifs.GetOEGraphMols():
alignres = oedepict.OEPrepareAlignedDepiction(fitmol, mcss)
if alignres.IsValid():
oechem.OEThrow.Info("%s mcs size: %d" % (fitmol.GetTitle(), alignres.NumAtoms()))
oechem.OEWriteMolecule(ofs, fitmol)
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(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 main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
smarts = itf.GetString("-smarts")
qmol = oechem.OEQMol()
if not oechem.OEParseSmarts(qmol, smarts):
oechem.OEThrow.Fatal("Invalid SMARTS: %s" % smarts)
oechem.OEGenerate2DCoordinates(qmol)
ss = oechem.OESubSearch(qmol)
if not ss.IsValid():
oechem.OEThrow.Fatal("Unable to initialize substructure search!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input molecule file!")
ofs = oechem.oemolostream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if not oechem.OEIs2DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output format for 2D coordinates")
for mol in ifs.GetOEGraphMols():
oechem.OEPrepareSearch(mol, ss)
alignres = oedepict.OEPrepareAlignedDepiction(mol, ss)
if not alignres.IsValid():
oechem.OEThrow.Warning(
"Substructure is not found in input molecule!")
oedepict.OEPrepareDepiction(mol)
oechem.OEWriteMolecule(ofs, mol)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oechem.OEConfigureSplitMolComplexOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ims = oechem.oemolistream()
if not itf.GetUnsignedInt("-modelnum") == 1:
ims.SetFlavor(
oechem.OEFormat_PDB,
oechem.OEGetDefaultIFlavor(oechem.OEFormat_PDB)
& ~oechem.OEIFlavor_PDB_ENDM)
if not ims.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oms = oechem.oemolostream()
if not oms.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Cannot read input file!")
opts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(opts, itf)
if itf.GetBool("-verbose"):
# don't bother counting sites unless we're going to print them
numSites = oechem.OECountMolComplexSites(inmol, opts)
oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Verbose)
oechem.OEThrow.Verbose("sites %d" % numSites)
for frag in oechem.OEGetMolComplexComponents(inmol, opts):
oechem.OEThrow.Verbose("frag %s" % frag.GetTitle())
oechem.OEWriteMolecule(oms, frag)
oms.close()
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line.")
ifname = itf.GetString("-in")
ofname = itf.GetString("-out")
stype = itf.GetString("-stype")
sort = itf.GetBool("-sort")
keeptitle = itf.GetBool("-keep-title")
nrthreads = itf.GetUnsignedInt("-nrthreads")
screentype = None
if stype == "MOLECULE":
screentype = oechem.OEGetSubSearchScreenType(
oechem.OESubSearchScreenType_Molecule)
elif stype == "MDL":
screentype = oechem.OEGetSubSearchScreenType(
oechem.OESubSearchScreenType_MDL)
elif stype == "SMARTS":
screentype = oechem.OEGetSubSearchScreenType(
oechem.OESubSearchScreenType_SMARTS)
if screentype is None:
oechem.OEThrow.Fatal("stype %s is not supported" % stype)
opts = oechem.OECreateSubSearchDatabaseOptions(screentype)
opts.SetSortByBitCounts(sort)
opts.SetKeepTitle(keeptitle)
opts.SetNumProcessors(nrthreads)
screenstr = screentype.GetName()
infomsg = "Using %d processor(s) to generate database with '%s'"
oechem.OEThrow.Info(infomsg % (opts.GetNumProcessors(), screenstr))
tracer = oechem.OEConsoleProgressTracer()
if not oechem.OECreateSubSearchDatabaseFile(ofname, ifname, opts, tracer):
oechem.OEThrow.Fatal(
"Substructure search database can not be generated!")
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-i")
oname = itf.GetString("-o")
ims = oechem.oemolistream()
if not ims.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oms = oechem.oemolostream()
if not oms.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Cannot read input file!")
allSites = itf.GetBool("-a")
filterLigand = itf.GetBool("-f")
# break out each scheme to better illustrate them
if filterLigand:
SplitMolComplexIterFilter(oms, inmol)
elif itf.HasString("-l"):
ligName = itf.GetString("-l")
if allSites:
SplitMolComplexIterAllSitesLigName(oms, inmol, ligName)
else:
SplitMolComplexIterLigName(oms, inmol, ligName)
else:
if allSites:
SplitMolComplexIterAllSites(oms, inmol)
else:
SplitMolComplexIter(oms, inmol)
oms.close()
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oemolprop.OEConfigureFilterParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ftype = oemolprop.OEGetFilterType(itf)
filt = oemolprop.OEFilter(ftype)
ver = itf.GetInt("-verbose")
oechem.OEThrow.SetLevel(ver)
oemolprop.OEWritePropertyDataToCSV(oname, ifs, filt)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ifname = itf.GetString("-ringdict")
ofname = itf.GetString("-out")
if not oechem.OEIsValid2DRingDictionary(ifname):
oechem.OEThrow.Fatal("Invalid ring dictionary file!")
ringdict = oechem.OE2DRingDictionary(ifname)
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
oedepict.OEWrite2DRingDictionaryReport(ofname, ringdict, ropts)
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if oechem.OECheckHelp(itf, argv):
return 0
if not oechem.OEParseCommandLine(itf, argv):
return 1
ifs = oechem.oemolistream()
if not ifs.open(itf.GetString("-i")):
oechem.OEThrow.Fatal("Unable to open %s for reading" %
itf.GetString("-i"))
ofs = oechem.oemolostream()
if not ofs.open(itf.GetString("-o")):
oechem.OEThrow.Fatal("Unable to open %s for writing" %
itf.GetString("-o"))
omega = oeomega.OEOmega()
maxConfs = 0
omega.SetMaxConfs(maxConfs)
omega.SetStrictStereo(False)
omega.SetSampleHydrogens(True)
omega.SetEnumNitrogen(oeomega.OENitrogenEnumeration_All)
mol = oechem.OEMol()
for mol in ifs.GetOEMols():
#print( mol.GetTitle() )
if not omega(mol):
print("omega failed on %s" % mol.GetTitle())
title = mol.GetTitle()
oechem.OETriposAtomNames(mol)
oequacpac.OEAssignPartialCharges(mol, oequacpac.OECharges_AM1BCCSym)
oechem.OEWriteConstMolecule(ofs, mol)
ofs.close()
return 0
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oemolprop.OEConfigureFilterParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oemolostream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot create output file!")
fmt = ofs.GetFormat()
if fmt not in [
oechem.OEFormat_SDF, oechem.OEFormat_OEB, oechem.OEFormat_CSV
]:
oechem.OEThrow.Fatal("Only SD, OEB, and CSV formats preserve SD data")
ftype = oemolprop.OEGetFilterType(itf)
filt = oemolprop.OEFilter(ftype)
ver = itf.GetInt("-verbose")
oechem.OEThrow.SetLevel(ver)
pwnd = False
filt.SetTable(oechem.oenul, pwnd)
filt.SetSDTag(True)
for mol in ifs.GetOEGraphMols():
filt(mol)
oechem.OEWriteMolecule(ofs, mol)