def get_protein_and_ligands(protein, ligand, itf):
if (itf.HasString("-complex")):
# separate ligand and protein in complex
iname = itf.GetString("-complex")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input complex file!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read complex from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
if not split_complex(protein, ligand, sopts, complexmol):
oechem.OEThrow.Fatal("Cannot separate complex!")
else:
# read ligand and protein from separate files
pname = itf.GetString("-protein")
ifs = oechem.oemolistream()
if not ifs.open(pname):
oechem.OEThrow.Fatal("Cannot open input protein file!")
if not oechem.OEReadMolecule(ifs, protein):
oechem.OEThrow.Fatal("Unable to read protein from %s" % pname)
lname = itf.GetString("-ligand")
ifs = oechem.oemolistream()
if not ifs.open(lname):
oechem.OEThrow.Fatal("Cannot open input ligand file!")
if not oechem.OEReadMolecule(ifs, ligand):
oechem.OEThrow.Fatal("Unable to read ligand from %s" % lname)
return ligand.NumAtoms() != 0 and protein.NumAtoms() != 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)
oechem.OEConfigureSplitMolComplexOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
if itf.GetBool("-verbose"):
oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Verbose)
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)
lig = oechem.OEGraphMol()
prot = oechem.OEGraphMol()
wat = oechem.OEGraphMol()
other = oechem.OEGraphMol()
if not oechem.OESplitMolComplex(lig, prot, wat, other, inmol, opts):
oechem.OEThrow.Fatal("Unable to split mol complex from %s" % iname)
if not lig.NumAtoms() == 0:
oechem.OEThrow.Verbose(" lig %s" % lig.GetTitle())
oechem.OEWriteMolecule(oms, lig)
if not prot.NumAtoms() == 0:
oechem.OEThrow.Verbose(" prot %s" % prot.GetTitle())
oechem.OEWriteMolecule(oms, prot)
if not wat.NumAtoms() == 0:
oechem.OEThrow.Verbose(" wat %s" % wat.GetTitle())
oechem.OEWriteMolecule(oms, wat)
if not other.NumAtoms() == 0:
oechem.OEThrow.Verbose("other %s" % other.GetTitle())
oechem.OEWriteMolecule(oms, other)
oms.close()
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(InterfaceData)
oechem.OEConfigureSplitMolComplexOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
if itf.GetBool("-verbose"):
oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Verbose)
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!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
if itf.GetBool("-verbose"):
oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Verbose)
opt = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(opt, itf)
# @ <SNIPPET-SPLIT-MOL-COMPLEX-LOWLEVEL-FRAGMENT>
# for input molecule mol and options opt ...
frags = oechem.OEAtomBondSetVector()
if oechem.OEGetMolComplexFragments(frags, mol, opt):
# ...
# @ </SNIPPET-SPLIT-MOL-COMPLEX-LOWLEVEL-FRAGMENT>
oechem.OEThrow.Verbose("Able to fragment mol complex from %s" % iname)
else:
oechem.OEThrow.Fatal("Unable to fragment mol complex from %s" % iname)
# @ <SNIPPET-SPLIT-MOL-COMPLEX-LOWLEVEL-COMBINE>
# for options opt and OEAtomBondSetVector frags produced earlier ...
numSites = oechem.OECountMolComplexSites(frags)
oechem.OEThrow.Verbose("sites %d" % numSites)
lig = oechem.OEGraphMol()
ligfilter = opt.GetLigandFilter()
if not oechem.OECombineMolComplexFragments(lig, frags, opt, ligfilter):
oechem.OEThrow.Warning("Unable to combine ligand frags from %s" %
mol.GetTitle())
protComplex = oechem.OEGraphMol()
p = opt.GetProteinFilter()
w = opt.GetWaterFilter()
if not oechem.OECombineMolComplexFragments(protComplex, frags, opt,
oechem.OEOrRoleSet(p, w)):
oechem.OEThrow.Warning("Unable to combine complex frags from %s" %
mol.GetTitle())
# @ </SNIPPET-SPLIT-MOL-COMPLEX-LOWLEVEL-COMBINE>
if not lig.NumAtoms() == 0:
oechem.OEThrow.Verbose(" lig %s" % lig.GetTitle())
oechem.OEWriteMolecule(oms, lig)
if not protComplex.NumAtoms() == 0:
oechem.OEThrow.Verbose(" prot %s" % protComplex.GetTitle())
oechem.OEWriteMolecule(oms, protComplex)
oms.close()
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(InterfaceData)
oechem.OEConfigureSplitMolComplexOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
opts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(opts, itf)
# @ </SNIPPET-SPLIT-MOL-COMPLEX-ITF>
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!")
bfixTitles = (oms.GetFormat() == oechem.OEFormat_SDF)
sTitleSDTag = "TITLE"
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Cannot read input file!")
lig = oechem.OEGraphMol()
prot = oechem.OEGraphMol()
wat = oechem.OEGraphMol()
other = oechem.OEGraphMol()
if not oechem.OESplitMolComplex(lig, prot, wat, other, inmol, opts):
oechem.OEThrow.Fatal("Unable to split mol complex from %s" % iname)
if not lig.NumAtoms() == 0:
if bfixTitles:
FixSDFTitle(sTitleSDTag, lig)
oechem.OEWriteMolecule(oms, lig)
if not prot.NumAtoms() == 0:
if bfixTitles:
FixSDFTitle(sTitleSDTag, prot)
oechem.OEWriteMolecule(oms, prot)
if not wat.NumAtoms() == 0:
if bfixTitles:
FixSDFTitle(sTitleSDTag, wat)
oechem.OEWriteMolecule(oms, wat)
if not other.NumAtoms() == 0:
if bfixTitles:
FixSDFTitle(sTitleSDTag, other)
oechem.OEWriteMolecule(oms, other)
oms.close()