示例#1
0
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
示例#2
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()
示例#3
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!")

    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()
示例#4
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)

    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()
示例#6
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
示例#7
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)
示例#8
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!")

    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()