def depict_complex(image, protein, ligand, opts, legend_frame=None):
"""
:type image: oedepict.OEImageBase
:type protein: oechem.OEMolBase
:type ligand: oechem.OEMolBase
:type opts: oedepict.OE2DMolDisplayOptions
:type legend_frame: oedepict.OEImageBase
"""
# 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)
# depiction
oegrapheme.OEPrepareActiveSiteDepiction(asite)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(image, adisp)
if legend_frame is not None:
lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(12, 1)
oegrapheme.OEDrawActiveSiteLegend(legend_frame, adisp, lopts)
def PoseInteractionsSVG(md_components, width=400, height=300):
"""Generate a OEGrapheme interaction plot for a protein-ligand complex.
The input protein may have other non-protein components as well so
the input protein is first split into components to isolate the protein
only for the plot. This may have to be changed if other components need
to be included in the plot.
"""
# # perceive residue hierarchy of total system
# if not oechem.OEHasResidues(proteinOrig):
# oechem.OEPerceiveResidues(proteinOrig, oechem.OEPreserveResInfo_All)
# print('Perceiving residues')
# split the total system into components
#protein, ligandPsuedo, water, other = oeommutils.split(proteinOrig)
protein = md_components.get_protein
ligand = md_components.get_ligand
# make the OEHintInteractionContainer
asite = oechem.OEInteractionHintContainer(protein, ligand)
if not asite.IsValid():
oechem.OEThrow.Fatal("Cannot initialize active site!")
# do the perceiving
oechem.OEPerceiveInteractionHints(asite)
# set the depiction options
opts = oegrapheme.OE2DActiveSiteDisplayOptions(width, height)
opts.SetRenderInteractiveLegend(True)
magnifyresidue = 1.0
opts.SetSVGMagnifyResidueInHover(magnifyresidue)
# make the depiction
oegrapheme.OEPrepareActiveSiteDepiction(asite)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
# make the image
image = oedepict.OEImage(width, height)
oegrapheme.OERenderActiveSite(image, adisp)
# Add a legend
#iconscale = 0.5
#oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight, iconscale)
svgBytes = oedepict.OEWriteImageToString("svg", image)
svgString = svgBytes.decode("utf-8")
return svgString
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % filename)
return mol
if len(sys.argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <ligand>" % sys.argv[0])
receptor = ImportMolecule(sys.argv[1])
ligand = ImportMolecule(sys.argv[2])
asite = oechem.OEInteractionHintContainer(receptor, ligand)
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)
# @ <SNIPPET-OERENDERACTIVESITE-IMAGE-ADISP>
# initializing asite oechem.OEInteractionHintContainer(receptor, ligand) object
image = oedepict.OEImage(800.0, 600.0)
opts = oegrapheme.OE2DActiveSiteDisplayOptions(image.GetWidth(), image.GetHeight())
opts.SetRenderInteractiveLegend(True)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(image, adisp)
oedepict.OEWriteImage("OERenderActiveSite-image-adisp.svg", image)
# @ </SNIPPET-OERENDERACTIVESITE-IMAGE-ADISP>
oedepict.OEWriteImage("OERenderActiveSite-image-adisp.pdf", image)
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, 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)