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)
########################################################################
#
########################################################################
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)
asite.SetTitle(ligand.GetTitle())
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)
opts = oegrapheme.OE2DActiveSiteDisplayOptions(600, 400)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
OEAddHighlighting_Predicate(adisp)
oegrapheme.OERenderActiveSite("OEAddHighlighting-ActiveSite-Predicate.png", adisp)
oegrapheme.OERenderActiveSite("OEAddHighlighting-ActiveSite-Predicate.pdf", adisp)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
OEAddHighlighting_AtomAndBondPredicate(adisp)
oegrapheme.OERenderActiveSite("OEAddHighlighting-ActiveSite-AtomAndBondPredicate.png", adisp)
oegrapheme.OERenderActiveSite("OEAddHighlighting-ActiveSite-AtomAndBondPredicate.pdf", adisp)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
OEAddHighlighting_OEMatch(adisp)
oegrapheme.OERenderActiveSite("OEAddHighlighting-ActiveSite-OEMatch.png", adisp)
oegrapheme.OERenderActiveSite("OEAddHighlighting-ActiveSite-OEMatch.pdf", adisp)
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
if not ifs.open(filename):
oechem.OEThrow.Fatal("Unable to open %s for reading" % filename)
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-FNAME-ADISP>
# initializing asite oechem.OEInteractionHintContainer(receptor, ligand) object
opts = oegrapheme.OE2DActiveSiteDisplayOptions(800.0, 600.0)
opts.SetRenderInteractiveLegend(True)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite("OERenderActiveSite-fname-adisp.svg", adisp)
# @ </SNIPPET-OERENDERACTIVESITE-FNAME-ADISP>
oegrapheme.OERenderActiveSite("OERenderActiveSite-fname-adisp.pdf", adisp)
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