def Draw2DSurfacePartialCharge(image, mol):
oedepict.OEPrepareDepiction(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
coloranion = oechem.OEColorStop(-1.0, oechem.OEColor(oechem.OEDarkRed))
colorcation = oechem.OEColorStop(+1.0, oechem.OEColor(oechem.OEDarkBlue))
colorg = oechem.OELinearColorGradient(coloranion, colorcation)
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEColor(oechem.OEWhite)))
arcfxn = AtomPartialChargeArcFxn(colorg)
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(image, disp)
def Draw2DSurface(image, mol):
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
arcfxn = AtomColorArcFxn()
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(image, disp)
def Draw2DSurfaces(image, mol):
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, 1.50))
disp = oedepict.OE2DMolDisplay(mol, opts)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_C), 1.00,
oechem.OEBlack)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_N), 1.25,
oechem.OEDarkBlue)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_O), 1.50,
oechem.OEDarkRed)
oedepict.OERenderMolecule(image, disp)
def DrawSurfaces(image, mol):
oechem.OEAssignCovalentRadii(mol)
minradius = oechem.OEGetCovalentRadius(oechem.OEElemNo_H)
radiusScales = oechem.OEDoubleVector(mol.GetMaxAtomIdx(), 0.0)
maxrscale = float("-inf")
for atom in mol.GetAtoms():
rscale = (atom.GetRadius() -
minradius) + oegrapheme.OESurfaceArcScale_Minimum
radiusScales[atom.GetIdx()] = rscale
maxrscale = max(maxrscale, rscale)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, maxrscale))
disp = oedepict.OE2DMolDisplay(mol, opts)
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
penA = oedepict.OEPen(oechem.OELightGrey, oechem.OELightGrey,
oedepict.OEFill_Off, 2.0,
oedepict.OEStipple_ShortDash)
arcfxnA = oegrapheme.OEDefaultArcFxn(penA)
for arc in oegrapheme.OEGet2DSurfaceArcs(
disp, oegrapheme.OESurfaceArcScale_Minimum):
arcfxnA(layer, arc)
penB = oedepict.OEPen(oechem.OEGrey, oechem.OEGrey, oedepict.OEFill_Off,
2.0)
arcfxnB = oegrapheme.OEDefaultArcFxn(penB)
for arc in oegrapheme.OEGet2DSurfaceArcs(disp, radiusScales):
arcfxnB(layer, arc)
oedepict.OERenderMolecule(image, disp)
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % filename)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OESuppressHydrogens(mol)
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])
oegrapheme.OEAddComplexSurfaceArcs(ligand, receptor)
oegrapheme.OEPrepareDepictionFrom3D(ligand)
width, height = 450, 350
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(ligand, opts))
disp = oedepict.OE2DMolDisplay(ligand, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule("DrawComplexSurface.png", disp)
# @ </SNIPPET-DRAW-COMPLEX-SURFACE>
oedepict.OERenderMolecule("DrawComplexSurface.pdf", disp)
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
# or its use.
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "OC(=O)c1cnc(c(Cl)c1)-c2ccccc2")
oedepict.OEPrepareDepiction(mol)
imagewidth, imageheight = 350, 250
# @ <SNIPPET-DRAW-2D-SURFACE>
opts = oedepict.OE2DMolDisplayOptions(imagewidth, imageheight,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
arcfxn = oegrapheme.OEEyelashArcFxn(
oedepict.OEPen(oechem.OEGrey, oechem.OEGrey))
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
# @ </SNIPPET-DRAW-2D-SURFACE>
oedepict.OERenderMolecule("Draw2DSurface.png", disp)
oedepict.OERenderMolecule("Draw2DSurface.pdf", disp)