def Draw2DSurface(disp, atompred, radius, color):
penA = oedepict.OEPen(color, color, oedepict.OEFill_Off, 2.0)
arcfxnA = oegrapheme.OEDefaultArcFxn(penA)
penB = oedepict.OEPen(oechem.OELightGrey, oechem.OELightGrey,
oedepict.OEFill_Off, 2.0,
oedepict.OEStipple_ShortDash)
arcfxnB = oegrapheme.OEDefaultArcFxn(penB)
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
for adisp in disp.GetAtomDisplays():
for arc in oegrapheme.OEGet2DSurfaceArcs(disp, adisp, radius):
if atompred(adisp.GetAtom()):
arcfxnA(layer, arc)
else:
arcfxnB(layer, arc)
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)
from openeye import oegrapheme
from openeye import oeshape
###############################################################
# USED TO GENERATE CODE SNIPPETS FOR THE GRAPHEME DOCUMENTATION
###############################################################
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <mol file>" % sys.argv[0])
ifs = oechem.oemolistream(sys.argv[1])
refmol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, refmol)
# @ <SNIPPET-RENDER-SHAPE-QUERY>
opts = oegrapheme.OEShapeQueryDisplayOptions()
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
arcpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_On,
2.0)
opts.SetSurfaceArcFxn(oegrapheme.OEDefaultArcFxn(arcpen))
cff = oeshape.OEColorForceField()
cff.Init(oeshape.OEColorFFType_ImplicitMillsDean)
disp = oegrapheme.OEShapeQueryDisplay(refmol, cff, opts)
image = oedepict.OEImage(420.0, 280.0)
oegrapheme.OERenderShapeQuery(image, disp)
# @ </SNIPPET-RENDER-SHAPE-QUERY>
oedepict.OEWriteImage("RenderShapeQuery.png", image)
oedepict.OEWriteImage("RenderShapeQuery.pdf", image)