def OEAddLabel_Predicate(disp):
ringhighlight = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, ringhighlight,
oechem.OEAtomIsInRing(), oechem.OEBondIsInRing())
ringlabel = oedepict.OEHighlightLabel("ring", oechem.OELightGreen)
oedepict.OEAddLabel(disp, ringlabel, oechem.OEAtomIsInRing())
chainhighlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, chainhighlight,
oechem.OEAtomIsInChain(), oechem.OEBondIsInChain())
chainlabel = oedepict.OEHighlightLabel("chain", oechem.OEBlueTint)
oedepict.OEAddLabel(disp, chainlabel, oechem.OEAtomIsInChain())
def OEAddHighlighting_OEAtomBondSet(disp):
mol = disp.GetMolecule()
abset = oechem.OEAtomBondSet(mol.GetAtoms(Pred6MemAromAtom()),
mol.GetBonds(Pred6MemAromBond()))
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, highlightstyle, abset)
def OEAddLabel_OEAtomBondSet(disp):
mol = disp.GetMolecule()
ringset = oechem.OEAtomBondSet(mol.GetAtoms(oechem.OEAtomIsInRing()),
mol.GetBonds(oechem.OEBondIsInRing()))
ringhighlight = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, ringhighlight, ringset)
ringlabel = oedepict.OEHighlightLabel("ring", oechem.OELightGreen)
oedepict.OEAddLabel(disp, ringlabel, ringset)
chainset = oechem.OEAtomBondSet(mol.GetAtoms(oechem.OEAtomIsInChain()),
mol.GetBonds(oechem.OEBondIsInChain()))
chainhighlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, chainhighlight, chainset)
chainlabel = oedepict.OEHighlightLabel("chain", oechem.OEBlueTint)
oedepict.OEAddLabel(disp, chainlabel, chainset)
def OEAddLabel_OEMatch(disp):
subs = oechem.OESubSearch("a1aaaaa1")
unique = True
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
for match in subs.Match(disp.GetMolecule(), unique):
oedepict.OEAddHighlighting(disp, highlightstyle, match)
label = oedepict.OEHighlightLabel("aromatic", oechem.OELightGreen)
oedepict.OEAddLabel(disp, label, match)
def highlight_atoms_in_mol(mol2, dihedralAtomIndices, width=200, height=200):
mol = mol2.CreateCopy()
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
for atom_idx in dihedralAtomIndices:
oedepict.OEAddHighlighting(disp, hstyle, oechem.OEHasAtomIdx(atom_idx))
oedepict.OERenderMolecule(img, disp)
return img
def plot_dihedral(mol2, width=200, height=200):
mol = mol2.CreateCopy()
dihedralAtomIndices = [
int(x) - 1 for x in get_sd_data(mol, "TORSION_ATOMS_FRAGMENT").split()
]
dih, tor = get_dihedral(mol, dihedralAtomIndices)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, hstyle, dih)
hstyle = oedepict.OEHighlightByColor(oechem.OERed)
oedepict.OEAddHighlighting(disp, hstyle, tor)
oedepict.OERenderMolecule(img, disp)
return img
def draw_subsearch_highlights(mol, subsearch, width=400.0, height=400.0):
"""
Draws the hits for the substructure in a given molecule.
Copied from http://notebooks.eyesopen.com/substructure-search-pandas-oenotebook.html
"""
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
mol = oechem.OEGraphMol(mol)
oedepict.OEPrepareDepiction(mol)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
disp = oedepict.OE2DMolDisplay(mol, opts)
unique = True
for match in subsearch.Match(mol, unique):
oedepict.OEAddHighlighting(disp, hstyle, match)
oedepict.OERenderMolecule(img, disp)
# return oenb.draw_oeimage_to_img_tag(img)
return img
def OEAddHighlighting_Predicate(adisp):
highlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oegrapheme.OEAddLigandHighlighting(adisp, highlight, Pred6MemAromAtom())
oegrapheme.OEAddLigandHighlighting(adisp, highlight, Pred6MemAromBond())
def OEAddHighlighting_OESubSearch(disp):
subsearch = oechem.OESubSearch("a1aaaaa1")
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, highlightstyle, subsearch)
def OEAddHighlighting_AtomAndBondPredicate(disp):
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, highlightstyle, Pred6MemAromAtom(),
Pred6MemAromBond())
unique = True
for match in ss.Match(mol, unique):
oedepict.OEAddHighlighting(disp, highlight, match)
image = oedepict.OEImage(disp.GetWidth(), disp.GetHeight())
oedepict.OERenderMolecule(image, disp)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
smiles = "c1ccc2c(c1)cc(O)cn2"
ss = oechem.OESubSearch("c1ncc(O)cc1")
highlight = oedepict.OEHighlightByBallAndStick(oechem.OEDarkBlue)
# @ <SNIPPET-OEHIGHLIGHTBYBALLANDSTICK-SETCOLOR>
highlight.SetColor(oechem.OEPinkTint)
# @ </SNIPPET-OEHIGHLIGHTBYBALLANDSTICK-SETCOLOR>
DepictMoleculesWithHighlight(smiles, ss, highlight,
"OEHighlightByBallAndStick_SetColor")
# @ <SNIPPET-OEHIGHLIGHTBYBALLANDSTICK-SETSTICKWIDTHSCALE>
highlight = oedepict.OEHighlightByBallAndStick(oechem.OEPinkTint)
highlight.SetStickWidthScale(5.0)
# @ </SNIPPET-OEHIGHLIGHTBYBALLANDSTICK-SETSTICKWIDTHSCALE>
DepictMoleculesWithHighlight(smiles, ss, highlight,
"OEHighlightByBallAndStick_SetStickWidthScale")
# @ <SNIPPET-OEHIGHLIGHTBYBALLANDSTICK-SETBALLRADIUSSCALE>
highlight = oedepict.OEHighlightByBallAndStick(oechem.OEPinkTint)