indigo, substructure search with tautomers

indigo, substructure search with tautomers.py

##### method 1, builtin highlighting
# experiment with substructure matching (when tautomers, show the scaffold as in the target)
indigo = Indigo()
renderer = IndigoRenderer(indigo)
indigo.setOption("render-output-format", "png")
smiles1 = 'CCC(O)=CCCCC'
mol1 = indigo.loadMolecule(smiles1)
smiles2 = 'CC(=O)CC'
mol2 = indigo.loadQueryMolecule(smiles2)
flag = 'TAU' # other flags 'RES', 'TAU', 'TAU INCHI', 'TAU RSMARTS'
matcher = indigo.substructureMatcher(mol1, flag) # here we specify the molecule
match = matcher.match(mol2) # here we specify the query (substructure)
print(flag, match)
if match:
    fig = plt.figure(figsize=(6, 4))
    axs = fig.subplots(3, 1)
    # target molecule
    img = renderer.renderToBuffer(mol1)
    img = Image.open(io.BytesIO(img))
    axs[0].imshow(img)
    axs[0].axis('off')
    axs[0].set_title('target molecule')
    # query
    img = renderer.renderToBuffer(mol2)
    img = Image.open(io.BytesIO(img))
    axs[1].imshow(img)
    axs[1].axis('off')
    axs[1].set_title('query')
    # get the first match
    res = match.highlightedTarget()
    img = renderer.renderToBuffer(res)
    img = Image.open(io.BytesIO(img))
    axs[2].imshow(img)
    axs[2].axis('off')
    axs[2].set_title('result')
    plt.show()


##### method 2, more flexible highlighting
# experiment with substructure matching (when tautomers, show the scaffold as in the target)
indigo = Indigo()
renderer = IndigoRenderer(indigo)
indigo.setOption("render-output-format", "png")
indigo.setOption("render-highlighted-labels-visible", False)
indigo.setOption("render-label-mode", 'terminal-hetero')
smiles1 = 'CCC(=O)CCCCC'
mol1 = indigo.loadMolecule(smiles1)
smiles2 = 'CC(O)=CC'
mol2 = indigo.loadQueryMolecule(smiles2)
flag = 'TAU'  # other flags 'RES', 'TAU', 'TAU INCHI', 'TAU RSMARTS'
matcher = indigo.substructureMatcher(mol1, flag)  # here we specify the molecule
match = matcher.match(mol2)  # here we specify the query (substructure)
print(flag, match)
if match:
    fig = plt.figure(figsize=(6, 4))
    axs = fig.subplots(3, 1)
    # target molecule
    img = renderer.renderToBuffer(mol1)
    img = Image.open(io.BytesIO(img))
    axs[0].imshow(img)
    axs[0].axis('off')
    axs[0].set_title('target molecule')
    # query
    img = renderer.renderToBuffer(mol2)
    img = Image.open(io.BytesIO(img))
    axs[1].imshow(img)
    axs[1].axis('off')
    axs[1].set_title('query')
    # get the first match
    res = mol1.clone()
    for atom in mol2.iterateAtoms():
        print("atom", atom.index(), "mapped to atom", match.mapAtom(atom).index())
        atom = res.getAtom(match.mapAtom(atom).index())
        atom.highlight()
        # for nei in atom.iterateNeighbors():
        #     if not nei.isPseudoatom() and not nei.isRSite() and nei.atomicNumber() == 1:
        #         nei.highlight()
        #         nei.bond().highlight()
    for bond in mol2.iterateBonds():
        bond = res.getBond(match.mapBond(bond).index())
        bond.highlight()
    img = renderer.renderToBuffer(res)
    img = Image.open(io.BytesIO(img))
    axs[2].imshow(img)
    axs[2].axis('off')
    axs[2].set_title('result')
    plt.show()