Hi Nick,
On Mon, Oct 28, 2013 at 3:34 PM, Nicholas Firth <[email protected]>wrote:
>
> I am seeing some weird behaviour from the adding an atom and a bond to an
> EditableMol. It works fine in most cases however for this particular
> fragment I'm getting an extra hydrogen being added on for some reason.
>
> >>> mol = Chem.MolFromSmiles('O=C1NC2=C(N1)C(=O)NC(=O)N2')
> >>> Chem.Kekulize(mol, clearAromaticFlags = True)
> >>> tempMol = Chem.EditableMol(mol)
> >>> firstIdx = tempMol.AddAtom(dumAtom)
> >>> tempMol.AddBond(8, firstIdx, Chem.BondType.SINGLE)
> 14
> >>> print Chem.MolToSmiles(tempMol.GetMol())
> [*][NH]1C(=O)NC2=C(NC(=O)N2)C1=O
>
> So this molecule is not RDKit friendly, I don't really know why this is
> happening. I guess some form of conversion of an implicit hydrogen to an
> explicit hydrogen...
>
> Is there any way of stopping the magic hydrogen from appearing? Or away of
> easily getting rid of it after it's appeared?
>
The problem is the aromatic N. Here's a simpler example that shows the same
thing:
>>> mol = Chem.MolFromSmiles('N1C=CC=C1')
>>> Chem.Kekulize(mol,clearAromaticFlags=True)
>>> tempMol = Chem.EditableMol(mol)
>>> idx = tempMol.AddAtom(Chem.Atom(0))
>>> tempMol.AddBond(idx,0,Chem.BondType.SINGLE)
6
>>> nm = tempMol.GetMol()
>>> print Chem.MolToSmiles(nm)
[*][NH]1C=CC=C1
Here's what's happening: when you build the initial molecule, aromaticity
is assigned and the N atom has an "explicit" H marker added. When you
kekuulize the structure, the aromaticity flags get cleared away, but that H
is still there. This causes problems when you form the dummy bond to the N.
I need to look at it a bit to be sure, but this feels like an easily
fixable bug to me. If so I will go ahead and fix it. If it turns out to be
more complicated than I think, you can clean up the mess manually in your
code by doing something like this:
>>> mol = Chem.MolFromSmiles('N1C=CC=C1',sanitize=False)
>>> Chem.Kekulize(mol,clearAromaticFlags=True)
>>> for atom in mol.GetAtoms():
... if atom.GetAtomicNum() in (7,15,16) and atom.GetNumExplicitHs()==1:
... atom.SetNumExplicitHs(0)
...
>>> tempMol = Chem.EditableMol(mol)
>>> idx = tempMol.AddAtom(Chem.Atom(0))
>>> tempMol.AddBond(idx,0,Chem.BondType.SINGLE)
6
>>> nm = tempMol.GetMol()
>>> print Chem.MolToSmiles(nm)
[*]N1C=CC=C1
-greg
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