I think the issue is that you're making an explicit bond to a Xenon atom,
and Xenon's valence model in the RDKit says that it has either zero bond or
it has two bonds. (Don't worry - it's not really something you should have
known *a priori *- valence models are funky.
<https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/>)
list( Chem.GetPeriodicTable().GetValenceList("Xe") ) # Returns [0, 2]
Since you have at least one bond to Xenon (to the carbon), you can't have
zero bonds, so you must have two bonds, so RDKit fills in the missing
valence with an implicit hydrogen:
atom.GetTotalValence() # returns 2
atom.GetNumImplicitHs() # returns 1
The hydrogen is implicit, so removing the hydrogens with Chem.RemoveHs()
won't do anything.
This then interacts with the Smiles code. The Smiles model says that if you
have an atom in brackets (which Xenon always is), you need to explicitly
record the hydrogens it has. (See here
<https://baoilleach.blogspot.com/2017/01/counting-hydrogens-in-smiles-string.html>
for more.)
Ways around it: The easiest would be if you could change your element to
something which takes a single valence, or something that doesn't have
valences for implicit hydrogen purposes. (Astatine is a decent choice for
the former, many of the the actinides work well for the latter.) If you
really do want to use Xenon, you can always manually flag the atom to not
have any implicit hydrogens.
*...*
xe = Chem.Atom(54) # 54 is Xenon
*xe.SetNoImplicit(True)*
idx = mw.AddAtom(xe)
mw.AddBond(0,6,Chem.BondType.SINGLE)
Chem.SanitizeMol(mw)
atom = mw.GetAtomWithIdx(idx)
atom.GetExplicitValence() # returns 1
atom.GetTotalValence() *# returns 1*
atom.GetNumImplicitHs() *# returns 0*
Chem.MolToSmiles(mw) *# returns '[Xe]c1ccccc1'*
On Wed, Sep 4, 2019 at 9:35 AM Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> I'm finding that if I add a Xenon atom to a molecule it seems to get an
> unwanted hydrogen added to it.
> Example notebook here:
> https://gist.github.com/tdudgeon/ba3497341d9de95b4d78f3e5ed9fc0f7
>
> Basic code is like this:
>
> from rdkit import Chem
> m = Chem.MolFromSmiles("c1ccccc1")
> mw = Chem.RWMol(m)
> xe = Chem.Atom(54) # 54 is Xenon
> idx = mw.AddAtom(xe)
> mw.AddBond(0,6,Chem.BondType.SINGLE)
> Chem.SanitizeMol(mw)
> atom = mw.GetAtomWithIdx(idx)
> atom.GetExplicitValence() # returns 1
> Chem.MolToSmiles(mw) # returns [XeH]c1ccccc1, expecting [Xe]c1ccccc1
>
> Even if I do a Chem.RemoveHs() the H remains.
>
> Any ideas why and how to fix?
>
>
>
>
>
> _______________________________________________
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> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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