Hi Sarah
On Wed, May 30, 2012 at 12:45 PM, Sarah Langdon <sarah.lang...@icr.ac.uk> wrote:
>
> I am trying to remove hydrogens from a molecule using RemoveHs, but the
> function isn't behaving as I expect.
>
> I am using it as part of some code that removes ring systems from a molecule
> and replaces them with a dummy atom, here are the SMILES for an example
> molecule and the 3 subsequent molecules as rings are removed
>
> 1 - O=C1NC(=O)N(C2CC3CCC2(CS(=O)(=O)N2CCC4(C5=CC=CC=C5CC4)CC2)C3(C)C)C1=O
> 2 - c1ccc2c(c1)CCC21CCN(SCC23C([*])([*])C(CC2)CC3N2C(=[*])NC(=[*])C2=[*])CC1
> 3 - [*]=C1NC(=[*])N(C2CC3CCC2([*])C3([*])[*])C1=[*]
> 4 - [*]C1([*])C2C[CH]C1([*])CC2
>
> On each of these I have used RemoveHs, but for some reason, in molecule 4,
> one of the carbons of the norbornane system is defined explicitly as CH. Does
> anyone have any idea why this is, or know how I can remove the hydrogen?
> Perhaps the hydrogen is added when I use MolToSmiles?
RemoveHs() removes explicit hydrogens from the molecule graph (i.e. Hs
that are actually present as atoms). Here's an example:
In [2]: m = Chem.MolFromSmiles('[H]OC([H])(Cl)F',sanitize=False)
In [3]: Chem.MolToSmiles(m)
Out[3]: '[H]OC(F)(Cl)[H]'
In [4]: nohm=Chem.RemoveHs(m)
In [5]: Chem.MolToSmiles(nohm)
Out[5]: 'OC(F)Cl'
H's that are written inside of square brackets with another atom, like
in your norbornane example, are usually there because the C is a
stereocenter. Since this one is *not* a stereocenter, something odd is
going on. Can you send the code that was used to generate these
molecular fragments so that I can try and figure out what's going on?
-greg
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