Hi Greg,
Thanks for your reply. The code used to generate these fragments is part of a
much larger set of code, so I have been putting together a shorter version to
recreate the problem for you. Strangely, now that I have isolated the code, I
don't get the same problem and the hydrogen is removed!
I think I will carry on playing around with this before I send you anything to
look at, I don't want to waste your time, hopefully I've got it fixed now.
Thanks for your help,
Sarah
On 30 May 2012, at 15:49, Greg Landrum wrote:
> 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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