Hi Eddie and Greg,
Thanks for your quick responses and solutions, they are really helpful.
Thanks,
Sarah
On 29 Sep 2011, at 03:51, Greg Landrum wrote:
> Sarah,
>
> On Wed, Sep 28, 2011 at 7:53 PM, Eddie Cao <cao.yi...@gmail.com>
> wrote:
>> I suggest the following alternative:
>> 1. first make a copy so you don't change the original molecule
>>>>> from copy import deepcopy
>>>>> mol2 = deepcopy(mol)
>> Now set the atoms you'd like to remove to dummy atoms with atomic
>> number 0
>>>>> mol2.GetAtomWithIdx(2).SetAtomicNum(0)
>>>>> mol2.GetAtomWithIdx(3).SetAtomicNum(0)
>> Now remove dummy atoms using a query
>>>>> mol3 = Chem.DeleteSubstructs(mol2, Chem.MolFromSmarts('[#0]'))
>> You get what you are looking for
>>>>> Chem.MolToSmiles(mol3)
>> 'CN'
>
> Eddie's solution is a nice one that should work pretty well.
>
> Another possible approach is to go ahead and use an EditableMol as you
> originally started, but to make sure that you remove the atoms
> starting with the highest numbers first:
>
>>>> m = Chem.MolFromSmiles('FCCCl')
>>>> em1 = Chem.EditableMol(m)
>>>> atomsToRemove=[0,3]
>>>> atomsToRemove.sort(reverse=True)
>>>> for atom in atomsToRemove:
> .. em1.RemoveAtom(atom)
> ..
>>>> m2 = em1.GetMol()
>>>> Chem.SanitizeMol(m2)
>>>> Chem.MolToSmiles(m2)
> 'CC'
>
> This should avoid the problem you were encountering.
>
> -greg
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