Hi Markus,
On Fri, Sep 16, 2016 at 11:35 AM, Markus Metz <metm...@gmail.com> wrote:
> Hello everybody:
>
> I am working on a script which removes the cores based on a given pattern
> and I am wondering how I can accomplish that if two matches are present in
> the parent molecule two outputs are generated with each matching pattern
> deleted once.
>
> ReplaceSubstructs seems to have an option like this: replaceAll=False
>
Indeed, adding that option to DeleteSubstructs() is a good idea.
I tried to use replaceSubstructs but using H as smiles string for
> replacement threw me an error.
> C worked.
>
The problem here may have been that you neglected the square brackets
around the 'H' in the SMILES?
This seems to work:
repl = Chem.MolFromSmiles('[H]')
frags = AllChem.ReplaceSubstructs(mol,pattern,repl)
for frag in frags:
print(Chem.MolToSmiles(frag))
[H]Cc1ccccc1
[H]Cc1ccccc1
Probably you want to call Chem.RemoveHs() on the outputs so that those Hs
disappear.
This isn't a great long-time solution (that is going to require the changes
to DeleteSubstructs()), but it may help in the short term.
-greg
> I have attached a notebook for you to better understand what I mean.
>
> Any suggestion you might have would be highly appreciated.
>
> Cheerio,
>
> Markus
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
