Hello:
Greg's suggestions worked out.
Best,
Markus
On Fri, Sep 16, 2016 at 1:44 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Glad to hear it. Would you mind replying to the list as well so that the
> thread is closed?
>
> Best,
> -greg
>
>
> On Fri, Sep 16, 2016 at 1:33 PM, Markus Metz <metm...@gmail.com> wrote:
>
>> Hi Greg:
>> Just tried it out and it works great.
>> Thank you very much!
>> Markus
>>
>> On Fri, Sep 16, 2016 at 12:21 PM, Greg Landrum <greg.land...@gmail.com>
>> wrote:
>>
>>> 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
>>>>
>>>>
>>>
>>
>
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