Which RDKit version do you have?
"print rdkit.__version__"
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-01-21 21:38 GMT+01:00 Janusz Petkowski <jjpet...@mit.edu>:
> Czesc again,
>
> Many thanks for the code snippet. I thought that I use it wrongly, I
> previously tried to use it exactly like you wrote, but I always got an
> error back. I think that maybe I am missing a module? I copied your snippet
> and tried to use it and got the same error
>
> m1 = Chem.MolFromSmiles('c1ccccc1')
> m1 = Chem.AddHs(m1, onlyOnAtoms=(2,3,4))
> print Chem.MolToSmiles(m1)
>
>
>
> The error is below:
>
> m1 = Chem.AddHs(m1, onlyOnAtoms=(2,3,4))
> Boost.Python.ArgumentError: Python argument types in
> rdkit.Chem.rdmolops.AddHs(Mol)
> did not match C++ signature:
> AddHs(class RDKit::ROMol mol, bool explicitOnly=False, bool
> addCoords=False)
>
> It looks like RDkit does not recognize the onlyOnAtoms function?
>
> Thanks again for all your help!
>
> Janusz
>
> ------------------------------
> *From:* Maciek Wójcikowski [mac...@wojcikowski.pl]
> *Sent:* Saturday, January 21, 2017 3:11 PM
>
> *To:* Janusz Petkowski
> *Cc:* rdkit-discuss@lists.sourceforge.net
> *Subject:* Re: [Rdkit-discuss] adding custom number of explicit H to
> specified non-hydrogen atoms
>
> Cześć,
>
> Following code will add Hs to atoms 2,3,4. These are the usual RDKit
> indices which you get from "Atom.GetIdx()".
>
>> In [5]: m1 = Chem.MolFromSmiles('c1ccccc1')
>> ...: m1 = Chem.AddHs(m1, onlyOnAtoms=(2,3,4))
>> ...: Chem.MolToSmiles(m1)
>> ...:
>> ...:
>> Out[5]: '[H]c1cccc([H])c1[H]'
>
>
>
> ----
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-01-21 15:54 GMT+01:00 Janusz Petkowski <jjpet...@mit.edu>:
>
>> Czesc Maciek,
>>
>> Thanks a lot for suggesting "onlyOnAtoms" option out. It looks like it is
>> exactly what I would need. If it is not too big of a problem would it be
>> possible for you to give me a simple example how to toggle that option on?
>> I am sorry if this question seems obvious but I am not a programmer and my
>> python skills are not yet advanced.
>>
>> Best regards,
>>
>> Janusz Petkowski
>> ------------------------------
>> *From:* Maciek Wójcikowski [mac...@wojcikowski.pl]
>> *Sent:* Saturday, January 21, 2017 5:35 AM
>> *To:* Janusz Petkowski
>> *Cc:* rdkit-discuss@lists.sourceforge.net
>> *Subject:* Re: [Rdkit-discuss] adding custom number of explicit H to
>> specified non-hydrogen atoms
>>
>> Hi Janusz,
>>
>> AddHs has a parameter "onlyOnAtoms" which takes a list of indices of
>> atoms to include. [http://www.rdkit.org/Python_D
>> ocs/rdkit.Chem.rdmolops-module.html#AddHs]
>>
>> ----
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>> 2017-01-20 23:21 GMT+01:00 Janusz Petkowski <jjpet...@mit.edu>:
>>
>>> Dear RDKit Community,
>>>
>>> By default H atoms are not explicit in the molecular graph and because
>>> of that the substructure matching is ignoring them when searching for
>>> substructures. It is possible to use Chem.AddHs(mol) to add explicit
>>> hydrogens to all atoms in the molecule and then perform substructure
>>> matching but is it possible, in RDkit, to add explicit hydrogens
>>> specifically to atoms of choice instead to all of them?
>>>
>>> So let's say if I do:
>>>
>>> m1 = Chem.MolFromSmiles('C=C')
>>> m1_H = Chem.AddHs(m1)
>>> print m1_H.GetNumAtoms()
>>> print Chem.MolToSmiles(m1_H)
>>>
>>> The result is:
>>>
>>> >>> 6
>>> >>> [H]C([H])=C([H])[H]
>>>
>>> What if I would like to add only one (1) explicit hydrogen atom to a
>>> specific non-hydrogen atom (let's say m1.GetAtomWithIdx(0). In that case I
>>> would want to have:
>>>
>>> print m1_H.GetNumAtoms()
>>> print Chem.MolToSmiles(m1_H)
>>>
>>> >>> 3
>>> >>> [H]C=C
>>>
>>> I tried to use the following method:
>>> m1.GetAtomWithIdx(0).SetNumExplicitHs(1)
>>> which correctly adds an explicit H to C=C molecule but somehow I cannot
>>> convert it to smiles with this one additional explicit H added or
>>> subsequently use for substructure matching.
>>>
>>> At the end I would like to do a substructure matching where the
>>> following query structures:
>>>
>>>
>>> [H]C=C or [H]C=CC match the following molecule:
>>> [H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
>>>
>>> but at the same time those query structures: [H]C=C([H])[H] or
>>> [H]C([H])=CC do not match [H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
>>>
>>> PS. Of course, the structure [H]C([H])=C([H])[H] converted from C=C
>>> using Chem.AddHs(mol) will not be matched onto
>>> [H]C(=C([H])C([H])([H])[H])C([H])([H])[H] which is correct.
>>>
>>> Thank you very much for your help,
>>>
>>> Best regards,
>>>
>>> Janusz Petkowski
>>>
>>>
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>>>
>>
>
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