I find installing RDKit using Conda the easiest and the most
straightforward across all platforms.
First install miniconda [http://conda.pydata.org/miniconda.html] and then
in terminal: "conda install -c rdkit rdkit"
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-01-21 23:33 GMT+01:00 Janusz Petkowski <jjpet...@mit.edu>:
> Ok, one last question. I try to update my RDKit to the current version
> (rdkit-Release_2016_09_3) which I downloaded from here
> https://github.com/rdkit/rdkit/releases so I can use onlyOnAtoms function.
>
> My current version (2015.03.1.) installed on Win 7 machine works perfectly
> well. I have downloaded the new one - rdkit-Release_2016_09_3 - I have set
> up environmental variables as described in Win installation guide (and as
> I had to set them up last time to get the previous 2015.03.1 version
> working) and at the end I have an import error like that:
>
> from rdkit import Chem
> File "C:\rdkit-Release_2016_09_3\rdkit\__init__.py", line 2, in <module>
> from .rdBase import rdkitVersion as __version__
> ImportError: No module named rdBase
>
> I presume that this is somehow related to missing DLLs? But I had them
> installed when I got the old version, so they should be there. When I try
> to download them from here http://www.microsoft.com/en-
> us/download/details.aspx?id=5555 anyway, I got a notification that newer
> DLLs are already installed.
>
> Reverting to my previous RDkit version 2015.03.1. allows everything to
> work again.
>
> Does anybody know how to circumvent this problem?
>
> Thank you once again!
>
> Janusz
> ------------------------------
> *From:* Peter Gedeck [peter.ged...@gmail.com]
> *Sent:* Saturday, January 21, 2017 3:44 PM
> *To:* Janusz Petkowski; Maciek Wójcikowski
>
> *Cc:* rdkit-discuss@lists.sourceforge.net
> *Subject:* Re: [Rdkit-discuss] adding custom number of explicit H to
> specified non-hydrogen atoms
>
> Looks like you have a very old version of RDkit. The additional option was
> included in RDkit 2016.03.1. Check
>
> import rdkit
> print(rdkit.__version__)
>
> Best,
>
> Peter
>
>
>
> On Sat, Jan 21, 2017 at 3:39 PM Janusz Petkowski <jjpet...@mit.edu> wrote:
>
>> 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_Docs/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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>
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