Re: [Rdkit-discuss] delete a substructure

[Chenyang Shi]

Thank you Chris. I found that one too; it is quite convenient to visualize
both SMARTS and SMILES strings.

On Thu, Mar 9, 2017 at 11:28 AM, Chris Swain  wrote:

> I use SMARTSviewer at Univ of Hamburg
>
> http://www.zbh.uni-hamburg.de/en/bioinformatics-server.html
>
> Chris
>
> On 9 Mar 2017, at 17:21, rdkit-discuss-requ...@lists.sourceforge.net
> wrote:
>
> One last question I have is do you guys have convenient online or local
> documents to look up desired SMARTS.
> Greg mentioned $RDBASE/Data/Functional_Group_Hierarchy.txt, which comes
> with the installation of RDKIT.
> Brian suggested daylight website,
> http://www.daylight.com/dayhtml_tutorials/languages/
> smarts/smarts_examples.html, which is a good place as well.
>
> Best,
> Chenyang
>
>
>
> 
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Re: [Rdkit-discuss] delete a substructure

[Chris Swain]

I use SMARTSviewer at Univ of Hamburg

http://www.zbh.uni-hamburg.de/en/bioinformatics-server.html 


Chris
> On 9 Mar 2017, at 17:21, rdkit-discuss-requ...@lists.sourceforge.net wrote:
> 
> One last question I have is do you guys have convenient online or local
> documents to look up desired SMARTS.
> Greg mentioned $RDBASE/Data/Functional_Group_Hierarchy.txt, which comes
> with the installation of RDKIT.
> Brian suggested daylight website,
> http://www.daylight.com/dayhtml_tutorials/languages/ 
> 
> smarts/smarts_examples.html, which is a good place as well.
> 
> Best,
> Chenyang

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Re: [Rdkit-discuss] delete a substructure

[Chenyang Shi]

Thanks Hongbin and Pavel for the suggestions. I am now confident that the
approach Hongbin proposed to remove duplicate counts is a robust one. Now I
need to revisit/recheck all my SMARTS definitions.

One last question I have is do you guys have convenient online or local
documents to look up desired SMARTS.
Greg mentioned $RDBASE/Data/Functional_Group_Hierarchy.txt, which comes
with the installation of RDKIT.
Brian suggested daylight website,
http://www.daylight.com/dayhtml_tutorials/languages/
smarts/smarts_examples.html, which is a good place as well.

Best,
Chenyang

On Thu, Mar 9, 2017 at 1:09 AM, 杨弘宾  wrote:

> Hi Chemyang,
>
> Your issue was caused by the definition of "-OH(phenol)", I think.  If
> you define this pattern as "cO", the atom *3* will be matched since it is
> the aromatic carbon bond to an oxygen.  I guess you just wanted to match
> exactly the oxygen and restrict it with "bonding with an aromatic carbon".
> So the SMARTS should ber "[$(Oc)]", which indicates an oxygen with the
> environment of "bonding with an aromatic carbon".
>
> m = Chem.MolFromSmiles('CC1=CC(=C(C=C1)C(=O)O)O')
> m.GetSubstructMatches(Chem.MolFromSmiles('[$(Oc)]'))
> >>> ((10,),)
>
> Then only atom *10* will be matched and it won't interfere with other
> counts.
>
> Reference: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
> 4.4
>
> --
> Hongbin Yang
>
>
> *From:* Chenyang Shi 
> *Date:* 2017-03-09 01:32
> *To:* Greg Landrum 
> *CC:* rdkit-discuss ; 杨弘宾
> 
> *Subject:* Re: [Rdkit-discuss] delete a substructure
> Dear Hongbin,
>
> I tried your method on a molecule, 4-Methylsalicylic acid
> (CC1=CC(=C(C=C1)C(=O)O)O). I looped through all groups defined in Joback
> method (using SMARTS), and used m.GetSubstructMatches to print out all
> atom positions. The result is summarized in the table.
>
> We can see there are duplicated counts--coming from COOH group. As
> suggested by Hongbin, we can remove duplicated atoms by looking at their
> positions--in this case, ((9),), ((7,8,),), ((7,),), and ((8,),) are
> subsets of ((7,8,9)) from -COOH. Indeed we can get rid of these duplicates.
> However, I also noticed that Atom (3,) from =C< (ring) group is also a part
> of -OH (phenol) ((10,3),). If we apply the same algorithm to remove
> duplicates, the =C<(ring) group will be only counted twice instead of three
> times.
>
> Greg, you mentioned as an alternative I can delete substructure using
> chemical reaction method. It would be greatly appreciated if you could show
> me (point me to) a simple example code, perhaps on a simple molecule? I
> find myself at a loss when browsing the manual. I would like to try also in
> that direction.
>
> Thanks,
> Chenyang
>
>
> [image: Inline image 1]
>
>
> On Mon, Mar 6, 2017 at 1:52 AM, Greg Landrum 
> wrote:
>
>> The solution that Hongbin proposes to the double-counting problem is a
>> good one. Just be sure to sort your substructure queries in the right order
>> so that the more complex ones come first.
>>
>> Another thing you might think about is making your queries more specific.
>> For example, as you pointed out "[OH]" is very general and matches parts of
>> carboxylic acids and a number of other functional groups. The RDKit has a
>> set of fairly well tested (though certainly not perfect) functional group
>> definitions in $RDBASE/Data/Functional_Group_Hierarchy.txt. The alcohol
>> definition from there looks like this:
>> [O;H1;$(O-!@[#6;!$(C=!@[O,N,S])])]
>>
>>
>> -greg
>>
>>
>> On Mon, Mar 6, 2017 at 7:20 AM, 杨弘宾  wrote:
>>
>>> Hi, Chenyang,
>>> You don't need to delete the substructure from the molecule. Just
>>> check whehter the mapped atoms have been matched. For example:
>>>
>>> m = Chem.MolFromSmiles('CC(=O)O')
>>> OH = Chem.MolFromSmarts('[OH]')
>>> COOH = Chem.MolFromSmarts('C(O)=O')
>>>
>>> m.GetSubstructMatches(OH)
>>> >> ((3,),)
>>> m.GetSubstructMatchs(COOH)
>>> >> ((1, 3, 2),)
>>>
>>> Since atom "3" has been already matched, it should be ignored.
>>> So you can create a "set" to record the matched atoms to avoid
>>> repetitive count.
>>>
>>> --
>>> Hongbin Yang 杨弘宾
>>>
>>>
>>> *From:* Chenyang Shi 
>>> *Date:* 2017-03-06 14:04
>>> *To:* Greg Landrum 
>>> *CC:* RDKit Discuss 
>>> *Subject:* Re: [Rdkit-discuss] delete a substructure
>>> Hi Greg,
>>>
>>> Thanks for a prompt reply. I did try "GetSubstructMatches()" and it
>>> returns correct numbers of substructures for CH3COOH. The potential problem
>>> with this approach is that if the molecule is getting complicated, it will
>>> possibly generate duplicate numbers for certain functional groups. For
>>> example, --OH (alcohol) group will be likely also counted in --COOH. A
>>> 

[Rdkit-discuss] show ROMol column in table

[Volkamer, Andrea]

Dear all,

I have trouble showing a table including a ROMol column.

# Add column to dataframe
PandasTools.AddMoleculeColumnToFrame(df, smilesCol='smiles')
# Remove compounds that couldn't be built
df = df[~df.ROMol.isnull()]

This works fine, but when I want to display it (df.head()), I get the following 
error:


AttributeError: 'module' object has no attribute 'format'


The first few columns are printed and have some image encoding in the 
respective column like:

https://physiologie-cbf.charite.de/en/institute/workgroups/team_volkamer/

Campus Mitte: Virchowweg 6, 10117 Berlin/ Philippstraße 13, Haus 18, 10115 
Berlin

Phone: +49 30 - 450 528 554 / 209 347 938
E-Mail: andrea.volka...@charite.de
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