Hi Chris,
You're missing one step: BRICS.BRICSBuild() is expecting molecules, not
SMILES.
If you add a call to Chem.MolFromSmiles() you should get what you want :
In [12]: mcat = [Chem.MolFromSmiles(x) for x in catalog]
In [13]: ms = BRICS.BRICSBuild(mcat)
In [14]: for m in ms: print Chem.MolToSmiles(m)
c1ncnc(-c2ncncn2)n1
c1ncnc(C2CC2)n1
c1ncnc(C2CNC2)n1
c1ncnc(Oc2ncncn2)n1
c1ncnc(OC2CC2)n1
c1ncnc(OC2CNC2)n1
C1CC1OC1CC1
C1CC1OC1CNC1
C1NCC1OC1CNC1
The other option is to call BRICS.BricsDecompose() with the returnMols
argument:
In [17]: catalog = BRICS.BRICSDecompose(base,returnMols=True)
In [18]: ms = BRICS.BRICSBuild(catalog)
In [19]: for m in ms: print Chem.MolToSmiles(m)
c1ncnc(C2CC2)n1
c1ncnc(C2CNC2)n1
c1ncnc(-c2ncncn2)n1
c1ncnc(Oc2ncncn2)n1
c1ncnc(OC2CC2)n1
c1ncnc(OC2CNC2)n1
C1CC1OC1CC1
C1CC1OC1CNC1
C1NCC1OC1CNC1
Best,
-greg
On Sat, Mar 14, 2015 at 2:34 PM, Chris Arthur <[email protected]>
wrote:
> Hi guys,
>
> i hope some can help.
>
> I am trying to run the code from
> <
> https://www.mail-archive.com/[email protected]/msg00479.html
> >
>
> from rdkit import Chem
> from rdkit.Chem import BRICS
> base = Chem.MolFromSmiles("n1cncnc1OCC(C1CC1)OC1CNC1")
>
> catalog = BRICS.BRICSDecompose(base)
> print catalog
>
> ms = BRICS.BRICSBuild(catalog)
> ms = list(ms)
> len(ms)
>
> for m in ms[:5]: print Chem.MolToSmiles(m)
>
>
> Brics is decomposing molecules correctly (as shown by print catalog)
> and ms reports as a
> <generator object BRICSBuild at 0x0000000009CBCA68>
>
> But I get errors whenever I try to get structures from ms (see the
> following trackback)
>
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File
> "C:\Anaconda\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
> line 580, in runfile
> execfile(filename, namespace)
> File "//
> ads.bris.ac.uk/filestore/myfiles/staff14/chxcja/Desktop/brics-test.py",
> line 11, in <module>
> ms = list(ms)
> File "c:\RDKit\rdkit\Chem\BRICS.py", line 532, in BRICSBuild
> if seed.HasSubstructMatch(rxn._matchers[0]):
> AttributeError: 'str' object has no attribute 'HasSubstructMatch'
>
> I am using Anaconda Python (Py2.7) on windows with RDKit_2014_09_02
>
> Can anyone suggest what I'm doing wrong?
>
> Thanks
>
> Chris
>
> --
> Dr Christopher J. Arthur
> School of Chemistry
> University of Bristol
> BRISTOL, BS8 1TS, UK
> E-mail: [email protected]
>
> Office: (+44 117) 331 7192
> Mass Spectrometry Lab: (+44 117) 331 7358.
> FAX: (+44 117) 927 7985
>
> WWW URL: http://www.chm.bris.ac.uk/staff/carthur.htm
> LinkedIn Profile: https://www.linkedin.com/in/drchrisarthur
>
>
>
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