Re: [Rdkit-discuss] PAINS

[Markus Hartenfeller]

Hi Nick, Here is some code to get you started: In: from rdkit import Chem from rdkit.Chem import AllChem molList = ['Nc1cc(C)cc(Br)c1','CNc1cc(C)cc(Cl)c1', 'CCC'] #create screening dataset mol_DB = [Chem.MolFromSmiles(m) for m in molList] #create query mol from smarts try:                                       substr = AllChem.MolFromSmarts('[#7;H2]c1ccccc1')   except:         print 'error parsing smarts query'         exit(1) #screen for m in mol_DB:     try:         if (m.HasSubstructMatch(substr)):               print Chem.MolToSmiles(m)              except:         print 'error during substructure matching with mol '+Chem.MolToSmiles(m)         continue Out: Cc1cc(N)cc(Br)c1 Is it that what you are looking for? You can find more examples here: http://www.rdkit.org/docs/GettingStartedInPython.html Cheers, Markus On 04/25/2013 02:36 PM, Nicholas Firth wrote: Hi RDKitters, I've just been made aware that the PAINS filters have been nicely put into SMARTS (http://www.macinchem.org/reviews/pains/painsFilter.php), my question is how do people think would be the most efficient way to implement this in RDKit? I don't have much experience with SMARTS matching in RDKit, but I thought I could create a list of molecules from SMARTS and iterate over these using the 'HasSubstructMatch()' function to show any failures. Does this sound sensible or is there a more efficient way? Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews Facebook www.facebook.com/theinstituteofcancerresearch Making the discoveries that defeat cancer The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

------------------------------------------------------------------------------
Try New Relic Now & We'll Send You this Cool Shirt
New Relic is the only SaaS-based application performance monitoring service 
that delivers powerful full stack analytics. Optimize and monitor your
browser, app, & servers with just a few lines of code. Try New Relic
and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss