Thanks Jameed and Adrian, I will have a look at those SMARTS, I have to admit I didn't know about them previous so thank you very much.
The SMARTS viewer had been really helpful, though it seemed to be showing me what I wanted. I was using the SMARTS editor from the Rarey group before using a temporary license, that was a really cool tool. 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 [email protected] | W www.icr.ac.uk | Twitter @ICRnews ________________________________________ From: Adrian Jasiński [[email protected]] Sent: 27 March 2014 19:30 To: Jameed Hussain Cc: Nicholas Firth; [email protected] Discuss Subject: Re: [Rdkit-discuss] SMARTS behaviour you can allways visualise yours SMARTS by using http://www.smartsview.de/ pozdrawiam Adrian 2014-03-27 17:44 GMT+01:00 Jameed Hussain <[email protected]<mailto:[email protected]>>: Try this: [*!H0;!$(*~[#0])] I don’t think you can do what you want without a recursive SMARTS. It’s well worth doing the Daylight exercises to get your head around recursive SMARTS – they are really useful. Cheers Jameed From: Nicholas Firth [mailto:[email protected]<mailto:[email protected]>] Sent: 27 March 2014 15:23 To: [email protected]<mailto:[email protected]> Discuss Subject: [Rdkit-discuss] SMARTS behaviour Hi RDKitters, This isn't strictly an RDKit based issue, but I guess someone here will be able to help me. I'm trying to identify the index of atoms in a molecule which have one or more hydrogen bonded to them but are not bonded to a dummy atom ([*]). >>> mol = Chem.MolFromSmiles('[*]CCC[*]') >>> patt = Chem.MolFromSmarts('[*H1,H2,H3,H4]!~[#0]') >>> print mol.GetSubstructMatches(patt) () I'd expect this to return (1). But it would appear that I'm in the wrong, as Pipeline Pilot give the same result. Is there a SMARTS query that will give me the matches that I want or do I have to go back to iterating over atoms? Many thanks in advance. 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 [email protected]<mailto:[email protected]> | W www.icr.ac.uk<http://www.icr.ac.uk/> | Twitter @ICRnews<https://twitter.com/ICRnews> Facebook www.facebook.com/theinstituteofcancerresearch<http://www.facebook.com/theinstituteofcancerresearch> Making the discoveries that defeat cancer [cid:[email protected]] 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. ________________________________ This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 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. ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
