The easiest way would be to do a substructure search as a subquery or WITH statement first and then do a SMARTS search on the result. This way you can keep your hydrogens and the speed (most of it).
Adrian On Thu, Mar 17, 2011 at 19:11, JP <jeanpaul.ebe...@inhibox.com> wrote: > Could the API possibly be altered to allow for H Removal (or not) ? > > On 17 March 2011 18:50, Greg Landrum <greg.land...@gmail.com> wrote: >> >> Hi JP, >> >> On Thu, Mar 17, 2011 at 2:55 PM, JP <jeanpaul.ebe...@inhibox.com> wrote: >> > I am using RDKit 2010_12_1, in particular the database cartridge - but I >> > am >> > quite positive this is an RDkit core problem. >> >> Well, problem... feature.. it's all a matter of perspective. :-S >> >> > Now - I am trying a substructure search (using '@>' operator on the >> > RDkit >> > molecule table) using smiles [H]N([H])C(=O)C(=O)C (so two explicit >> > hydrogens >> > on the N which is bound to a C with double bond to O) the following >> > molecule is returned: >> > I have the following smiles string: >> > O=C(C(=O)N1CC[NH2+]CC1)c1ccc(cc1C)C >> > Which RDKit::mol object >> > Cc1ccc(C(C(N2CC[NH2+]CC2)=O)=O)c(C)c1 >> > But it shouldn't ! (No ?) >> > Any help will be as usual - much appreciated. >> >> Here's what happens: when you construct the query molecule from SMILES >> the Hs are removed, so the queries for [H]N([H])C(=O)C(=O)C and >> NC(=O)C(=O)C end up being identical. >> >> At the moment, if you want to include the Hs in the query you have to >> do a SMARTS query. This has the unfortunate side effect of making the >> query substantially slower. >> >> I agree that this behavior is "suboptimal". I'm going to have to think >> (and read) a bit to come up with a reasonable solution. >> >> -greg > > > > -- > > Jean-Paul Ebejer > Early Stage Researcher > InhibOx Ltd > Pembroke House > 36-37 Pembroke Street > Oxford > OX1 1BP > UK > (+44 / 0) 1865 262 034 > > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > Any unauthorised dissemination or copying of this email or its attachments, > and any use or disclosure of any information contained in them, is strictly > prohibited and may be illegal. If you have received this email in error > please notify the sender and delete all copies from your system. > > We and our group companies accept no liability or responsibility for > personal emails or emails unconnected with our business. > > Internet communications including emails and access and use of web sites > cannot be guaranteed to be secure or error free as information can be > intercepted, corrupted, lost or arrive late. Furthermore, while we have > taken steps to control the spread of viruses on our systems, we cannot > guarantee that this email and any files transmitted with it are virus free. > No liability is accepted for any errors, omissions, interceptions, corrupted > mail, lost communications or late delivery arising as a result of receiving > this message via the Internet or for any virus that may be contained in it. > > > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
