I don't have access to the sources right now, so I don't exactly remember how i did it, but the CDK pharmacophore matching code is doing this (ie identifying atoms matching the pharmacophore SMARTS pattern).
On Sep 14, 2010, at 5:12 AM, Thomas G. Kristensen wrote: > Hi all, > > I'm trying to use CDK for detecting pharmacophores. It's easy enough > to get SMARTSQuery to find patterns but a major problem is, that the > returned atom (indices) do not respect the ordering of molecules in > the original SMARTS string. For example, the query string "[O;X2]C" > will, in one of my examples, return two atoms in this order: > > #<Atom Atom(745381933, S:C, 3D:[(-4.8833, 0.8605, 0.0308)], > AtomType(745381933, N:C.sp3, FC:0, H:SP3, NC:4, EV:4, > Isotope(745381933, Element(745381933, S:C, ID:C1))))> > #<Atom Atom(1362034980, S:O, 3D:[(-3.6751, 1.6658, 0.029)], > AtomType(1362034980, N:O.sp3, FC:0, H:SP3, NC:2, EV:2, > Isotope(1362034980, Element(1362034980, S:O, ID:O1))))> > > That is, the carbon is returned before the oxygen. I'm only interested > in the oxygen as that is the defining point of this feature but I > cannot assume that it will be the first atom returned (or the last, > for that matter). The order in which SMARTSQuery returns matched atoms > is arbitrary, rendering it useless as a feature extraction tool. > > I have been looking trough the source code of SMARTQuery, SMARTSParser > and UniversalIsomorphismTester to no avail. As far as I can tell from > the source it is impossible to extract the atoms in the correct order > without completely rewriting the SMARTS matching functionality include > the isomorphism tester. > > Does anybody know if I am mistaken? It would really make life much > easier for me if it was possible to extract the atoms in the order in > which they are matched. > > Best regards, > > Thomas > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- After a number of decimal places, nobody gives a damn. ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
