On 15/11/2010 12:17, Fredrik Wallner wrote: > Hi all! > > I'm having some problems with SMART matching... > > # This is the query I would like to have worked, without modifications > on either molecule or SMARTS > $ echo "OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O" | obabel -ismi -ocan > -s'[#6]-1(-[#6](~[!#6&!#1]~[#6]-[!#6&!#1]-[#6]-1=[!#6&!#1])~[!#6&!#1])=[#6;!R]-[#1]' > 0 molecules converted > > # Here the explicit hydrogen is removed from the query > $ echo "OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O" | obabel -ismi -ocan > -s'[#6]-1(-[#6](~[!#6&!#1]~[#6]-[!#6&!#1]-[#6]-1=[!#6&!#1])~[!#6&!#1])=[#6;!R]' > OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O > 1 molecule converted > > # Here the hydrogen is required, but implicit are allowed > $ echo "OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O" | obabel -ismi -ocan > -s'[#6]-1(-[#6](~[!#6&!#1]~[#6]-[!#6&!#1]-[#6]-1=[!#6&!#1])~[!#6&!#1])=[#6;!R;H]' > OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O > 1 molecule converted > > # Here the molecule to be tested has had an added hydrogen > $ echo "OCCOc1ccccc1[CH]=C1C(=O)NC(=S)NC1=O" | obabel -ismi -ocan > -s'[#6]-1(-[#6](~[!#6&!#1]~[#6]-[!#6&!#1]-[#6]-1=[!#6&!#1])~[!#6&!#1])=[#6;!R]-[#1]' > OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O > 1 molecule converted
Be careful, according to a recent post by Andrew Dalke, this is not explicit hydrogen, just explicitly stated implicit hydrogen. (At least one OB developer did not realize the difference, and at least one does not think it should matter.) > > # I also tried with the -h switch to add hydrogens to the molecule > with no luck (does it add the hydrogens before or after the SMARTS > matching? > $ echo "OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O" | obabel -ismi -ocan -h > -s'[#6]-1(-[#6](~[!#6&!#1]~[#6]-[!#6&!#1]-[#6]-1=[!#6&!#1])~[!#6&!#1])=[#6;!R]-[#1]' > 0 molecules converted > > I find it kind of unintuitive that query no 1 and 3 gives different > results and I would have thought that all should match. > > Have I missed something or do anyone among you have an idea how to > solve my problem without rewriting every SMART... The proper solution *should* be to add hydrogen with a -h option if the SMARTS query has explicit hydrogen. The order the options are applied is (which needs recording in the documentation): ops in alphabetical order. These are the plugin options. -h -b -r etc. Most hardwired options. --filter -s -v The original versions of the SMARTS filter. So in versions earlier than 2.3.0 -h would add hydrogens before the SMARTS test in -s. But In 2.3.0 there is an enhanced -s option that is an op and which overrides the old version. Because it is an op it is applied *before* the hydrogens are added by -h. On a Windows install giving plugin_ops.obf a different extension removes the new -s and allows query 5 to succeed, as expected. A workaround is to add the hydrogens first in a format which takes explicit hydrogen: obabel -:OCCOc1ccccc1C=C1C(=O)NC(=S)NC1=O -osdf -h | obabel -isdf -ocan -s"[#6]-1(-[#6](~[!#6&!#1]~[#6]-[!#6&!#1]-[#6]-1=[!#6&!#1])~[!#6&!#1])=[#6;!R]-[#1]" Sorry that the new -s option was not completely thought through. It would give extra flexibility if the order of the options on the command line was significant, but that would require significant code changes. Chris ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
