ChemAxon Forum Archive » Storage & search: JChem Base and JChem Oracle Cartridge

problem search

User 870ab5b546

01-08-2007 15:14:16

Query:





Code:
<?xml version="1.0" ?>


<MDocument>


  <MChemicalStruct>


    <molecule molID="m1">


      <atomArray


          atomID="a1 a2 a3 a4 a5 a6 a7"


          elementType="P C H C C C C"


          mrvQueryProps="0 0 0 A: 0 0 0"


          x2="-7.241320687437101 -5.907641565609065 -5.90671259150665 -4.818697122581782 -7.241320687437101 -8.728846459922266 -7.6399020168949825"


          y2="1.9366666269302368 1.1666666269302368 -0.37333309287724314 2.25561106995752 3.476666626930237 2.335247956388119 0.40114349898395085"


          />


      <bondArray>


        <bond atomRefs2="a1 a7" order="1" />


        <bond atomRefs2="a1 a5" order="1" />


        <bond atomRefs2="a1 a2" order="2" />


        <bond atomRefs2="a1 a6" order="1" />


        <bond atomRefs2="a2 a4" order="1" />


        <bond atomRefs2="a2 a3" order="1" />


      </bondArray>


    </molecule>


  </MChemicalStruct>


</MDocument>






Target:





Code:
<?xml version="1.0" ?>


<MDocument>


  <MChemicalStruct>


    <molecule molID="m1">


      <atomArray


          atomID="a1 a2 a3 a4 a5 a6 a7"


          elementType="P C H H C C C"


          x2="-7.241320687437101 -5.907641565609065 -5.90671259150665 -4.818697122581782 -7.241320687437101 -8.728846459922266 -7.6399020168949825"


          y2="1.9366666269302368 1.1666666269302368 -0.37333309287724314 2.25561106995752 3.476666626930237 2.335247956388119 0.40114349898395085"


          />


      <bondArray>


        <bond atomRefs2="a1 a7" order="1" />


        <bond atomRefs2="a1 a5" order="1" />


        <bond atomRefs2="a1 a2" order="2" />


        <bond atomRefs2="a1 a6" order="1" />


        <bond atomRefs2="a2 a4" order="1" />


        <bond atomRefs2="a2 a3" order="1" />


      </bondArray>


    </molecule>


  </MChemicalStruct>


</MDocument>






The query is not found in the target. Why not? Does not H count as "any" atom?

ChemAxon a3d59b832c

01-08-2007 19:31:33

bobgr wrote:
The query is not found in the target. Why not? Does not H count as "any" atom?
In fact, it does not. See the documentation:


http://www.chemaxon.com/jchem/doc/user/Query.html#generatom





However, from the next major release there will be a new AH query atom for matching any atom including hydrogen. In the meantime, you can use an R-atom (e.g. R1) with no definition.

User 870ab5b546

01-08-2007 20:13:18

Hm, last I heard, H was an atom, but OK.





Perhaps for the next minor release you could put a tooltip in, so hovering above the Any atom in the periodic table causes a popup that says, "Any atom except H" to appear.

ChemAxon a3d59b832c

02-08-2007 08:40:13

OK, we will enhance the tooltip. We are currently redesigning the whole More window, and the AH button will be next to Any.

User 870ab5b546

08-08-2007 15:29:59

Szabolcs wrote:
In the meantime, you can use an R-atom (e.g. R1) with no definition.
That doesn't work when I want to map the R atom as well. So I really need that AH button.

ChemAxon a3d59b832c

08-08-2007 15:42:17

It seems to work for me:
Quote:
$ jcsearch --allHits -q "CC
  • |$;;_R1$|" CCC


    Query has 5 matches:


    Match 1:[ 1, 2, 3 ]


    Match 2:[ 1, 2, -2 ]


    Match 3:[ 2, 1, -1 ]


    Match 4:[ 2, 3, -3 ]


    Match 5:[ 3, 2, -2 ]


    CCC
    		•
    It is important that the R-atom does not have a definition. Otherwise, only the non-Rgroup portion of the scaffold is included in the hit array indeed.

    User 870ab5b546

    08-08-2007 15:47:38

    I mean, I can't apply a map number to the R atom.

    ChemAxon a3d59b832c

    08-08-2007 15:54:40

    Oh, I see. You are right, it is disabled for R-atoms.