You did not specify the JChem version, so I was trying with one of the latest.
(Please also attach mol files as files, it is much easier to manage them)
The not list query in mol file format works as expected.
The mol query you have pasted on the other hand contains an QH query atom.
This seems like a bug, my colleagues will investigate this and get back to you.
Until then you may use the not list in mol format for the same purpose.
I wanted to post MOL as a file, but believe it or not, I had a very weird situtation. I use Marvin Sketch to save the MOL file, the MOL file is visible within Marvin Sketch Open dialog, but not visible to the Windows Explore (when saved under Desktop or My Document). So I was not able to attach the MOL file. Very strange indeed. My colleague had exactly the same issue last week. We are using Vista Ultimate X64. I was doing some quick Google search, did not find useful link. Anyway, I will try more when I get time.
I was using Marvin in jchem_5_0_02_1. But I just tried the example on the ChemAxon web site, when I try to get the query MOL format, it uses QH as element name as well.
Szilard ChemAxon personnel
Joined: 21 May 2004
The first issue seems to be some strange Windows "feature".
Regarding the conversion, I'm not sure I understand you correctly.
If I take the query SMARTS "[#6]C([!#6])CBr" and paste it into a Marvin Sketch (e.g. one of the applets on our website) I get the "not list" format on either file export or in the Edit -> Source window when I select mol format in "View".
It applies for both V2000 and V3000 mol formats.
Maybe You have converted an other SMARTS string (they all look alike to me :) ) or you have used some other method ?
In any case the search behavior of the QH must be investigated regardless.
I did not write the smarts, I actually draw the query using "QH" atom, then obtain the MOL file and use the MOL in the jc_compare search. If you draw the query (Table 3) and try to get MOL, you will see QH in the atom list.
Szabolcs ChemAxon personnel
Joined: 03 Jun 2004
The page below does not really explain what I saw (because I saved the file in Desktop, and my Document, not into Program Files folder). However, it seems offer a good theory - the MOL file Marvin Sketch wrote was actually saved in another location. I have to uninstall Java 6 Upgrade 10, I cannot reproduce the problem at this point. (I guess it has something to do with Vista x64 + Java 6 Upgrade 10).
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