Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.

Support Ticket System is replacing forum

This forum was converted into a searchable archive. You cannot add posts here any more. For support please use our new Ticket System.

Create your first ticket
Example in the query feature document
To watch this topic for replies  Register (enables digests) or give email address:
This topic is locked: you cannot edit posts or make replies.
Display posts from previous:   
    View previous topic :: View next topic    
Author Message
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 8:49 amPost subject: Example in the query feature document Reply with quote

http://www.chemaxon.com/jchem/doc/user/query_features.html

In Table 3, the 4th query does not seem to match the 2nd target.
Szabolcs
ChemAxon personnel
Joined: 03 Jun 2004
Posts: 1924

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 9:21 amPost subject: Reply with quote

It should be OK.

Please note that QH (hetero or hydrogen) matches the implicit H.

Regards,
Szabolcs
Tamas
ChemAxon personnel
Joined: 03 Jan 2007
Posts: 131

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 9:41 amPost subject: Reply with quote

Hi,

It matches because of the presence of the implicit H (see attached picture).

Best regards,
Tamás



 Filename: MatchImplicitH.png    Filesize: 2.81 KB    Viewed: 16101 Time(s)
 Description:  
MatchImplicitH.png
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 6:04 pmPost subject: Reply with quote

Thank you. Just out of curiosity, I tried jc_compare
The following statement returns 0, no match.
I also try to represent query in MOL format, same result. I must have a mistake somewhere.

select jc_compare('CC(Cl)C(O)C1CCCC(C1)C(C)CBr', '[#6]C([!#6])CBr', 't:s') FROM dual;
Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 7:29 pmPost subject: Reply with quote

Hi,

In SMARTS format these should not match, as only isotopic and charged Hydrogens match not list according to Daylight conventions.
Please see:

http://www.chemaxon.com/jchem/doc/user/query_appendix.html#daylMDLDiff

However in mol format there should be a match according to the documentation.

Could you attach the files in mol/SDF format and let us know you JChem version please ?

Best regards,

Szilard
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 7:37 pmPost subject: Reply with quote

<pre>

Marvin 11110808542D

5 4 0 0 0 0 999 V2000
-1.5616 0.3241 0.0000 QH 0 0 0 0 0 0 0 0 0 0 0 0
-0.8471 0.7366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1327 0.3241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5818 0.7366 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-0.8471 1.5616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
2 5 1 0 0 0 0
M END
</pre>
Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 8:07 pmPost subject: Reply with quote

Hi,

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.

Best regards,

Szilard
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 8:27 pmPost subject: Reply with quote

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
Posts: 1668

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 8:45 pmPost subject: Reply with quote

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.

Szilard
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Tue Nov 11, 2008 10:27 pmPost subject: Reply with quote

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
Posts: 1924

View user's profile

Back to top
Link to postPosted: Wed Nov 12, 2008 8:20 amPost subject: Reply with quote

Hi Yingyao,

You are right, our SMARTS export is buggy, [!#6] is not the correct representation for QH. We will change that to [#1,!#6].

As a workaround, you could use cxsmarts instead, that preserves the QH query atom:
Code:
[#6]C([!#6])CBr |$;;QH_p;;$|


Best regards,
Szabolcs
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Wed Nov 12, 2008 5:33 pmPost subject: Reply with quote

Just want to make sure, it sounds the MOL export for QH atom is buggy as well.
Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

View user's profile

Back to top
Link to postPosted: Wed Nov 12, 2008 6:41 pmPost subject: Reply with quote

Hi,
Quote:
Just want to make sure, it sounds the MOL export for QH atom is buggy as well.
Yes it seems that is the problem that's preventing you from getting the desired search result.

We are investigating this issue and will get back to you soon.

Until then as a workaround you may use the MRV format for searching with QH query atoms.

Best regards,

Szilard
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Thu Nov 13, 2008 7:42 amPost subject: Reply with quote

I did a bit more Google search, first I need to convince you that I am not out of my mind. Others have similar problem with the ghost files.

http://www.vistax64.com/vista-general/41666-java-6-creates-directories-files-explorer-cant-see.html

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).

http://stackoverflow.com/questions/280600/java-filecanwrite-on-vista-and-super-hidden-files

I post the info here just in case someone else experience the same.


Last edited by Yingyao on Thu Nov 13, 2008 7:43 am; edited 1 time in total
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Thu Nov 13, 2008 7:54 amPost subject: Reply with quote

Although I cannot reproduce it, I believe the answer is AUC.

http://www.eggheadcafe.com/software/aspnet/32468146/cant-see-swf-files-save.aspx

Why Java can create a file that people in the Administrator group cannot see (but should be visible by Administrator account)? I don't know.
Szilard
ChemAxon personnel
Joined: 21 May 2004
Posts: 1668

View user's profile

Back to top
Link to postPosted: Thu Nov 13, 2008 8:21 pmPost subject: Reply with quote

Quote:
Just want to make sure, it sounds the MOL export for QH atom is buggy as well.
Actually the bug was in the MOL import, not the export.
We have fixed it, the fix will be available in the next minor release (JChem 5.1.4)

Thank you for the bug report.

Best regards,

Szilard
Yingyao

Joined: 30 Sep 2004
Posts: 205

View user's profile

Back to top
Link to postPosted: Mon Dec 08, 2008 9:34 pmPost subject: Reply with quote

Do you have a rough estimation on when 5.1.4 will be released? Thanks
Szabolcs
ChemAxon personnel
Joined: 03 Jun 2004
Posts: 1924

View user's profile

Back to top
Link to postPosted: Wed Dec 10, 2008 12:35 amPost subject: Reply with quote

Hi,

It is planned to be out next week.

Best regards,
Szabolcs
This topic is locked: you cannot edit posts or make replies.
Page 1 of 1


To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You can download files in this forum