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rdf standardization
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lutz

Joined: 29 Apr 2005
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Link to postPosted: Wed Jan 28, 2009 7:39 pmPost subject: rdf standardization Reply with quote

using JChem standardizer 5.1.2 to aromatize molecules in an reaction rdf file, the standardizer changes the $RFMT $RIREG 12345 line towards $RFMT only in the resulting file, means the reaction number is kicked out... could I get this back?

cheers

Lutz
Gyorgy
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Joined: 21 May 2004
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Link to postPosted: Fri Jan 30, 2009 10:33 amPost subject: Reply with quote

Could you please attach an example reaction file (input) to be able to reproduce the problem?
lutz

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Link to postPosted: Fri Jan 30, 2009 11:33 amPost subject: Reply with quote

here it is: inputfile test.rdf and after aromatization testout.rdf


 Filename: testout.rdf    Filesize: 7.83 KB    Downloaded: 570 Time(s)
 Description:  

 Filename: test.rdf    Filesize: 8.13 KB    Downloaded: 446 Time(s)
 Description:  
Gyorgy
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Link to postPosted: Fri Jan 30, 2009 1:48 pmPost subject: Reply with quote

Thanks, it is a general rdf import/export problem, not related to aromatization or standardization. It can be reproduced with molconvert.

Code:
molconvert rdf test.rdf -o testout2.rdf


We are investigating it further.
lutz

Joined: 29 Apr 2005
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Link to postPosted: Thu Feb 05, 2009 4:09 pmPost subject: Reply with quote

Dear Gyuri,

can you give us an indication if you could send us a preliminary version of the standardizer that leaves the RIREG numbers intact? Would be great because otherwise we need to program a workaround soon.

best regards

lutz
Akos
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Joined: 09 Mar 2007
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Link to postPosted: Thu Feb 05, 2009 5:52 pmPost subject: RIREG field import Reply with quote

Hi Lutz,




We are investigating this problem right now. Theoretically, Marvin should be able to import the RIREG field, but for some reason it is not imported from your file. Unfortunately, I don't know whether we will have capacity for the bugfix before the release of 5.2.





Best regards,




Akos
Gyorgy
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Link to postPosted: Thu Mar 26, 2009 9:47 amPost subject: Reply with quote

The problem has been corrected, both $RIREG and $REREG fields are kept intact during conversions now. It will be available in version 5.2.1 approximately in the middle of April. Thank you for pointing out this issue!
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