How to uncompress compressed molfiles in batch?

Hi





I import a few moleculars to database, and found their cd_structure are in "ChemAxon Compressed Molfile" format. I would like their cd_structure are in normal 'mrv' fromat. Could I change them in batch?





Thanks,





Xu

Hi,





the cd_structure field contains the structures according to original source file. You cannot change the formats of structures in cd_structures, you can import that molecules again with MRV source. I recommend to use our molconvert tool for change source format. You can find the starting script of it in the jchem/bin directory, see the maual:


http://www.chemaxon.com/marvin/help/applications/molconvert.html








Regards, Edvard

Hi Xu,





For this, you need to convert your input molecules from mol/sd format to mrv.








You can use molconvert for this. (It is part of JChem distribution.) See:








http://www.chemaxon.com/marvin/help/applications/molconvert.html

















Alternatively, you can switch off molfile conversion for a JChem table, using JChem Manager.





In that case, your newly inserted structures will be stored in its original mol format.








See: http://www.chemaxon.com/jchem/doc/admin/#options














Best regards,





Szabolcs

Hi,





I checked my SD file from which I imported into database, and the molecular structure are in normal format, not chemaxon compressed molfiles format. Is there any parameter for 'import' to let me remain the molfiles in cd_structure same as that original in SD file instead of cervert them to compressed molfiles format?





Thanks,





Xu

Hi Xu,





Applying compression is a "global" option. Once you disable compression in JChem Manager (i.e. uncheck the checkbox "Compress MOL, RXN and SDF formats during import" -- http://www.chemaxon.com/jchem/doc/admin/#options ), structures will be imported uncompressed for all subsequent imports (until you enable compression again).





Peter

Hi,





Is there such an parameter to contral the imported structure in orginial format when I use 'jcman' command line?





Besides, after I modify a molecular with compressed molfile in cd_structutre from http (edit.jsp, update.jsp), the molfile in cd_id would change to uncompressed format. How could I contral the molfile format of structure into cd_structure when I modify or insert a new molecular from web-page?





Thanks,





Xu

Quote:

Is there such an parameter to contral the imported structure in orginial format when I use 'jcman' command line?

There is no option, it is a global option in the property table.


Once set, all of our programs behave accordingly.





BTW we plan to abolish this automatic compression altogether for the sake of simplicity.

Quote:

How could I contral the molfile format of structure into cd_structure when I modify or insert a new molecular from web-page?

Whatever format is sent to the UpdateHandler class, it will be stored as is in cd_structure (except uncompressed molfile is compressed if the option is set that way).


So if get the source from the applet in "csmol" format with getMol() and send that to the server it will be compressed regardless of the option.





Best regards,





Szilard