Is there a way to generat MDL by Instant Jchem

User 6ba4d9dd23

03-03-2014 15:59:50

I have a database containing 500 chemicals. Is ther a way to generate MDL for these chemicals using Instant Jchem? Thanks.

ChemAxon 2bdd02d1e5

03-03-2014 17:28:50

Do you want to export to multiple files or just to single MOL file?

You can export to a single MDL mol file by using jcman utility from JChem package.


User 6ba4d9dd23

04-03-2014 02:35:46

Hi Filip,

I want to export 500 chemiclas' MDL in a single file. Can you show me some more detailed information. Thanks.

ChemAxon 2bdd02d1e5

04-03-2014 07:47:20


For JChem manager documentation see You can export to MDL Molfile from there.

Within IJC you can export to MDL SDfile but not to MDL Molfile. I'm sorry for that, hope that JChem manager helps in this case.


ChemAxon 2bdd02d1e5

04-03-2014 09:16:27

One more thought... 

Don't you want to use SDF file instead? This is almost the same as MOL but more suitable for multiple structures.

If you export only single structure field in IJC to SD file. It will give you structures in MOL format one after another separated by $$$$. If you need to use mol suffix instead just rename the file and try to use it in an application you need.

User 6ba4d9dd23

04-03-2014 17:22:15

Hi Filip, 

Actually I want add a column containg MDL number in SDF file. Sorry I did not express correctly.

ChemAxon 2bdd02d1e5

05-03-2014 09:15:23


I'm sorry, I'm little confuse. There is such number in structure definition in SDF file? Or you want to add a new column with this number?

IJC can not generate this number. Neither showing it (if it's in structure definition) as I am aware of. Maybe you can obtain it from a web service? 

ChemAxon fa971619eb

05-03-2014 09:21:32

I think you refer to the MFCD number that is provided in the ACD database?

If so then this is proprietary to MDL/Accelrys. We do not have a mechansim for looking these up.