Different Mol format between import with jcman and update

Hi all,





if I import an structure using JChem Manager it creates a different content in column CD_STRUCTURE than if I update the structure from a Marvin View using UpdateHandler and molecule.tobinformat.





The import creates something encrypted like:








Marvin 04070514492D





32 34 0 0 1 0 999 V2000


+S+VaI-V62


aE0WVI+V64


ukyVVI+V64


+S+V3L1W64


4Q+V05zV90


gy1WaI-V62


aE0WmHyV60


ukyVmHyV60


S+wVaI-V60


ukyVSj0W60


aE0WkL2W60


efyVnk2W80


gy1W3L1W64


Qs3WYh+V60


+S+VMFxV60


S+wVMFxV60


mFvVVI+V60


5q3WWx1W64


mv1WTX3W60


5+4WPK0W64


mFvVmHyV60


5q3WpH4W60


Vv5WBr2W80


UA7W8M0W60


kitVKTxV80


DY5W3J5W60


zQ2WYT5W80


DJ7WpH4W80


vG0W3W0W10


mv1W05zV10


r-sV-T8W60


-QuVs27W60


10201


10301


10401


1050n


20601


20701


30801


30901


30A09


40B01


40C09


60D01


60E01


70F01


80G02


90H02


D0I01


D0J09


E0K01


G0L01


I0M01


I0N0n


K0O0n


L0P02


M0Q01


M0R02


Q0S01


80F01


B0D01


H0L01


I0K01


20T09


60U0n


V0W01


M END








But the update from java program creates a real mol file representation like:








Marvin 04070514492D





32 34 0 0 1 0 999 V2000


-0.6338 -0.2908 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0


0.0932 -0.7009 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0


-1.3384 -0.7009 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0


-0.6338 0.5443 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0


-0.6524 -1.1968 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0


0.7978 -0.2908 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0


0.0932 -1.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.3384 -1.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.0580 -0.2908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.3384 0.2908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.0932 0.9582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.3720 1.1185 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


0.7978 0.5443 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0


1.5770 -0.5406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-0.6338 -1.9498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.0580 -1.9498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.7664 -0.7009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.5621 0.7904 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0


0.7792 1.4429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.0357 0.1305 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0


-2.7664 -1.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.5621 1.7523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.4159 1.1595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


2.9342 0.1416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-3.4002 -1.8604 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


2.2669 2.1699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.9917 2.2370 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


2.9901 1.7523 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


0.1081 0.2051 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


0.7792 -1.1968 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-3.6875 3.4687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-3.1041 2.8854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1 2 1 0 0 0 0


1 3 1 0 0 0 0


1 4 1 0 0 0 0


1 5 1 6 0 0 0


2 6 1 0 0 0 0


2 7 1 0 0 0 0


3 8 1 0 0 0 0


3 9 1 0 0 0 0


3 10 1 1 0 0 0


4 11 1 0 0 0 0


4 12 1 1 0 0 0


6 13 1 0 0 0 0


6 14 1 0 0 0 0


7 15 1 0 0 0 0


8 16 2 0 0 0 0


9 17 2 0 0 0 0


13 18 1 0 0 0 0


13 19 1 1 0 0 0


14 20 1 0 0 0 0


16 21 1 0 0 0 0


18 22 1 0 0 0 0


18 23 1 6 0 0 0


20 24 1 6 0 0 0


21 25 2 0 0 0 0


22 26 1 0 0 0 0


22 27 2 0 0 0 0


26 28 1 0 0 0 0


8 15 1 0 0 0 0


11 13 1 0 0 0 0


17 21 1 0 0 0 0


18 20 1 0 0 0 0


2 29 1 1 0 0 0


6 30 1 6 0 0 0


31 32 1 0 0 0 0


M END





$$$$








I'd like to have the second representation in both cases. Is that possible at all?





Thanks in advance.

Hi,





We apply some text-based compression to the structure, that's why you see the difference.


(The structure is stored in "ChemAxon Compressed Molfile" format)





Currently there is no way of changing this behavior, but I will discuss with my colleagues if we should add an option for this in the future.





Until then if you need the structure in the original format for some reason, you can uncompress it with:





http://www.jchem.com/doc/api/chemaxon/formats/MdlCompressor.html





Best regards,





Szilard

Thank you very much.