molfile v3000 bond bug

Hi everybody!





There seems to be a bug somewhere in Marvin and its molfile v3000 support: The following V2 molfile has a either cis/trans bond (the second bond):





== Molfile V2 ==











  Marvin  02190914152D         





  4  3  0  0  0  0            999 V2000


   -3.2705    1.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


   -2.5561    1.8268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


   -1.8416    1.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


   -1.1271    1.8268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  1  2  1  0  0  0  0


  2  3  2  3  0  0  0


  3  4  1  0  0  0  0


M  END


== Molfile V2 ==





This molfile is displayed correctly. But its v3000 counterpart:








=== MOLFILE V3 ===











  Marvin  02190914162D         





  0  0  0     0  0            999 V3000


M  V30 BEGIN CTAB


M  V30 COUNTS 4 3 0 0 0


M  V30 BEGIN ATOM


M  V30 1 C -6.1049 2.64 0 0


M  V30 2 C -4.7714 3.41 0 0


M  V30 3 C -3.4377 2.64 0 0


M  V30 4 C -2.1039 3.41 0 0


M  V30 END ATOM


M  V30 BEGIN BOND


M  V30 1 1 1 2


M  V30 2 2 2 3 CFG=2


M  V30 3 1 3 4


M  V30 END BOND


M  V30 END CTAB


M  END


=== MOLFILE V3 ===





has a wavy bond instead. The same happens when I use MarvinBeans to render v3000 molfiles to an image.





Can you please give me a hint how to handle molfile v3000 with special bond types in MarvinBeans?





Thanks in advance





Helge

Hi Helge,





I cannot imagine how could you produce that V3000 molfile with Marvin because the current version does not support the storage of double cis|trans bonds. CFG=2 means either up|down, that's why you see a wavy bond when you import the file.





The problem is that MDL's documentation does not describe how to store cis|trans. Although page 89 of http://www.mdl.com/downloads/public/ctfile/ctfile.pdf lists the possible values of the CFG attribute,


 0 = none (default)


 1 = up


 2 = either


3 = down


the "cis" and "trans" words do not appear on this page or anywhere in this chapter. Hence the obvious interpretation is that CFG=2 means either up|down bonds and there is no way to store cis|trans.





On the other hand, the best way to store cis|trans in such a format would be with the same CFG option but bond type=2. At least I would do it this way, so I assume that they also did it this way, just forgot to document it.








I corrected Marvin's V3000 import/export, it will work as you expect it in Marvin 5.2.





Peter

Hi Peter,





you are correct; the description of the molfile v3000 format is a little bit unclear at this point.





However, our molfile guru here (he was involved in the development of molfile v3000 some years ago) told me that the CFG=2 option has different meanings, dependend on the bond type - as you guessed.





If the bond type is single CFG=2 should result in a wavy bond, but if it's a double bond this should result in a crossed bond.





You were also correct with your assumption that the molfile v3000 I supplied to you was not generated by Marvin, it was genereated by a program by our molfile guru...





I'm looking forward to Marvin 5.2 to get the "bug" fixed.





Thank you very much for your help!














Helge

Hi Helge,





Marvin 5.2 correctly imports and exports the double either bond, but this bug has not been fixed in the 5.1.6 version.





Best regards,





Akos

Hi Peter, Hi Akos,





I've tested the Import/Export functions of Marvin 5.2 and it seems that the molfiles v3000 are now handled correctly.





Thanks you very much for your help!





Best regards





Helge