OpenBabel's current implementation for V3000 mol and sdf files does not support the S group block contained in this file, and causes the conversion to fail. I have altered the development code so that the rest of the molecule is converted properly.
With the current code, a work around would be to use the (far more common) V2000 mol file or prevent the generating program from using an S group (aka alias, abbreviated group), which just controls the display. The S group block could be manually deleted, which would affect the display, e.g. the C and O of the OCH3 group would have the same coordinates. The properties towards the end of the file do not look right and are ignored. Chris On 10/03/2011 10:11, nms_uk wrote: > Hi all, > I'm trying to use babel to convert a valid sdf file to mol file but it > doesn't work. > Can anyone take a look and help please? > here are the contents of the sdf file: > > > > 0 0 0 0 0 999 V3000 > M V30 BEGIN CTAB > M V30 COUNTS 13 13 3 0 0 > M V30 BEGIN ATOM > M V30 1 C 7.90196 6.19608 0.00000 0 > M V30 2 C 9.29412 5.37255 0.00000 0 > M V30 3 C 6.50980 5.37255 0.00000 0 > M V30 4 C 6.50980 3.76471 0.00000 0 > M V30 5 C 9.31373 3.78431 0.00000 0 > M V30 6 C 7.90196 2.94118 0.00000 0 > M V30 7 C 7.90196 1.35294 0.00000 0 > M V30 8 C 9.21569 0.52941 0.00000 0 > M V30 9 O 7.58824 8.09804 0.00000 0 > M V30 10 H 7.58824 8.09804 0.00000 0 > M V30 11 C 10.27451 1.78431 0.00000 0 > M V30 12 C 10.37255 6.49020 0.00000 0 > M V30 13 O 10.37255 6.49020 0.00000 0 > M V30 END ATOM > M V30 BEGIN BOND > M V30 1 1 2 1 > M V30 2 1 3 4 > M V30 3 1 5 6 > M V30 4 1 6 7 > M V30 5 1 8 7 > M V30 6 2 3 1 > M V30 7 2 5 2 > M V30 8 2 6 4 > M V30 9 1 9 10 > M V30 10 1 1 9 > M V30 11 2 8 11 > M V30 12 1 12 13 > M V30 13 1 2 13 > M V30 END BOND > M V30 BEGIN SGROUP > M V30 1 SUP 0 ATOMS=(2 9 10) XBONDS=(1 10) LABEL=OH > M V30 2 SUP 0 ATOMS=(1 11) XBONDS=(1 11) LABEL=CH2 > M V30 3 SUP 0 ATOMS=(2 12 13) XBONDS=(1 13) LABEL=OCH3 > M V30 END SGROUP > M V30 END CTAB > M END >> > 51.00000 > >> > 000300@ > > $$$$ > > -- ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
