If I remember correctly, that column is for atom stereo information - I don't think the CDK supports this properly yet, hence it doesn't include it in the output.
On Sat, Dec 17, 2011 at 7:24 PM, lochana menikarachchi <[email protected]> wrote: > > I have noticed either cdk MDLV2000 reader or sdf writer looses some > information in the sdf file. (column 7) This breaks compatibility with other > programs that rely on this information. Both oechem and marvin keep all > information in sdf. Is there anyway to solve this. Is it a limitation in the > CDK?? > > Ex: A part from a sdf file downloaded from pubchem > > 5701990 > -OEChem-12131111192D > > 57 60 0 1 0 0 0 0 0999 V2000 > 8.6500 1.4952 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.0000 -2.8124 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 10.2963 0.9572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 7.3931 -0.7600 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 > 7.3931 0.2400 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 > 6.5271 -1.2600 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 > 5.6610 -0.7600 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 > 4.7510 -1.2669 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 > 6.5271 0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.6610 0.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.3393 0.5447 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 > 8.3393 -1.0648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > CDK generated > > 5701990 > CDK 1217111900 > > 57 60 0 0 0 0 0 0 0 0999 V2000 > 8.6500 1.4952 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.0000 -2.8124 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 10.2963 0.9572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 7.3931 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.3931 0.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.5271 -1.2600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.6610 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.7510 -1.2669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.5271 0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.6610 0.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.3393 0.5447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.3393 -1.0648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
