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
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