Recently I knew KCF file format. The format represents molecules as graph structure. And it is used in KEGG.
KCF uses atom label and orientation, and bond information.
RDKit or Openbabel can not convert sdf 2 kcf.
Someone who want to convert sdf to kcf. KEGG site provide us API for file format conversion.
Example is following.
I have a sdf file.
iwatobipen$ head cdk2.sdf
ZINC03814457
3D
Structure written by MMmdl.
30 31 0 0 1 0 999 V2000
5.4230 -0.4412 0.7616 C 0 0 0 0 0 0
4.2434 0.3667 0.1880 C 0 0 0 0 0 0
4.5978 0.9630 -1.1852 C 0 0 0 0 0 0
2.9575 -0.4703 0.1074 C 0 0 0 0 0 0
2.9988 -1.6999 0.0580 O 0 0 0 0 0 0
1.6357 0.2975 0.0804 C 0 0 0 0 0 0
Know convert the file to kcf format using REST API.
iwatobipen$ curl -F sdffile=@cdk2.sdf http://rest.genome.jp/sdf2kcf/ > cdk2.kcf
iwatobipen$ head cdk2.kcf
ENTRY cdk21 Compound
ATOM 17
1 C1a C 5.4230 -0.4412
2 C1c C 4.2434 0.3667
3 C1a C 4.5978 0.9630
4 C5a C 2.9575 -0.4703
5 O5a O 2.9988 -1.6999
6 C1b C 1.6357 0.2975
7 O2a O 0.5374 -0.6063
8 C8y C -0.7229 -0.0532
API works fine. But if user want to convert large dataset, API is too slow.
I will try to make converter someday.
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