Hi,
I am a very new to CDK. I am trying to use the FileConvertor that came
with cdk1.0.1 to convert smiles strings to 2d structure and get
following error message:
Converting benzene.smi ... The format of the input file is not
recognized or not supported.
failed!
here is my benzene.smi
c1ccccc1 benzene
my command line:
java -cp ~/jar/cdk-1.0.1.jar org.openscience.cdk.applications.
FileConvertor
-2 -o mol benzene.smi
When I used sd format for the input file, it works fine.
for example if I take benzene.sdf:
benzene
--OE--
6 6 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0
1 6 2 0 0 0
1 2 1 0 0 0
2 3 2 0 0 0
3 4 1 0 0 0
4 5 2 0 0 0
5 6 1 0 0 0
M END
$$$$
and run the following command:
java -cp ~/jar/cdk-1.0.1.jar org.openscience.cdk.applications.
FileConvertor
-2 -o mol benzene.sdf
I got the 2D coordinate.
Is there anything wrong with my smiles input or command?
Thanks
Yongjin
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