Hi all, I am having trouble reading a mol file. The mol file was written from GaussView. The mol file describes benzene with aromatic bonds between the carbons. I read the mol file using CDK (MDLReader) and printed the smiles string. The smiles doesn't contain the aromatic bonds, neither does it contain the alternating single/double bonds in the ring. Does MDLReader parse aromatic bond types (the bond type is listed as 4 in mol file)? I am using Java 1.5.0, RHEL 4, CDK 1.0.1. The same problem persists with CDK 1.0.3 as well.
I am attaching the mol file and the java file I used to printout the smiles string. Thanks, Bala.
Mol2Smiles.java
Description: Binary data
benzene.mol
Description: Binary data
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