Problematic mol file parsing

Hi

 

with JChem 6.2.0, we encounter problems with some molfiles (attached).

Command line tools (and Java API)  returns different errors for each mofiles:

- Amylose_(minus_2_units)

java.util.concurrent.ExecutionException:
chemaxon.formats.MolFormatException: Array index out of range: 108

...

- Intracellular-Sulfur

java.util.concurrent.ExecutionException:
chemaxon.formats.MolFormatException: Invalid atom indices in bond
definition (1, 1) 

...

 

Do you have an idea of what happens with those molfiles?

Regards

Hi,

In the first file (Amylose), line 213 contains a reference to the 109. bond. There are only 103 bond in the structure, this cause the problem. If you remove this line, the import works correctly.

In the second file there is only one atom, and one bond. This bond tries to connect the atom with itself.

Did you create the files with our API?

Janos

Hi

 

We have not created those files by ourselves.

the Amylose molfile comes from the BioPath database, and the Sulfur molfile from the MetaCyc database.

Hi,

In the first file I think its a bug (if I understand right the MDL file specification).

The loop bond in the second file can be a valid, but it has no chemical meaning. We do not support loop bonds or parallel bonds.

Janos

Hi

 

Thanks for all these explanations.

We will see with data provider how to fix that for molfile 1.

 

Regards