Hi all,
Thanks all! I should have been a bit more explicit. This is the context
of the offending line:
try {
smi = rdmol.MolToSmiles();
} catch (org.RDKit.MolSanitizeException e) {
System.err.println("Bad Mol Found: " + smi);
}
I thought after reading the comments, that maybe I was being too specific.
So, I tried the same try/catch block with a more general exception (which I
hadn't tried before):
try {
smi = rdmol.MolToSmiles();
} catch (Exception e) {
System.err.println("Bad Mol Found: " + smi);
}
Nothing changed (I reached the same error):
Exception in thread "main" org.RDKit.MolSanitizeException
at org.RDKit.RDKFuncsJNI.RWMol_MolFromSmiles__SWIG_3(Native Method)
at org.RDKit.RWMol.MolFromSmiles(RWMol.java:422)
Hopefully my issue is a bit more clear now. There is another route around
this issue, reading the input file line by line and excising those
offending lines. This would work, but I would rather not have to buffer my
RDKit code. :)
Thanks!
Matt
On Sun, Jun 1, 2014 at 12:55 AM, Toby Wright <toby.wri...@inhibox.com>
wrote:
> If you just want to ignore the error add a try...catch block around the
> offending line.
>
> Yours,
>
> Toby Wright
>
>
> On 31 May 2014 00:03, Matthew Lardy <mla...@gmail.com> wrote:
>
>> Hi all,
>>
>> I am having this issue with the Java wrapper while trying to create a
>> smiles string from a RWMol class object. I don't care about trying to
>> figure out what is going wrong, I just want to bypass this record without
>> my application closing. Any ideas?
>>
>> Here is the offending line:
>>
>> rdmol.MolToSmiles();
>>
>> The error:
>>
>> Exception in thread "main" org.RDKit.MolSanitizeException
>> at org.RDKit.RDKFuncsJNI.RWMol_MolFromSmiles__SWIG_3(Native Method)
>> at org.RDKit.RWMol.MolFromSmiles(RWMol.java:422)
>>
>> Thanks in advance!
>> Matt
>>
>>
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