Hi Jan,
The exception should be a org.RDKit.MolSanitizeException, but the following
code fails too:
String smi = "";
try {
smi = rdmol.MolToSmiles();
} catch (Exception e) {
System.err.println("Bad Mol Found: ");
}
Shouldn't this catch everything? Because that isn't working either. That's
why I am confused as to what to do (in fact that type of catch works fine
with other APIs [eg. ChemAxon]).
Matt
On Mon, Jun 2, 2014 at 11:12 AM, Jan Holst Jensen <j...@biochemfusion.com>
wrote:
> Hi Matt,
>
> You are catching exceptions for Mol*To*Smiles(), but the exception that
> is giving you trouble is caused by Mol*From*Smiles():
>
>
> > at org.RDKit.RDKFuncsJNI.RWMol_Mol*From*Smiles__SWIG_3(Native Method)
> > at org.RDKit.RWMol.Mol*From*Smiles(RWMol.java:422)
>
> So my guess is that 'smi' is used in downstream code with an invalid value
> that causes the error ? And it might be fixed by
>
>
> try {
> smi = rdmol.MolToSmiles();
> } catch (org.RDKit.MolSanitizeException e) {
> *smi = "CC"; // Some valid dummy value in case of read errors.*
>
> System.err.println("Bad Mol Found: " + smi);
> }
>
> ?
>
> Does the catch-clause work ? Does it output an error to stderr ?
>
> Cheers
> -- Jan
>
>
> On 2014-06-02 19:46, Matthew Lardy wrote:
>
> 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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>
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