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
<mailto: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
<mailto: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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