On Wed, Jun 1, 2011 at 2:45 PM, Andrew Dalke <da...@dalkescientific.com> wrote:
> I'm really not a Java programmer. Should that be:
>
> IteratingMDLReader mdliter = new IteratingMDLReader(sdfile,
> DefaultChemObjectBuilder.getInstance();
>
> while (mdliter.hasNext()) {
> ...
> }
Yes, this is correct
> Also, what does CDK do if there's an error in one of the records? For
> example, some of the other toolkits' readers skip bad records and report to
> stderr. If CDK ignores bad records, is there a way to get the count of
> records skipped? If CDK raises an exception, is there a way to ignore the
> error and keep on processing?
I think an exception will be thrown, which you could catch and decide
what to do - but I'm not sure
--
Rajarshi Guha
NIH Chemical Genomics Center
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