No, "cutting out a chunk of lines from a file" might be simple, but can become an expensive operation if you want to deal with thousands of files and million of records. That is one of the reasons why I (unfortunately) couldn't consider rdkit any further for one of my projects a few years ago. So, I support Michael's idea :-)
On Sat, May 2, 2015 at 12:17 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > On 04/30/2015 05:01 PM, Michael Reutlinger wrote: > >> However, in some cases this does not help. E.g. when an unknown atom (most >> of the time this is X) is found in the MolBlock the import fails with an >> Post-condition Violation and None is yielded. This is fine to detect the >> problem BUT it is impossible to get any information about the molecule >> which failed. > > I'd say the best you can do skip over to the next molecule and report > "molecule in lines X to Y is corrupt". Cutting out a chunk of lines from > a file is trivial, and if you're reading from a stream rather than a > file then, well, don't. Without a valid mol block you don't have a > molecule and you shouldn't be making one up. As in "conservative in what > you produce". > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > ------------------------------------------------------------------------------ > One dashboard for servers and applications across Physical-Virtual-Cloud > Widest out-of-the-box monitoring support with 50+ applications > Performance metrics, stats and reports that give you Actionable Insights > Deep dive visibility with transaction tracing using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
