User 677b9c22ff
20-08-2013 02:30:26
Hi,
the Structure Checker v6 does not catch errors from certain broken SD files.
One solution could be to catch the errors that are thrown by MVIEW and use the error output as fix.
FILE: error-broken-SDF.sdf
Example: "Invalid counts line" output in mview (its not thrown all the time)
Mview 6 reports 4 molecules, but Structure Checker v6 thinks there is only one molecule in the file.
Other errors include, that should be fixed by Structure Checker:
Example: chemaxon.formats.MolFormatException: Invalid header block.
Basically any MolFormatException should be fixed.
The broken SD files are very common if assembled from multiple sources,
so I think that is an highly probable feature that should be included into the
standard settings. That extends not only to broken headers, but basically
all "crude errors" such as wrong element names, broken SD attachments etc.
Other example data can be downloaded here (public)
http://www.smpdb.ca/public/system/current/metabolites.sdf
Also if one activates all options in structure checker v6, using the configure checker,
the substructure checker still makes problems because its not marked as requesting input, even if set
ignore one can not proceed with "NEXT". Quite annoying if one has to go throuh all options manually.
One other solution I came up with when structure checker fails is to use Instant-Jchem,
because it would catch and ignore such crude errors, maybe similar functionalities could be
implemented into the Structure Checker, that would be quite helpful.
Cheers
Tobias