Hi KNIME team,
an earlier post (http://tech.knime.org/node/20568) says that the data when using the external tool node is exported in quotes (" ").
This unfortunately also applies to sd-files (with csv-files once can understand :-). For sd-file this is not the standard format as so I would simply not quote chemical structure data (same way as when using sd-writer).
However, as written in above earlier post one can overcome by removing the quotes in the external tool / script. This as such is no issue, but the file (Output Data file) which should be read back generates an error - both for quoted and also non-quoted sd-files. Even a copy-paste of the exported sd-file is not re-imported and results in:
ERROR External Tool Execute failed: New line in quoted string (or closing quote missing). In line 1.
So this node requires adaptations with regard to sd-files and thus I would recommend to export with no quotes in order to generate a standard sd-file which could also be used by other applications than scripts.
PS. Also when generating mol files I would not have them quoted. Always use the standard definition.
Thanks for considering and fixing.