Closed Aariq closed 4 months ago
These messages seem to come primarily from ChemmineR::propOB()
Conversation on how to capture OpenBabel errors: https://github.com/girke-lab/ChemmineR/issues/14
A good example of where this gives misleading results is with phosphatidylcholine. The structure on KEGG has "R" groups for the fatty acid chain that OpenBabel can't parse. So it gets read in as only having 10 carbons and the volatility is way overestimated putting it in the "high" category. This really should result in NA
s across the board for functional groups and calculations.
Warnings and errors from OpenBabel are unfortunately difficult to capture, but it would be nice if there was some indication of parsing problems in the output of
calc_vol()
. Either that or just turning the OpenBabel errors into R errors and OpenBabel warnings into R warnings.An example: