WIP: detect and handle errors from OpenBabel via propOB #96
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Closed
|
Decided it is likely better to check for the symptoms of invalid SDFs rather than to try to capture the errors. See discussion in #85. Will leave this open until we are sure that this alternative approach is better, then will close this PR. |
|
Closing this as it was superseded (mostly) by #104 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Attempt at solving #56 by using
callrto runpropOBin an isolated R session where I can capture stderr. The downside is that it appears to be quite a bit slower, but it does appear to work. Still much to do:get_fx_groups()ob_err_passfromget_fx_groups()(actually, maybe this argument shouldn't be part of safe_propOB() but rather higher up and have the effect of choosing betweenChemmineR::propOB()andsafe_propOB(). That way can use faster option when there aren't errors.)