Query bond funcs - #938
Merged
Merged
Conversation
johnmay
force-pushed
the
query-bond-funcs
branch
from
November 29, 2022 09:42
0bef349 to
d3ba05e
Compare
|
SonarCloud Quality Gate failed. |
egonw
approved these changes
Sep 8, 2023
egonw
left a comment
egonw
left a comment
Member
There was a problem hiding this comment.
I am happy with this patch. One thing I am wondering if it should not just fail when an IQueryAtomContainer is given.
| IAtomType type; | ||
| if (atom instanceof IPseudoAtom || atom.getAtomicNumber() == null) { | ||
| if (atomContainer instanceof IQueryAtomContainer || atom instanceof IQueryAtom) | ||
| logger.warn("A query molecule/atom was provided to the atom type matcher"); |
Member
Author
|
Possible but I didn't want to make that decision. I figurered warning that "things might not work as you expect" was a reasonable middle ground. |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
At some point these went out of sync with the main AtomContainer, the order.numeric() should be compared and not the ordinal() since "unset" has the largest enum in the ordinal. We also make this function null safe since it's highly likely Query molecules have unset bond order.
Fixes #920.
I then was pondering an exception for providing a query molecule to the atom type matcher, but since we have the fall-back "X" atom type I think logging a warning makes most sense. If a caller wants to avoid the warning they should check if the molecule is a query before hand.