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SonarCloud Quality Gate failed. |
egonw
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Sep 8, 2023
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egonw
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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"); |
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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. |
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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.