Query bond funcs #938
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Query bond funcs #938
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SonarCloud Quality Gate failed. |
egonw
approved these changes
Sep 8, 2023
| @@ -125,9 +130,10 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) | |||
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| private IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom, RingSearch searcher, List<IBond> connectedBonds) throws CDKException { | |||
| 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.