allowOptionalAttachments should also include terminal query atoms matching hydrogen#6280
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…en in additional to terminal dummy atoms - added relevant unit tests
greglandrum
approved these changes
Apr 12, 2023
| return atom->getDegree() == 1 && | ||
| (atom->getAtomicNum() == 0 || | ||
| (atom->hasQuery() && | ||
| describeQuery(atom).find("AtomAtomicNum 1 = val") != |
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using describeQuery() here is a nice solution to something that's otherwise a pain in the ass to deal with
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At first it seemed too easy, but I tried a few different ways to break it and couldn't ;-)
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Currently the
allowOptionalAttachmentsparameter ingenerateDepictionMatching2DStructure()and theallowRGroupsparameter ingenerate_aligned_coords()only cover terminal dummy atoms, which are allowed not to match (or to match hydrogen). However, this should also include terminal query atoms when the query includes hydrogen.This PR extends
allowOptionalAttachments/allowRGroupsaccordingly, such that now a scaffold such asmatches a molecule such as