Valence clean-up #7397
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Valence clean-up #7397
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…mbership Al(IIIb), Si(IVb), P(Vb), As(Vb), Sb(Vb), Bi(Vb) - address elements with d orbitals (P, As, Sb, Si) which can accommodate bonds supported by lone pairs from halogens and chalcogens with requiring adding extra valences to periodic table - add test to make sure that PX6-, AlX63-, AsX6-, SbX6-, BiF6- do not raise an AtomValenceException while PX6, AlX6, AsX6, SbX6, BiX6 and peracids of the same elements which cannot exist raise an AtomValenceException - correct SmilesTests.java and rdkit/Chem/UnitTestSmiles.py where CCC[Al+3] should rather read CCC[Al+2] - comment out incorrect entries in rdkit/Chem/test_data/NCI_aromat_regress.txt and rdkit/Chem/test_data/NCI_5K_TPSA.csv - add -1 valence to alkali elements which were missing it (Rb, Cs, Fr)
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This PR cleans up valences in
atomic_data.cpp. In addiition to a few missing-1valences for some alkali metals (Rb, Cs, Fr), which I believe should be added in analogy to Li, Na and K, there were a number of higher valences for Al (6), Si (6), P, As, Sb, Bi (7) which I believe are incorrect. Al has only valence 3 (not 6), Si has only valence 4 (not 6), P, As, Sb, Bi can have 3 and 5 (not 7).The incorrect valences lead to non-existing compounds such as AlX6, PF6, AsF6, SbF6, BiF6 to be accepted.
The fact that these elements may form negatively charged complexes which higher valence thanks to their d orbitals can be more appropriately accounted for by modifying the code in
Atom.cpp. With these modifications, all existing unit tests pass, while preventing species such as AlX6, PF6, AsF6, SbF6, BiF6 to be accepted.Two Java tests which were failing with the new code in this PR upon inspection turned out to refer to species which are actually incorrect and should be rejected. I have therefore amended such tests.
Incorrect species were:
while it should have rather been Al2(C2O42-)3
while it should have been
while it should have been