* add a test
* change stereo bond canonicalization
* update canonicalization watch test with fixed cases
* make canonicalization test stricter (compare CIP codes)
* add reverse symmetry condition
* rewrite double bond canonicalization code
* update tests
* fix multiline comment
* update java tests
* update python test
* nix switchBondDir (unused)
* fix and rename flipBondDir
* refactor comment
* fix shadowed var name, casting
* fix neighbor sorting
* make seen_bonds a vector
* abstract setDirectionFromNeighboringBond
* handle both sides of the bond have directions
* move getNeighboringStereoBond
* check seen_bonds after popping connectedBondsQ
* use references for arguments
* add release note
* add example required by Dan
* add example requested by Dan
* change valence model to use isolobal analogy
Remove support for five-coordinate C+ and, by analogy, five-coordinate N+2
Removes support for charge states that take atoms past the end of the periodic table
i.e. [Lv-4] is no longer supported
* update the tests for that
* remove valence state of 6 for Al
* fix representation of phosphate in the mol2 parser
this is a correction of what was done during #5973
* cleanup the exceptions for P, S, As, and Se
* drop valence states:
Si 6, P 7, As 7
* a couple of additional changes from #7397
* update java tests
* fix an inconsistency: Rb now supports valence -1
* documentation
* - replace operator[] with at() for bounds check
- extract some code into a function to avoid duplication
- use TAB as separator throughout in the periodic table data for consistency
* removing the .at() usage
We know that these vectors aren't empty, so there's no need for the bounds check.
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Co-authored-by: ptosco <paolo.tosco@novartis.com>
