4 Commits

Author SHA1 Message Date
Ricardo Rodriguez
680520e0ad Follow up to PR #8968 (#9168)
* implement consistency check

* add more consistency checks

* check direction consistency accross double bond

* clean up directions for non-stereo bonds

* fix counts for second from atom dirs; add check

* handle inconconsistent bond dirs

* add more tests, pubchem cases, and update existing

* drop statics

* fix typo

* make sourceBond arg const

* fix consistency check
2026-03-20 04:28:17 +01:00
Ricardo Rodriguez
d5aa90e18f Fix for issue #8965 (#8968)
* 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
2026-02-26 08:58:36 +01:00
Ricardo Rodriguez
d4641c1f58 Fix removing (non)redundant bond dir specs when exporting SMILES (#9066)
* increase counts to avoid removing non-redundant bond dirs

* update tests
2026-01-24 07:15:00 +01:00
Ricardo Rodriguez
fa68ea2ef2 convert smiTest1 to catch (#9004) 2025-12-13 20:21:00 +01:00