* - Abbreviations::applyMatches() sets the _abbreviationMapping molecule property to relate the atom indices in the molecule with abbreviations to the atom indices in the original molecule
* added support for bond index mappings
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* backup
* simple first pass, passes all tests
* cleanup a bunch of existing uses
* ensure that we can safely add atoms/bonds while in edit mode
* add context manager on python side
* handle exceptions properly in those
* changes in response to review
* support read-only access to cstates from python
* expose GetBrackets
* expose getAttachPoints too
remove vestigial SubstanceGroupCState_VECT
* backup
* backup
* basics working
* backup
* add label_mol_abbreviations
* fix a bug in the chirality handling
* add linkers, needs more testing
* add another peptide test
* sanitize results by default
* just need rings
* getting started with the C++ form of abbreviations
* a bit of error handling
* add findApplicableMatches
* actually apply the abbreviations
* make the getDefault functions more efficient
* add labeling (creating s groups)
* docs
* basic python wrappers (maybe this is enough?)
* add _displayLabel and _displayLabelW support to MolDraw2D
update the docs for that
* use displayLabel props
* add more default abbrevs
* change default linker defns
add parseLinkers convenience function
* make sure attachment point atoms aren't aromatic
* change the color of dummies to be darker gray
* remove python implementation
* support abbreviations in the java wrappers
* add abbreviations to the csharp wrappers
* add abbreviations to the js wrappers
* add molParity to the list of atom props not written to CXSMILES
* support condensing SUP substance groups
* add that to the python wrappers
* Update testAbbreviations.py
* clear ring info if we added it
* document that the molecules with abbreviations removed have not been sanitized
