Greg Landrum d2d87909de Add support for abbreviations (#3406) ...

* 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

2020-09-28 17:09:46 -04:00

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