Commit Graph

4 Commits

Author SHA1 Message Date
tadhurst-cdd
f00a8cbb4c ScsrHbondMrvError (#8646)
* fix MRV for Hbonds

* add test file

* add test file

* enforce chirality in DistGeom catch test

* Added test for correct hbond retention

* removed debug print statement

* retrigger checks

* testing  java AromaticTests

* testing java aromaticTests

* removed testing code
2025-09-29 17:30:50 +02:00
Greg Landrum
724716b2c6 Switch to isoelectronic valence model (#7491)
* 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>
2024-06-25 15:38:49 +02:00
Greg Landrum
86b9e6b089 Fixes #72 2013-08-25 06:36:10 +02:00
Greg Landrum
c7ef21088b add initial version of new swig wrappers 2011-04-07 05:22:00 +00:00