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

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