Description:

Expand the default DREIDING ruleset to cover common monatomic ions encountered in biomolecular and crystallographic systems. Keep behavior for existing ions unchanged, and add clear documentation in the rule system reference.

Tasks:

• Ruleset Additions

  • In resources/default.rules.toml, append low-priority ion rules for common monatomic ions (no oxidation-state variants), e.g., Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba, Ag, Au, Cu, Zn, Cd, Ni, Co, Pd, Pt.
  • Keep priorities aligned with existing metal/ion section; preserve deterministic ordering.

• Documentation

  • Update docs/05_rule_system.md with a concise table listing the new ion types, their element condition, and priority.