new commands: isolde validate

[arohou]

isolde validate: a read-only validation command suite (agent-friendly)

What this PR delivers

Four new ChimeraX commands that expose the same scoring as the subpanels of
ISOLDE's GUI Validate tab as structured, programmatically-consumable
tool calls:

• isolde validate peptidebonds [model]
• isolde validate rama [model] [include outliers|allowed|all]
• isolde validate rotamers [model] [include outliers|nonfavored|all]
• isolde validate clashes [model]

Plus no-op isolde validate and isolde preflight parent commands that
return a useful "expected one of: ..." error instead of ChimeraX's generic
Unknown command: isolde validate #1.2.

The primary intended consumer is an LLM agent driving ChimeraX through the
MCP server, but the commands are equally useful from scripts:
they're read-only, never start a simulation, and return a Python dict of
summary counts plus an itemised list.

Design decisions

Shared output keywords across all four subcommands, matching the pattern
of ChimeraX's existing clashes / hbonds commands:

• log true — dump the full per-item table to the ChimeraX HTML log
  (capped at 500 rows so a 5000-clash structure doesn't trash the Reply Log).
• saveFile <path> — write the full unclipped table to disk.
  .json → structured JSON; anything else → plain UTF-8 text via
  chimerax.io.open_output.
• limit <n> — cap the inline items list so a giant structure doesn't blow
  up the caller's context window. The returned dict carries truncated,
  returned_count, total_count whenever clipping happens. clashes
  defaults to limit=200; the others have no default cap.

Summary lines tell the caller how to see the full list. Every summary
gets a one-line hint pointing at log true / saveFile <path> whenever
there's something to list. This was added after observing an agent see "499 unique clashes" with no clue how to drill
in.

Friendly parent commands. isolde validate <model> and
isolde preflight <model> (with no subcommand) now raise a UserError
listing the available subcommands instead of ChimeraX's generic
Unknown command. Implemented by registering the parents with a no-op
handler that always raises. Fixing this in ChimeraX's cli.py parser was
considered — it would benefit every hierarchical command in ChimeraX — but
rejected as out of scope here: cli.py is too central to change without
dedicated test coverage.

Overlap with existing rama and rota

There is a deliberate, contained overlap with the older rama and rota
commands. They are not removed and not deprecated:

• rama / rota (existing) add live 3D annotators to the model and,
  with report=True, dump non-favored residues as a free-text log message.
  They're an interactive convenience for human ISOLDE users — toggle the
  coloured 3D markup, with an optional text dump.
• isolde validate rama / rotamers (new) are pure read-only data
  accessors — no annotators, no model side effects, structured output,
  paginated, optionally saveable. Intended for agents and scripts.

The two are kept side by side because they serve genuinely different
consumers. The new commands' docstrings point users at the existing
rama / rota for the live-annotator use case.

Minimising the duplication

To avoid two divergent implementations of the same scoring, the actual
compute is factored into pure helpers that both surfaces consume:

Helper	Used by
_compute_rama_report(...)	isolde validate rama and rama report=true (refactored)
_compute_rotamer_report(...)	isolde validate rotamers and rota report=true (refactored)
classify_peptide_bonds(pdm, residues)	isolde validate peptidebonds, rama report=true cis/twisted dump, and the GUI PeptideBondDialog (refactored)
clash_atom_label(atom)	isolde validate clashes and the GUI ClashesDialog (refactored)

RamaMgr.cis() / twisted() were also tweaked to read their cutoffs from
defaults.CIS_PEPTIDE_BOND_CUTOFF / defaults.TWISTED_PEPTIDE_BOND_DELTA
rather than hardcoded radians(30) / radians(150), so the value lives in
one place.

Net effect: the new isolde validate commands, the GUI Validate panels,
and the legacy rama / rota report=true text dumps all classify
residues / bonds / clashes through the same code paths and give the same
answer.

Files touched

• isolde/src/validation/cmd.py — new validators, parent commands, shared
  compute helpers, file/log output helpers.
• isolde/src/validation/clashes.py — extracted clash_atom_label.
• isolde/src/molobject.py — RamaMgr.cis() / twisted() use
  defaults.* constants.
• isolde/src/cmd/cmd.py — register the new command group.
• isolde/src/ui/validation_tab/{clashes.py,peptide_bond.py} — GUI panels
  switched to the shared helpers.
• isolde/docs/source/commands/isolde.rst — full command reference for
  the new validators.

Out of scope

• Fixing ChimeraX's cli.py to emit Incomplete command: instead of
  Unknown command: for hierarchical commands missing a sub-action.
  Would benefit every ChimeraX bundle, but cli.py needs more deliberate
  testing than this PR can provide.
• Tightening the misleading Command 'isolde' is not recognized hint in
  the chimerax MCP bridge. The new parent commands neutralise it for
  isolde validate / isolde preflight, but the bridge heuristic itself
  could still be improved separately.