md-analyze

MD Analyze

Read skills/common/preamble.md, skills/common/tool-output.md, skills/common/node-cli-patterns.md, and skills/common/run-loop.md before acting. Use mdclaw plan_next --job-dir <job_dir> to confirm the job is ready for analysis and to get the leaf prod parent.

Analysis is always user-initiated. Production does not chain into analysis; the user or harness invokes this skill when ready. In harnesses with slash commands, /md-analyze is the shortcut.

If the job belongs to a study with study_plan.json, use the plan's analysis list as the starting point for metric selection. Treat it as scientific intent, not as a brittle execution contract: missing or incomplete plan fields should not block normal analysis.

Route To The Right Guidance

• Combine a production lineage into an analysis trajectory: skills/md-analyze/concat.md
• RMSD, RMSF, contacts, distances, hydrogen bonds, or energy summaries: skills/md-analyze/metrics.md
• Errors, missing artifacts, bad selections, or empty DCDs: skills/md-analyze/troubleshooting.md
• Legacy notes for current analysis helpers: skills/md-analyze/analysis.md

Step 0 Summary

Confirm these fields before running analysis:

Parameter	Value
Target	job directory
Analysis data scope	segment, production_chain, or comparison
Analysis subjects	optional for segment/production_chain; required for comparison
Comparison mapping	required for different chains/topologies; initial types: residue_number, atom_selection
Validation	require analysis_data_scope; comparison is binary/pairwise with two unique subject labels
Leaf prod node	requested node or deepest continuation leaf
Atom selection	mdtraj selection, default "protein"
Stride	integer, default 1

For comparison analyses, create the node with explicit subjects and mapping: Use two completed production_chain analyze nodes as parents. Put analysis_subjects and comparison_mapping on the comparison node itself, not on the parent production_chain analyze nodes. The resolver still exposes multi-parent analyze inputs as branches_input for tool compatibility. For residue_number mappings, each reference uses subject_label:residue_id; the residue_id is a string, not a number. For atom_selection mappings, selection values are mdtraj selection strings.

mdclaw create_node --job-dir <job_dir> --node-type analyze \
  --parent-node-ids <analyze_apo> <analyze_holo> \
  --label "apo_vs_holo" \
  --conditions '{"analysis_data_scope": "comparison",
                 "analysis_subjects": [
                   {"label": "apo"},
                   {"label": "holo"}
                 ],
                 "comparison_mapping": {
                   "type": "residue_number",
                   "pairs": [["apo:10", "holo:10"]]
                 }}'

Create an analyze node first, then run analysis tools with both --job-dir and --node-id.

Structure Preview and Visual QA

The structure-preview and visual-review procedure is shared across all stages. Follow skills/common/visual-qa.md when the user wants a structural snapshot or a completed prod/analyze artifact would benefit from a quick obvious-accident check.