القائمة
Analysis of molecular dynamics trajectories (RMSD, RMSF, contacts, hotspot analysis)
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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| name | trajectory-analysis |
| description | Analysis of molecular dynamics trajectories (RMSD, RMSF, contacts, hotspot analysis) |
| metadata | {"openclaw":{"requires":{"env":["OPENAI_API_KEY"],"bins":["python3"],"pip":["MDAnalysis","numpy"]},"primaryEnv":"OPENAI_API_KEY"}} |
Analyze molecular dynamics trajectories to extract structural and dynamic properties. Supports both static (PDB-only) and dynamic (trajectory + topology) analysis modes.
The skill follows the two-axis config_master schema:
| data_type | analysis_type | What it computes |
|---|---|---|
| static | basic | Contact map from PDB distance matrix |
| static | advanced | (reserved for future analyses) |
| dynamic | basic | RMSD, RMSF, radius of gyration |
| dynamic | advanced | Residue contact frequency / hotspots |
| dynamic | both | All dynamic analyses combined |
# Static contact analysis
python skills/trajectory-analysis/scripts/run_analysis.py \
--data-type static --analysis-type basic \
--paths structure.pdb --distance-cutoff 4.5
# Dynamic RMSD/RMSF/RoG
python skills/trajectory-analysis/scripts/run_analysis.py \
--data-type dynamic --analysis-type basic \
--paths trajectory.dcd --topology system.pdb
# Dynamic hotspot analysis
python skills/trajectory-analysis/scripts/run_analysis.py \
--data-type dynamic --analysis-type advanced \
--paths trajectory.dcd --topology system.pdb \
--distance-cutoff 4.5 --n-top 10
# Full dynamic analysis with artifact DAG provenance
python skills/trajectory-analysis/scripts/run_analysis.py \
--data-type dynamic --analysis-type both \
--paths trajectory.dcd --topology system.pdb \
--artifact-dir ./artifacts -o results.json
--data-type: static (PDB only) or dynamic (trajectory + topology)--analysis-type: basic, advanced, or both--paths: Trajectory file(s) (DCD, XTC, TRR) or PDB file(s)--topology: Topology file (PDB or PSF) — required for trajectory formats--selection: MDAnalysis atom selection string (default: protein and name CA)--reference-frame: Reference frame for RMSD alignment (default: 0)--distance-cutoff: Distance cutoff in Angstroms for contact analysis (default: 4.5)--n-top: Number of top contact pairs to report (default: 10)--artifact-dir: Directory for Artifact DAG storage (enables provenance tracking)--parent-artifacts: Parent artifact IDs for DAG lineage--output / -o: Output JSON file (default: stdout)pip install MDAnalysis) — trajectory I/O, RMSD/RMSF, contact analysisWhen --artifact-dir is provided, the skill:
ProvenanceTrackerArtifact (type: ANALYSIS) with full results--parent-artifacts are specified_artifact_id and _run_id in the output JSON