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Analysis of molecular dynamics trajectories (RMSD, RMSF, contacts, hotspot analysis)
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Basado en la clasificación ocupacional SOC
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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