mdtraj-trajectory-analysis SKILL.md skillA
mdtraj-trajectory-analysis from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/mdtraj-trajectory-analysis@git:20260528.63fd25cPins git:20260528.63fd25c in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/mdtraj-trajectory-analysis/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260528.63fd25c, committed May 28, 2026
- First version recorded
- May 28, 2026
- Size
- 26,184 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# mdtraj Trajectory Analysis ## Overview mdtraj is a fast, dependency-light Python library for reading, writing, and analyzing molecular dynamics (MD) trajectories. It handles every common MD format (DCD, XTC, TRR, NetCDF, H5, AMBER, GROMACS, CHARMM, OpenMM) into a single `Trajectory` object backed by NumPy arrays, then exposes geometry, RMSD/Rg/RMSF/SASA, contacts, hydrogen bonds, torsions, and 8-state DSSP secondary structure as pure-Python functions. This skill covers the analysis-side workflows: structural stability metrics, contact frequency maps, Ramachandran plots (general + Gly/Pro), and DSSP time series across multi-replicate ensembles. > **Unit note**: mdtraj works in **nanometers** and **picoseconds** internally. Multiply distances by 10 for Ångström output. Torsions are in **radians** — convert with `np.degrees()`. ## When to Use - Computing RMSD vs time, radius of gyration, and per-residue RMSF to assess structural stability across MD replicates - Building residue-residue contact frequency maps from a trajectory ensemble - Extracting backbone phi/psi torsions to plot Ramachandran diagrams (general, glycine-specific, proline-specific) …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/mdtraj-trajectory-analysis@sha256:fa80011d435fdfabThe line at the top of this page pins the label git:20260528.63fd25c, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_atic2vgzloske3hx)
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Versions
The registry has recorded 3 versions of this file, all committed on May 28, 2026.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260528.63fd25c latest | 2026-05-28 | 63fd25c | 26,184 B | A | view · diff |
| git:20260528.6b09274 | 2026-05-28 | 6b09274 | 20,046 B | A | view · diff |
| git:20260528.d3d04b2 | 2026-05-28 | d3d04b2 | 27,422 B | A | view |
Audit of the latest version
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- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (26184 bytes)
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- pass: No link to an exfiltration or paste host
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- pass: No instruction to send local credentials anywhere
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Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_atic2vgzloske3hx GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/mdtraj-trajectory-analysis GET https://markdownregistry.com/api/v1/blob/fa80011d435fdfabf2ff3f0ab8830686f8672bed2ab789ae3ba209b98a4e3a3c
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