mdanalysis — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited mdanalysis (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
MDAnalysis 2.10.0 (2025). Core pattern: Universe (topology + trajectory) → AtomGroup (selection) → AnalysisBase.run() → .results.
import MDAnalysis as mda
from MDAnalysis.analysis import rms, align
# Load topology + trajectory
u = mda.Universe('protein.prmtop', 'traj.dcd')
print(u) # <Universe with 45000 atoms>
print(len(u.trajectory)) # number of frames
# Select atoms
protein = u.select_atoms('protein')
ca = u.select_atoms('protein and name CA')
ligand = u.select_atoms('resname LIG')
# Iterate trajectory
for ts in u.trajectory:
print(ts.frame, ts.time, ca.positions.mean(axis=0))| Task | Reference |
|---|---|
| Universe, topology formats, selections, trajectory I/O, writing | references/universe-selections.md |
| RMSD, RMSF, alignment, radius of gyration | references/rmsd-rmsf-alignment.md |
| Hydrogen bonds, native contacts, binding residues | references/contacts-hbonds.md |
| Dihedrals, DSSP, PCA, RDF, density, MSD | references/structure-dynamics.md |
| Protein-ligand interaction analysis workflow | references/protein-ligand.md |
| Module | Import | Role |
|---|---|---|
rms | from MDAnalysis.analysis import rms | RMSD, RMSF |
align | from MDAnalysis.analysis import align | Structural alignment |
contacts | from MDAnalysis.analysis import contacts | Native contacts |
hydrogenbonds | from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis | H-bonds |
dihedrals | from MDAnalysis.analysis.dihedrals import Ramachandran, Janin | Dihedral angles |
dssp | from MDAnalysis.analysis.dssp import DSSP | Secondary structure |
pca | from MDAnalysis.analysis.pca import PCA | Conformational PCA |
rdf | from MDAnalysis.analysis.rdf import InterRDF | Radial distribution |
density | from MDAnalysis.analysis.density import DensityAnalysis | Density maps |
msd | from MDAnalysis.analysis.msd import EinsteinMSD | Diffusion |
distances | from MDAnalysis.analysis.distances import dist, between | Distances |
Topology: PSF, PRMTOP (Amber), GRO (GROMACS), PDB, MOL2, TPR, CRD, XML
Trajectory: DCD, XTC, TRR, NC (Amber), LAMMPSDUMP, H5MD, TNG, XYZ, PDBpip install MDAnalysis MDAnalysisData
conda install -c conda-forge mdanalysis
# Verify
python -c "import MDAnalysis; print(MDAnalysis.__version__)"analysis = SomeAnalysis(atomgroup, **params)
analysis.run(start=0, stop=None, step=1, verbose=True)
results = analysis.results # dict-like Results objectase — ASE MD trajectories, structure building (complementary)scientific-skills:matplotlib — plotting RMSD, RMSF curvesscientific-skills:seaborn — heatmaps for contact mapsscientific-skills:plotly — interactive conformational space plotsscientific-skills:biopython — PDB fetching and sequence tools~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.