Feature Computation

mdxplain provides six feature types for molecular dynamics analysis:

• Distances

• Contacts

• Torsions

• DSSP secondary structure

• Solvent accessible surface area (SASA)

• Atomic coordinates

It is recommended to save computed features to disk for large datasets to avoid recomputation. (Saving and Loading)

# Residue-residue distances (closest heavy-atom pairs)
pipeline.feature.add.distances(excluded_neighbors=1)

# Binary contacts (interaction indicator)
pipeline.feature.add.contacts(cutoff=4.5)

# Backbone and side-chain torsion angles
pipeline.feature.add.torsions()  # phi, psi, omega, chi1-4

# Secondary structure assignment
pipeline.feature.add.dssp()

# Solvent accessible surface area
pipeline.feature.add.sasa()

# Atomic coordinates (xyz positions)
pipeline.feature.add.coordinates()