Programatic access to the CLI methods

residue_neighborhoods(residues, trajectories)

Per-residue neighborhoods based on contact frequencies between pairs of residues.

interface(trajectories[, topology, …])

Contact-frequencies between two groups of residues

sites(site_inputs, trajectories[, topology, …])

Compute distances between groups of contact-pairs that are already pre-defined as sites

compare(datasets[, graphic_ext, …])

Compare contact frequencies across different sets of data

residue_selection(expression, top[, …])

Find residues in an input topology using Unix filename pattern matching like in an ‘ls’ Unix operation.

pdb(code[, filename, verbose, url])

Return a Trajectory from a four-letter PDB code via RSCB PBB lookup

fragment_overview(topology[, methods, AAs])

Prints the fragments obtained by get_fragments for the available methods.