mdciao.contacts

Computation, bookkeeping, and manipulation of residue-residue contacts.

The methods wrap around a modified version of mdtraj.compute_contacts to extract residue-residue distances. The modifications consist in including the indices of the closest atom-pairs in the returned values.

The classes contain and abstract these distances into sense-making groups, offering methods to operate directly on all residue-residue distances.

It is recommended to use higher-level methods of the API, like those exposed by mdciao.cli to create ContactPair or ContactGroup objects and then use the methods stated above, but of course experienced users can instantiate them directly.

Classes

`Residues`	Container for `mdtraj.Topology.Residues` objects
`ContactPair`	Container for a contacts between two residues
`ContactGroup`	Container for `ContactPair`-objects
`GroupOfInterfaces`	Container for `ContactGroup` objects

Functions

`per_traj_ctc`	Wrapper for `mdtraj.compute_contacts` for strided, chunked computation of contacts.
`trajs2ctcs`	Time-traces of residue-residue distances from a list of trajectories
`select_and_report_residue_neighborhood_idxs`	Group residue pairs into neighborhoods using pre-computed contact frequencies
`per_traj_mindist_lower_bound`	Strided, chunked computation of lower bounds for all-atom residue-residue distances.
`trajs2lower_bounds`	Return a lower bound for all-atom residue-residue distances for each pair in ctc_residxs_pairs, for all trajectories in trajs.