Interactions

molsysmt.Interactions stores observations from one analysis method over a molecular system. It supports hydrogen-bond triples, disulfide candidate pairs, ring groups, and relations with more participants. The class is experimental. Detectors retain their established outputs by default; both hydrogen-bond and the disulfide candidate detectors can also return an Interactions analysis explicitly.

The new experimental ionic detector returns sparse analyses by default, using selected-state formal-charge centers and an explicit minimum-distance cutoff. The experimental pi-pi detector uses declared aromatic rings, fitted planes, and explicit distance, angle, offset and planarity cutoffs for its custom proposal. Attributed ProLIF and Mol*/MDTraj geometric profiles are available separately. The new hydrogen-bond entry point offers named per-structure scientific criteria; its default sparse output is independent of the established Buch/Luzard–Chandler defaults.

• get_metal_coordination — observing directed metal-ligand proximity candidates.

• get_water_bridges — joining two simultaneous hydrogen bonds through indexed water.

• get_hydrophobic_interactions — calculating typed hydrophobic atom proximity.

• get_halogen_bonds — calculating four-role halogen geometry.

• Get attributed hydrogen bonds — calculating attributed hydrogen-bond observations.

• Querying interaction results — building, querying, and saving sparse interaction results.

• get_ionic_interactions — calculating scoped formal-charge contacts.

• Get pi-pi interactions — calculating parallel and edge-to-face ring geometry.

• Get cation-pi interactions — reproducing ProLIF cation–π observations and examining a separate proposal.