Molecular system

In MolSysSuite, a molecular system has:

• a topology (atoms, bonds, residues, chains, etc.), and

• one or more structures (spatial information: coordinates, optional periodic box, optional time).

This matters because MolSysViewer is driven by MolSysMT concepts such as selection and structure_indices.

Terminology

Molecular system

Topology + structures.

Structure

One set of coordinates (and optional box/time). In other libraries this is often called a “frame”. In MolSysSuite, a structure can also represent a model (not necessarily time-ordered).

Structure indices

Which structures you are working with (for example, to pick a subset from a trajectory-like dataset).

Selection

A MolSysMT selection expression used to pick atoms/residues from the molecular system.