Selection Syntaxes

MolSysMT provides a native declarative selection engine and selected interoperability with third-party syntaxes. Support is directional: parsing a query and translating a set of indices are separate capabilities.

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Supported syntaxes and shortcuts

Syntax	Selection input	Translation output	Scope
MolSysMT (native)	Yes	No	Any supported molecular-system form
MDTraj	Yes	Yes	Inputs convertible to mdtraj.Topology
MDAnalysis	Yes	No	Inputs convertible to MDAnalysis.Universe
NGLView	No	Yes	Atom, group, and chain translations

The input direction is selected with syntax=...; the output direction is requested with to_syntax=.... A syntax listed in one direction is not implicitly supported in the other. Use msm.supported.syntaxes() to inspect this matrix in the running version.

The native syntax includes attributes such as atom_name, atom_type, group_name, group_id, chain_id, and molecule_type, together with and, or, and not. Shortcuts such as "protein", "water", "ions", and "backbone" are configured through msm.configure.selection_shortcuts.