MolSys

molsysmt.MolSys is the primary native unified molecular system container in MolSysMT. It composes the topological graph, 3D structures sequence or ensemble, and molecular mechanics parameter contracts into a single immutable state object.

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Overview and Role

As a user, molsysmt.MolSys is the central object returned when loading, converting, or processing molecular systems. By composing dedicated sub-containers, MolSys ensures strict separation of concerns while providing a unified gateway for selections, spatial queries, and form transformations.

molsysmt.MolSys instances are treated as immutable state objects. Modifying system composition or atom inventories is handled via molsysmt.MolSysBuilder before compiling back to a fresh MolSys.

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Internal Attributes

Inside a molsysmt.MolSys instance, three primary core component objects are composed:

Attribute	Internal Object Class	Description
topology	molsysmt.Topology	Topological graph containing atom, residue, group, component, molecule, and chain inventories.
structures	molsysmt.Structures	Structural container holding 3D coordinates (n_structures, n_atoms, 3), periodic box matrices (n_structures, 3, 3), and frame timestamps.
molecular_mechanics	molsysmt.MolecularMechanics	Forcefield parameters, partial charges, atom masses, and non-bonded interaction rules.

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Invariants and Performance

• String Identifier Invariant: All element IDs (atom_id, group_id, chain_id) inside topology are normalized to string representations.

• Fast Digestion Bypass: Compatible with skip_digestion=True for high-frequency internal algorithm passes.

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API Documentation

Detailed methods, converters, and getters for molsysmt.MolSys are documented in the [molsysmt.MolSys API Reference].