The Molecular System

Welcome to The Molecular System, the conceptual heart of MolSysMT. This section defines the constitutional architecture of molecular models: how systems are formally defined, how physical items differ from data representation forms, and how orthogonal elements and attributes are structured.

Understanding these foundational concepts ensures seamless interoperability when handling structures across different file formats, computational engines, and external libraries.

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Contents

• The Molecular System
  Core definition of a molecular system and the form-agnostic architecture of MolSysMT.

• Items and Forms
  Understanding physical molecular items and the catalog of supported data representation forms.

• Elements
  The orthogonal structural hierarchy: atoms, groups, components, chains, molecules, entities, and bioassemblies.

• Attributes
  Detailed guide to structural, topological, mechanical, and physicochemical molecular attributes.