Elements#

In MolSysMT, a molecular system is organized into a clean, orthogonal hierarchy of structural elements. These elements define different levels of resolution, semantic grouping, and covalent connectivity within a molecular model.

Hierarchy of Structural Elements#

The primary structural and semantic hierarchy flows from individual atoms up to the entire system:

atom ──────> group ──────> molecule ──────> entity ──────> system
 │
 ├────────> component
 │
 └────────> chain

  • Primary Hierarchy: Every atom belongs to a group, every group belongs to a molecule, every molecule belongs to an entity, and all entities belong to the system.

  • Orthogonal Associations: component (covalent connectivity) and chain (structural assignment) are atom-aligned properties rather than strict parent containers of groups or molecules.

Atom#

Atoms are the indivisible structural units of a classical molecular model. Attributes associated with atoms include atomic coordinates, element names, atomic numbers, partial charges, and formal masses.

Group#

Groups are chemical building blocks composed of one or more atoms. Typical examples of groups include amino acid residues (such as ALA, TRP), nucleic acid residues (such as A, G), solvent molecules (such as HOH), mono-atomic ions (such as NA, CL), or small-molecule ligand residues.

Component#

Components are covalently connected atom subgraphs (the connected components of a molecular graph). A single polymer chain, an isolated small molecule, or a water molecule is a component. If two molecules form a covalent bond (such as a covalent drug-receptor adduct), they become a single component while remaining two distinct molecules.

Molecule#

Molecules are distinct physical or functional molecular units. A molecule can be composed of a single polypeptide chain, a protein quaternary assembly, a double-stranded DNA fragment, a ligand, or a water molecule.

Chain#

Chains are operational structural groupings historically assigned in structural databases such as the Protein Data Bank (e.g., Chain A, Chain B).

Entity#

Entities represent unique chemical species or natures within the system. For example, all water molecules in a simulation box belong to a single "Water" entity, while all copies of a specific protein belong to a single protein entity.

System#

The root container that encompasses all entities, molecules, components, chains, groups, and atoms.