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Gerardo Tauriello authoredGerardo Tauriello authored
The Molecular Entity
This document describes the :class:`EntityHandle` and the related classes.
The Handle Classes
The entity class represents a molecular structure. Such a structure is in general made up of one or more chains of residues, which in turn are formed by one or more atoms.
The interface of entities is tailored to biological macromolecules, but this does not prevent it to be used for molecules in general: An entity also represent a ligand or a collection of water molecules - hence the rather generic name.
A chain of one or more :class:`residues <ResidueHandle>`. Chains are always part of an entity.
The residue is either used to represent complete molecules or building blocks in a polymer, e.g. in a protein, DNA or RNA. A residue consists of one or more :class:`atoms <AtomHandle>`. Residues are always part of a :class:`ChainHandle`, even if they are ligands or water molecules where the concept of a chain does not apply.
Represents an atom in a molecular structure. Atoms are always part of a residue.
The View Classes
An entity view represents a structural subset of an :class:`EntityHandle`. For an introduction ,see :doc:`../../intro-01`.