entity.rst

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`.

A view representation of an :class:`AtomHandle`. Mostly, the same functionality is provided as for the handle.

Functions

Boolean Operators

Other Entity-Related Functions

Residue Numbering

Number for a residue. The residue number has a numeric part and an (optional) insertion-code. You can work with this object as if it was an integer and comparison will look first at the numeric part and then the insertion-code. All access to existing objects is read-only.

param num:	Numeric part of residue number.
type num:	:class:`int`
param ins_code:	Alpha-numeric part of residue number (optional insertion code). Only first character kept.
type ins_code:	:class:`str`

ChainType

A ChainType fills the :attr:`ChainHandle.type` attribute. Different types are described in the :ref:`ChainType enum <chaintype_enum>`. Functions for setting a type belong to the :class:`EditorBase` class, getting is provided by the :class:`ChainHandle` class, further convenience functions are described here.

The ChainType enum

The ChainType enum enumerates all types defined by the PDB for the MMCif file format. Following values are supported:

CHAINTYPE_POLY, CHAINTYPE_NON_POLY, CHAINTYPE_WATER, CHAINTYPE_POLY_PEPTIDE_D, CHAINTYPE_POLY_PEPTIDE_L, CHAINTYPE_POLY_DN, CHAINTYPE_POLY_RN, CHAINTYPE_POLY_SAC_D, CHAINTYPE_POLY_SAC_L, CHAINTYPE_POLY_DN_RN, CHAINTYPE_UNKNOWN, CHAINTYPE_N_CHAINTYPES

Where CHAINTYPE_N_CHAINTYPES holds the number of different types available.

Setter & Getter functions

:func:`EditorBase.SetChainType`, :func:`ChainHandle.GetType`

ChainType functions

ViewAddFlags

Those are the flags controlling behaviour of routines adding handles to views.

• INCLUDE_ATOMS - Include all atoms when adding a residue handle to a view
• INCLUDE_RESIDUES - Include all residues when adding a chain to a view
• INCLUDE_CHAINS - Include all chains when creating a new entity view
• INCLUDE_ALL = INCLUDE_ATOMS | INCLUDE_RESIDUES | INCLUDE_CHAINS - Convenience flags to include all substructures
• CHECK_DUPLICATES - If set, it will be checked that no duplicates are created when adding a new handle