Residue type

type Residue

A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.

function Residue(name::String, id = nothing)

Create a new residue with the given name and optional residue identifier id.

function Residue(topology::Topology, index::Integer)

Get a copy of the residue at index from a topology.

The residue index in the topology is not always the same as the residue identifier.

function residue_for_atom(topology::Topology, index::Integer)

Get a copy of the residue containing the atom at index in the topology.

This function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.

function deepcopy(residue::Residue)

Make a deep copy of a residue.

function name(residue::Residue)

Get the name of a residue.

function id(residue::Residue)

Get the identifier of a residue in the initial topology.

function size(residue::Residue)

Get the number of atoms in a residue.

function add_atom!(residue::Residue, index::Integer)

Add the atom at the given index in the residue.

function contains(residue::Residue, index::Integer)

Check if the atom at the given index is in the residue.

function deepcopy(residue::Residue)

Make a deep copy of a residue.

function property(residue::Residue, name::String)

Get a named property for the given residue.

function set_property!(residue::Residue, name::String, value)

Set a named property for the given residue.

function properties_count(residue::Residue)

Get the number of properties associated with a residue.

function list_properties(residue::Residue)

Get the names of all properties associated with a residue.