Select (Node)

Select a list of pre-defined sites on molecules


Context	Analysis
Name Required?	Yes
Branches	`ForEach`

Overview

The Select node assembles a list of sites from a species, and which can then be iterated over and reference by other nodes (e.g. the Calculate* nodes).

Description

The Select node assembles a list of coordinates (and axes, if present) for one or more defined sites. The mechanism of selection can be controlled to provide exclusions with other sites (e.g. based on the parent molecule containing the site) or select only sites within a given distance of another reference point. Iteration over the sites is performed via the ForEach branch.

When nesting Select nodes in analysis routines, the selection of sites can be carefully controlled in order to avoid unwanted groups of selected nodes. For instance, the SameMoleculeAsSite keyword allows another Select node to be reference, and which will force the current Select node to only select a site if it is present in the same molecule as the other site.

Branching

The hidden ForEach keyword / branch is executed for each site selected by the node, and may contain any other analysis-style nodes, including other Select nodes.

Configuration

Control

Keyword	Arguments	Default	Description
`Site`	`name` `[name...]`	–	A list of `name`d sites to select.
`DynamicSite`	`name` `[name...]`	–	A list of `name`d `DynamicSite`s to select.
`SameMoleculeAsSite`	`name`	–	Request that selected sites come from the molecule containing the current site in the `name`d `Select` node.
`ExcludeSameMolecule`	`name` `[name...]`	–	Exclude sites from the selection if they are present in the same molecule as the current site in any of the `name`d `SelectNode`s.
`ExcludeSameSite`	`name` `[name...]`	–	Exclude sites from the selection if they are the current site in any of the `name`d `SelectNode`s.
`ReferenceSite`	`name`	–	Site from the `name`d `Select` node to be used as a reference point when determining inclusions / exclusions.
`InclusiveRange`	`min` `max`	–	Distance range from `ReferenceSite` within which sites are selected.

Last modified March 10, 2023: Web docs styling (#1350) (43924dc)