PickCylinder (Node)

Context	Generation
Name Required?	Yes
Branches	–

Overview

The Pick node picks (selects) all molecules of a given species type from the current configuration, for further processing by other nodes.

Description

Any molecule is picked if the distance between it’s centre of geometry and the closest point on the line defining the cylinder position is less than or equal to the radius of the cylinder.

The two points defining the line on which the cylinder exists are given by:

$l_0 = (o_x, o_y, o_z) $

$l_1 = (o_x + x, o_y + y, o_z + z) $

…where $(o_x, o_y, o_z)$ are the coordinates of the origin in real-space, determined from the fractional cell coordinates $(f_x, f_y, f_z)$ provided with the OriginFrac keyword.

The shortest distance $d$ from the point $p$ (the molecule center of geometry) to the line is then:

$d = \frac{\lvert(p - l_0) \times (p - l_1)\rvert}{\lvert l_1 - l_0 \rvert} $

For the full derivation of this equation see https://mathworld.wolfram.com/Point-LineDistance3-Dimensional.html.

Configuration

Control

Keyword	Arguments	Default	Description
OriginFrac	fx fy fz	0.0 0.0 0.0	Fractional cell coordinates representing one point on the line describing the cylinder.
Radius	double	5.0	Radius, in Angstroms, of the cylinder.
Source	name	–	The name of an existing picking node from which to pick molecules for the current selection. If not specified, any molecule in the current configuration may be picked.
Vector	x y z	0.0 0.0 1.0	Defines the direction of orientation of the cylinder from the origin point.