Module: refdist

Description	Usage
tools for calculating the distance between trajectory frames
Authors: Gareth Tribello

Details

This module contains methods for calculating the distance between two configurations as well as the distances between multiple configurations. The functionality within this module is used in both the mapping and dimred modules.

Actions

The following actions are part of this module

Tags

MCOLVAR FUNCTION

MCOLVAR: actions for calculating a vector of colvars FUNCTION: actions that take in one or multiple arguments and that return one or multiple arguments

Name	Description	Tags
DIFFERENCE	Calculate the differences between two scalars or vectors	FUNCTION
DISPLACEMENT	Calculate the displacement vector between the pair of input vectors	MCOLVAR
EUCLIDEAN_DISTANCE	Calculate the euclidean distance between two vectors of arguments	MCOLVAR
KERNEL	Transform a set of input coordinates using a kernel function	FUNCTION
MAHALANOBIS_DISTANCE	Calculate the Mahalanobis distance between two points in CV space	FUNCTION
MATRIX_PRODUCT_DIAGONAL	Calculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector	FUNCTION
NORMALIZED_EUCLIDEAN_DISTANCE	Calculate the normalised euclidean distance between two points in CV space	FUNCTION