namespace bond

Overview

Functions for bond-related analyses. More…

Detailed Documentation

Functions for bond-related analyses.

This namespace contains functions that are used for determining the hydrogen bonds, or lists of bonded atoms for write-outs to data files and visualization.

These functions are distinct from the neighbour-list building functions. Bonds can be built from cages, ring lists etc.

Hydrogen bonds are determined using a strict geometric criterion.

A hydrogen bond between two water molecules exists when:

  1. The distance between the donor oxygen atom and the acceptor hydrogen atom is less than 2.42 Angstrom

  2. The angle between the O O vector and the O-H vector should be less than 30 degrees

Changelog