Module: Bond Calculation ()

Description:

The module calculates bonds in a given molecular structure by analyzing the distances between the individual atoms of the structure. A maximal distance value will be used to determine whether two atoms are connected or not.

This module is especially useful when being used with a molecule that is derived from a trajectory. Each newly displayed time step will cause the bonds to be recalculated. A similar module for bond calculation is available via the Molecule Editor. This editor module offers advanced functionality but cannot be used dynamically in the work flow of the Project View.

Connections:

Data [required]
Molecule for which a new molecule with a complete bond structure should be computed.

Ports:

Mode

Select bond calculation method. For more information on bond calculation methods please refer to Molecule Editor's documentation.

Maximal atom distance

Available only when 'Mode' is set to 'distance'. The value determines the maximal distance between two atoms (in Å) below which they are considered to be connected by a bond.

Action

Starts the computation of the new molecule. "Add" will compute new bonds according to the chosen parameters and add the newly computed bonds to the molecule, "Remove" will remove bonds that match the respective parameters. Some of these bonds might not be present in the molecule, but this is not a problem. "Replace" will first remove all bonds and then add those that match the given parameter configuration.