Module: Compute H Bonds ()

Description:

This module creates a molecule with a new level (the hydrogen bond level 'hBonds') containing possibly found hydrogen bonds. Chemical criteria are used to identify potential donors and acceptors. All non carbon heavy atoms with at least one hydrogen (explicit or implicit) are used as donors and all atoms with at least one lone electron pair are used as acceptors. Several geometric criteria are then checked including distance and angle between donor and acceptor atoms. The hydrogen bond calculation represents the base for further computations, such as the secondary structure detection.

Press the Apply button to start the calculation of hydrogen bonds.

Connections:

Molecule [required]
A molecule for which the hydrogen bond level should be generated.

Ports:

Minimum Angle

This angle determines the minimum angle a hydrogen bond must have. The angle of each bond is defined as the angle between the three atoms involved in the bond (donor - acceptor - heavy atom bonded to the acceptor).

Maximum Distance

This value determines the maximum distance between the donor and the acceptor atom.

Restrictions

Specifies optional restrictions for the hydrogen bond calculation. Removing atoms from HET residues and/or water molecules may produce a cleaner result. You can also restrict the computation to the enriched backbone to obtain hydrogen bonds between the backbone carbonyl and amine groups only.