vmd.topology.addbond

vmd.topology.addbond()

Add a bond between two atoms with given indices. If bond is already present, nothing will be done.

Parameters:

• i (int) – Index of first atom
• j (int) – Index of second atom
• molid (int) – Molecule ID to add bond to. Defaults to top molecule.
• order (float) – Bond order. Defaults to 1.0
• type (str) – Bond type. Can be from output of topology.bondtypes(), or can define a new bond type. Defaults to None