vmd.topology.bonds

vmd.topology.bonds()

Get all unique bonds within a specified molecule. Optionally, can get bond type and order by modifying the type parameter

Parameters:

• molid (int) – Molecule ID to query. Defaults to top molecule
• type (bool) – Whether to include bond type information in the result Defaults to False.
• orders (bool) – Whether to include bond order information in the result Defaults to False.

Returns:

(list of lists) Information about each bond in the system. Each bond

will be a list with the indices of the two atoms in the bond, followed by bond type (as a string) and order (as a float) if requested