opencadd.structure.core.Structure.add_bonds

Structure.add_bonds(values, types=None, guessed=False, order=None)

Add new Bonds to this Universe.

Parameters

  • values (iterable of tuples, AtomGroups, or Bonds; or TopologyGroup) – An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms, or Bonds. If every value is a Bond, all keywords are ignored. If AtomGroups, Bonds, or a TopologyGroup are passed, they must be from the same Universe.

  • types (iterable (optional, default None)) – None, or an iterable of hashable values with the same length as values

  • guessed (bool or iterable (optional, default False)) – bool, or an iterable of hashable values with the same length as values

  • order (iterable (optional, default None)) – None, or an iterable of hashable values with the same length as values

Example

Adding TIP4P water bonds with a list of AtomGroups:

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import GRO
u = mda.Universe(GRO)
sol = u.select_atoms('resname SOL')
ow_hw1 = sol.select_atoms('name OW or name HW1').split('residue')
ow_hw2 = sol.select_atoms('name OW or name HW2').split('residue')
ow_mw = sol.select_atoms('name OW or name MW').split('residue')
u.add_bonds(ow_hw1 + ow_hw2 + ow_mw)

You can only add bonds from the same Universe. If you would like to add AtomGroups, Bonds, or a TopologyGroup from a different Universe, convert them to indices first.

from MDAnalysis.tests.datafiles import PSF
u2 = mda.Universe(PSF)

#  assuming you have already added bonds to u
u2.add_bonds(u.bonds.to_indices())

New in version 1.0.0.