Bond¶

This module defines Bond for dealing with bond information provided by using AtomGroup.setBonds() method.

class Bond(ag, indices, acsi=None)[source]¶

A pointer class for bonded atoms. Following built-in functions are customized for this class:

• len() returns bond length, i.e. getLength()
• iter() yields Atom instances

getACSIndex()[source]¶

Return index of the coordinate set.

getAtomGroup()[source]¶

Return atom group.

getAtoms()[source]¶

Return bonded atoms.

getIndices()[source]¶

Return indices of bonded atoms.

getLength()[source]¶

Return bond length.

getVector()[source]¶

Return bond vector that originates from the first atom.

setACSIndex(index)[source]¶

Set the coordinate set at index active.