Possible bond orders are:
BondOrder.Unknown: the bond order is not specified
BondOrder.Single: bond order for single bond
BondOrder.Double: bond order for double bond
BondOrder.Triple: bond order for triple bond
BondOrder.Quadruple: bond order for quadruple bond (present in some metals)
BondOrder.Quintuplet: bond order for quintuplet bond (present in some metals)
BondOrder.Amide: bond order for amide bond
BondOrder.Aromatic: bond order for aromatic bond
Topologycontains the definition of all the atoms in the system, and the liaisons between the atoms (bonds, angles, dihedrals, …). It will also contain all the residues information if it is available.
Create a new empty
add_bond(i, j, order=None)¶
Add a bond between the atoms at indexes
Topology, optionally setting the bond
Get the bonds order corresponding to the bond between atoms i and j
Remove all existing bonds, angles, dihedral angles and improper dihedral angles in this topology.
Remove any existing bond between the atoms at indexes
This function does nothing if there is no bond between
countatoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type. If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.