cgexplore.terms.Bond

class cgexplore.terms.Bond(atom_names, atom_ids, bond_r, bond_k, atoms, force, funct=0)[source]

Bases: object

Class containing bond defintion used in Forcefield.

Parameters:

  • atom_names (Sequence[str]) – Element and ID+1 of atoms in bond.

  • atom_ids (Sequence[int]) – ID of atoms in bond.

  • bond_r (Quantity) – r quantity of bond force.

  • bond_k (Quantity) – k quantity of bond force.

  • atoms (Sequence[Atom] | None) – stk.Atom instances of the atoms in bond.

  • force (str) – The force to apply to a bond, usually “HarmonicBondForce”.

  • funct (int) – For some forcefields (e.g., Martini), this term can change the force function. For harmonic bonds, set to 0.

Methods

Attributes

atom_names

atom_ids

bond_r

bond_k

atoms

force

funct

atom_ids: Sequence[int]
atom_names: Sequence[str]
atoms: Sequence[Atom] | None
bond_k: Quantity
bond_r: Quantity
force: str
funct: int