ichor.core.calculators.connectivity package
Submodules
ichor.core.calculators.connectivity.distance_connectivity_calculator module
- connectivity_calculator_distance(atoms: ichor.core.atoms.Atoms) ndarray
Calculates the connectivity matrix (showing which atoms are bonded as 1 and those that are not bonded as 0. It uses the Van Der Waals radius an Atom (see Atom class) to determine if atoms should be bonded or not.
:param : atoms: Atoms instance
- Returns:
- type: np.ndarray
The connectivity matrix between atoms of shape len(atoms) x len(atoms)
Note
This is a class method because the connectivity only needs to be calculated once per trajectory. The connectivity remains the same for all timesteps in a trajectory.
ichor.core.calculators.connectivity.valence_connectivity_calculator module
- connectivity_calculator_valence(atoms: ichor.core.atoms.Atoms) ndarray
Calculates the connectivity matrix (showing which atoms are bonded as 1 and those that are not bonded as 0. It uses the Van Der Waals radius an Atom (see Atom class) to determine if atoms should be bonded or not.
:param : atoms: Atoms instance
- Returns:
- type: np.ndarray
The connectivity matrix between atoms of shape len(atoms) x len(atoms)
Note
This is a class method because the connectivity only needs to be calculated once per trajectory. The connectivity remains the same for all timesteps in a trajectory.