CodeEntropy.ClassCollection.DataContainer.DataContainer

class CodeEntropy.ClassCollection.DataContainer.DataContainer(u, start=None, end=None, step=1)

This is the main data container for CodeEntropy Solute calculation This host framewise information of positions and forces on all the atoms, in lab and local frames. The vectors in the local frames are obtained after transforming the lab frame vectors using orthonormal bases that also stored framewise for each atom.

The properties of its molecule (base molecule) is linked to a molecule class object that contains the info about its topology.

__init__(u, start=None, end=None, step=1)

Create a data container for CodeEntropy and load data from MDAnalysis.Universe

Parameters:

• u (MDAnalyse.Universe) – A Universe object will all topology, dihedrals,coordinates and force information Check Example/create_new_universe.py on how to create a universe from existing data

• start (int or None, Optional, default: None) – Frame id to start analysis. Default None will start from frame 0

• end (int or None, Optional, default: None) – Frame id to end analysis. Default None will end at last frame

• step (int, Optional, default: 1) – Steps between frame.

Methods

__init__(u[, start, end, step])	Create a data container for CodeEntropy and load data from MDAnalysis.Universe
add_dihedral(arg_dihedral)
get_center_of_mass(arg_atomList, arg_frame)	compute and return the center of mass of the input atoms in the lab frame
get_minmax(arg_token, arg_indices[, ...])	Return the minimum and maximum value of an array with name given by arg_token at frame arg_frame for selected indices.
get_moment_of_inertia_tensor_lab(...)	return the 3 x 3 moment of inertia tensor for the body defined by the collection of atoms in the input atom List.
get_principal_axes(arg_atomList, arg_frame, ...)	Returns a pricipal moments of inertia and a 3 x 3 matrix with each row as the principal axes sorted in the descending order of the corresponding eigen values (principal moments of inertia).
initialize_ndarrays()	The number of frames for which the container will hold the data must be provided before hand
print_attributes()
reset_rotationAxesArray()	Reset the rotational axes value of every atom per frame while maintaining the shape of the array.
reset_translationAxesArray()	Reset the translational axes value of every atom per frame while maintaining the shape of the array.
update_localCoords(arg_type, arg_atomList)
update_localCoords_of_all_atoms(arg_type)
update_localForces(arg_type, arg_atomList)
update_localForces_of_all_atoms(arg_type)
update_rotationAxesArray_at(arg_frame, ...)	Update the rotational axes at a given frame for the selected atoms with the input values.
update_translationAxesArray_at(arg_frame, ...)	Update the translational axes at a given frame for the selected atoms with the input values.