getCoordinates()

Description

getCoordinates() is a function used to transform the atom positions into coordinates by centering them around their center of masses and rotation along a common axis.

The position array can be obtained using the function extractPositions(). The molecule type information dictionary can be obtained using the function getMolInfos.

Argument, keywords and outputs

Input(s) / Argument(s)

Name	Flag	Type	Description
Positions		np.ndarray	Array of the positions of the atoms of the molecules. Dimension(s) should be in (N frames, N molecules, N atoms per molecule, 3).
Type info		dict	Dictionary containing all the informations on the molecule type. Can be extracted with read_simulation.getMolInfos()
Up	up=	bool	(Opt.) Check that the molecules are always orientated pointing “up”.

Output(s)

Name	Type	Description
New Positions	np.ndarray	Array of the coordinates of the atoms of the molecules. Dimension(s) are in (N frames, N molecules, N atoms per molecule, 2).

Examples

Convert a position array

The following example will convert the position array atom_positions, using the dictionary of information on the molecule type mol_types, into the array of coordinates coordinates_array that can be used in ML-LPA.

import mllpa

coordinates_array = mllpa.getCoordinates(atom_positions, mol_types)