getDistances()
Description
getDistances() is a function used to transform the atom positions into intra-molecular distances by measuring the distances between atom pairs at a given rank.
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() | |
| Rank | rank= | int | (Opt.) Number of atoms (-1) between two neighbours along the same line used for distance calculations. At rank 1, the neighbours of an atom are all atom sharing a direct bond with it. Default is 6. |
Output(s)
| Name | Type | Description |
|---|---|---|
| Distances | np.ndarray | Array of the distances of the atoms of the molecules. Dimension(s) are in (N frames, N molecules, N distances). |
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 distances distances_array that can be used in ML-LPA.
import mllpa
distances_array = mllpa.getDistances(atom_positions, mol_types)
Select the neighbor rank
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 distances distances_array that can be used in ML-LPA. Here, a neighbor rank of 4 instead of 6 for the generation of the intra-molecular distances will be used
distances_array = mllpa.getDistances(atom_positions, mol_types, rank=4)