systemFromPositions()
Description
systemFromPositions() is a function similar to openSystem() used to load the simulation files to be analysed. The function will use position arrays instead of simulation files. More informations on the System class can be found in the related API reference.
Similarly to the openSystem() function, systemFromPositions() can only load one molecule type at a time.
The position and simulation box arrays 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 | str | Molecule type to load from the simulation file. | |
| Type infos | dict | Dictionary containing all the informations on the molecule type. Can be extracted with getMolInfos() | |
| Boxes | np.ndarray | Array of the box dimensions. Dimension(s) are in (N frames, 3). | |
| Up | up= | bool | (Opt.) Check that the molecules are always orientated pointing “up”. Default is True. |
| 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 |
|---|---|---|
| System | class System | Instance of the system classes containing all the informations on the system as well as the positions and configurations. |
Examples
Load the position in the System class
The following example will load for the given molecule type DPPC a position array, atom_positions, a dictionary of type information, mol_infos, and the array of dimensions of the simulation boxes, simulation_boxes, into an instance of the System class named here loaded_system.
import mllpa
types_list = mllpa.systemFromPositions(atom_positions, 'DPPC', mol_infos, simulation_boxes)
Select the neighbor rank
The following example will load for the given molecule type DPPC a position array, atom_positions, a dictionary of type information, mol_infos, and the array of dimensions of the simulation boxes, simulation_boxes, into an instance of the System class named here loaded_system. Here, a neighbor rank of 4 instead of 6 for the generation of the intra-molecular distances will be used.
types_list = mllpa.systemFromPositions(atom_positions, 'DPPC', mol_infos, simulation_boxes, rank=4)
Related tutorials
The following tutorial(s) detail further the use of the systemFromPositions() function: