Tessellation
Description
The class Tessellations is used to store all informations required to perform a Voronoi tessellation on the molecules of the system, along with all elements obtained through the tessellation. After a neighbor analysis, the information are also stored in the instance of the class.
Attributes and Methods
Initialisation
Instances of the Tessellation class can be generated in ML-LPA via the function doVoro().
It is recommended to use this function to generate the instances of the class. However, if one wants to generate it by calling the class, the following data are required:
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The array of names of all the molecules.
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The array of ids of all the molecules.
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The array of the centers of mass of all the molecules.
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The array of dimensions of the simulation box over time, in the correct dimensions, as extracted by the extractPositions() function.
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The array of the phases of the molecules, as extracted by the functions getPhases() or setPhases().
Please be aware that ghost lipids, required for most of the membrane geometries, cannot be generated within the Tessellation class.
Attributes
| Name | Type | Description |
|---|---|---|
| tessellation.names | np.ndarray | Name of the molecule type of each molecule of the system. |
| tessellation.ids | np.ndarray | Indices of all the molecules of the system. |
| tessellation.positions | np.ndarray | 3D positions of the centers of mass of all the molecules of the system. |
| tessellation.boxes | np.ndarray | Dimensions of the simulation box. |
| tessellation.phases | np.ndarray | Phases of all the molecules of the system. |
| tessellation.leaflets | np.ndarray | Name of the leaflets in which all the molecules can be found, if applicable |
| tessellation.ghosts | np.ndarray | 3D positions of the centers of mass of the ghosts of all the molecules of the system, if applicable |
| tessellation.volumes | np.ndarray | Volumes - or Areas in 2D - found through the tessellation of all the molecules. |
| tessellation.vertices | np.ndarray | Positions of the vertices of the cell of each molecule. |
| tessellation.neighbors | np.ndarray | List of the neighbors of all the molecules of the system. |
| tessellation.geometry | str | Geometry selected for the tessellation during the generation. |
| tessellation.threshold | float | Threshold used to remove sporious neighbors found during the tessellation. |
| tessellation.neighbors_phases | np.ndarray | Phases of the neighbors of each molecules of the system. |
| tessellation.phases_list | np.ndarray | Name of the phases, in the order provided in tessellation.neighbors_phases. |
Methods
| Name | Argument(s) | Description |
|---|---|---|
| tessellation.getLeaflets() | <ul><li>geometry=, {str}, (Opt.) geometry of the system. Default is bilayer.</li></ul> | Find the leaflet in which all the molecules are located. |
| tessellation.doVoronoi() | <ul><li>geometry=, {str}, (Opt.) geometry of the system. Default is bilayer.</li><li>threshold=, {float}, (Opt.) threshold used to remove sporious neighbors found during the tessellation. Default is 0.01.</li></ul> | Perform the Voronoi tessellation on the system to find the individual cells of each molecules. |
| tessellation.checkNeighbors() | Determine the state of the neighbors of each molecule of the system. | |
| tessellation.toTable() | Collect all the attributes of the instance and convert them into a pandas dataframe. | |
| tessellation.save() | <ul><li>file_path, {str}, Path and name of the file to generate.</li><li>format, {str}, File extension and format to use for the output file.</li></ul> | Save the instance of the Tessellation class in a file. |
The .save() method uses the same argument and generates the same files than the saveVoro() function.
Examples
Initialise an instance of the class
The following example will initialise an instance of the Tessellation class, named here voronoi, from the name array mol_names, the position array mol_positions, the array of indices mol_ids, the array of dimensions of the simulation boxes, simulation_boxes and the array of phases mol_phases.
from mllpa.system_class import Tessellation
voronoi = Tessellation(mol_names, mol_ids, mol_positions, simulation_boxes, mol_phases)
Assign molecules to their respective leaflets
The following example will assign the molecules in the instance of the Tessellation class voronoi with the leaflets they can be found in, based on the geometry bilayer. The results will be stored directly in the instance.
voronoi.getLeaflets(geometry='bilayer')
Do the tessellation
The following example will tessellate the molecules in the instance of the Tessellation class voronoi, based on the geometry bilayer_3d, and cures the results from spurious neighbors with a threshold at 1% (0.01). All the results will be stored directly in the instance.
voronoi.doVoronoi(geometry='bilayer_3d', threshold=0.01)
Analyse the local environment
The following example will use a tessellation previously made in the instance of the Tessellation class voronoi to analyse the local environment. The results are both stored in the instance and returned as the array of the phase environment for each molecule neighbor_phases and the list of the phase names phases_list given in the same order than in neighbor_phases
neighbors_phases, phases_list = voronoi.checkNeighbors()
Convert the content into a pandas data frame
The following example will convert the attributes of the instance of the Tessellation class voronoi in a pandas table-like structure dataframe.
dataframe = voronoi.toTable()
Save the instance in a file
The following example will save the content of the instance of the Tessellation class voronoi in a file test_file.xml
voronoi.save(file_path='test_file.xml')
Related functions
The following function(s) uses the System class either in their input our output:
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Common functions
Related tutorials
The following tutorial(s) detail further the use of the getStates() function through the .getStates() method of the system class: