Element_PI.Generate_PI

Element_PI.GeneratePI(savefile=False, pixelx=100, pixely=100, myspread=2, bounds={'maxBD': 3, 'minBD': - 0.1})

Outputs a visual representation of a persistence image based on file given.

Parameters

  • xyz (string) –

    • Name for local file containing data on coordinates representing atoms in compound

  • savefile (bool, optional) –

    • Default value = False

    • Options:

      • True = plot of PI is saved

      • False = plot is not saved

    • Saves file to: <xyz>_img.png

  • pixelx (int, optional) –

    • Default value = 100

    • Number of pixels on x-axis

  • pixely (int, optional) –

    • Default value = 100

    • Number of pixels on y-axis

  • myspread (float, optional) –

    • Default value = 2

    • Parameter for kernel

    • For Gaussian kernel, this specifies the variance

  • bounds (dictionary, optional) –

    • Default value = {"maxBD": 2, "minBD":0}

    • Specifies boundary extent in Angstroms

    • Format:

      {
    "maxBD": <float>,
    "minBD": <float>
}

    • maxBD: upper boundary of persistence image (in Angstroms)

    • minBD: lower boundary of persistence image (in Angstroms)

Returns

  • None (none)

  • No explicit return value. Outputs the plot of the PI to the screen.

Note

This function offers an alternative method to generate a PI that does not output the matrix-representation of the PI. Therefore, this should only be used for visualization purposes.

Example

In this example, we will generate a PI for the following molecule:

../../_images/GeneratePI_molecule_image

To generate this PI, we will set our filename and then call the GeneratePI function.:

import Element_PI

fname = 'babel/95.xyz'  # This file included in original repository
Element_PI.GeneratePI(fname, savefile = True, pixelx = 20, pixely = 20,
    myspread = 2, bounds = {"maxBD": 3, "minBD": 0})

The PI generated from this code is shown below:

../../_images/babel95_PI