Element_PI.PersDiagram

Element_PI.PersDiagram(lifetime=True, showplot=True)

Creates a visual representation for a persistence diagram

Parameters

• xyz (string) –

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

• lifetime (bool, optional) –

  • Option to set the y-axis to lifetime value

  • Options:

    • True: set coordinates to (birth, death - birth)

    • False: set coordinates to (birth, death)

• showplot (bool, optional) –

  • Option to output PD plot automatically to screen or not

  • Options:

    • True: show plot

    • False: do not show plot

Returns

• rips (Rips object from the ripser module) –

  • See ripser documentation for this return value.

  • This object has the data specified in xyz fit to it.

• Note

  If showplot = True, then a plot of the PD will be output to the screen.

Example

In the example below, we will show how to create a persistence diagram and output it to the screen. We will use the file babel/1.xyz which contains coordinate data on the atoms in the pyridine compound.:

import Element_PI

filename = 'babel/1.xyz'
Element_PI.PersDiagram(filename, lifetime = True, showplot = True)

If we specify lifetime = True (as above), then our plot will look like the following. This plot represents the PD that is used to generate the PI.:

If we specify lifetime = False, then our plot will look slightly different.: