Element_PI.Makexyzdistance

Element_PI.Makexyzdistance()

Prepares a file with geometric chemical data for use in Vietoris-Rips filtration.

Parameters

t (string) –

• Name of source file for coordinate data for a compound

• See documentation’s specifications for file structure

• File contains (x, y, z) coordinates for each atom in compound

Returns

• Distance (Numpy array) –

  • Distance matrix for every atom in the compound

  • Used as input to Vietoris-Rips filtration function (ripser)

• element (string) –

  • Name of the element being read

Example

Generating distance matrix for chemical compound stored in a file named compound.xyz:

from PersistentImages_Chemistry.Element_PI import Makexyzdistance

file_name = 'compound.xyz'
dist_matrix, name = Makexyzdistance(file_name)