Persistent Generators AT

Pipeline description

This example computes the persistent one-dimensional generators of the electronic density of the Adenine-Thymine molecular complex. These generators characterize the cycles in the interactions between atoms, whether they are covalent (cycles in the carbonate chains), or weaker non-covalent interactions (cycles in the hydrogen bonds).

Generators are computed using PersistentGenerators. For context, the one-dimensional separatrices of the MorseSmale complex are computed using MorseSmaleComplex and shown in the ParaView example.

The python script simply computes the generators and saves the result as a .vtp file.

ParaView

To reproduce the above screenshot, go to your ttk-data directory and enter the following command:

paraview states/persistentGenerators_at.pvsm

Python code

#!/usr/bin/env python

from paraview.simple import *

# create a new 'XML Image Data Reader'
atvti = XMLImageDataReader(FileName=["at.vti"])

# create a new 'TTK PersistentGenerators'
tTKPersistentGenerators1 = TTKPersistentGenerators(Input=atvti)
tTKPersistentGenerators1.ScalarField = ["POINTS", "density"]

SaveData("PersistentGeneratorsAt.vtp", tTKPersistentGenerators1)

To run the above Python script, go to your ttk-data directory and enter the following command:

pvpython python/persistentGenerators_at.py

Inputs

• at.vti: A molecular dataset: a three-dimensional regular grid with 1 scalar field, the electronic density in the Adenine Thymine complex.

Outputs

• PersistentGeneratorsAt.vtp: the raw one-dimensional generators of the field.

C++/Python API

MorseSmaleComplex

PersistentGenerators