Psikit update/Draw ESP, HOMO LUMO #RDKit #Chemoinformatics #quantumchemistry

I just updated psikit which is package for quantum-chemoinformatics ;)

It can be installed from conda / pypi :)

I added and updated new function for molecular property rendering.

Current version of psikit can draw not only frontier orbital but also ESP and dual descriptor. Dual descriptor is calculated by psi4. What is dual descriptor? From original ducment.

Calculates the dual descriptor from frontier orbitals: 𝑓2(𝐫)=𝜌LUMO(𝐫)−𝜌HOMO(𝐫)f2(r)=ρLUMO(r)−ρHOMO(r). The dual descriptor is a good measure of nucleophilicity and electrophilicity, containing information essentially equivalent to both Fukui functions combined. More details on the dual descriptor itself can be found in [Morell:2005:205], while the current implementation is described in [Martinez-Araya:2015:451]. This feature is currently only supported for closed shell systems.

It is very easy to get these images!

Let’s test the functions with acetic acid as an example.

Following code is almost borrowed form the UGM material. Thanks for sharing nice code. Import packages, read Reaction data and reaction objects at first. For convenience, I recommend to install ipymol at first.

 
import ipymol
from psikit import Psikit
pk = Psikit()
v = ipymol.viewer
v.start() # pymol will launch

Calculate energy of acetic acid.

Then call getMOview() for getting some cube files.


pk.getMOview()

Now data preparation is finished. I can get several views just call view_on_pymol with target option which I would like to draw in pymol.

 
pk.view_on_pymol(target='ESP')
pk.view_on_pymol(target='DUAL', maprange=0.001)
pk.view_on_pymol('FRONTIER')

Now I could get 3 views in pymol. Following images are results.

ESP
DUAL
LUMO
HOMO

Visualization of quantum chemistry properties are useful for medchem I think. Any comments, requests and suggestions are greatly appreciated.

code example

Today’s code is uploaded my repo and URL is below.

https://github.com/iwatobipen/playground/blob/master/new_function_psikit.ipynb

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