octadist 2.5.3

OctaDist: A tool for calculating distortion parameters in coordination complexes.

OctaDist

Octahedral distortion calculator: A tool for calculating distortion parameters in coordination complexes. https://octadist.github.io/

Standard abilities

OctaDist is computer software for inorganic chemistry and crystallography program. It is written entirely in Python 3 binding to Tkinter GUI toolkit. OctaDist can be used for studying the structural distortion in coordination complexes. With the abilities of OctaDist, you can:

• identify the type of octahedral coordination complexes.
• compute octahedral distortion parameters.
• display 3D molecule and other stuff.
• implement its functions in your or other programs.
• broaden the program with your ideas as needed.

Documents

User document: Online manual.

Reference document: HTML | PDF | Epub

Installing

The easiest way to install OctaDist is to use pip.

pip install octadist

or use conda for those who have Anaconda installed on your system.

conda install -c rangsiman octadist

Now you can check if octadist package is installed correctly.

import octadist

print(octadist.__version__)     # '2.5.3'

Running the tests

import octadist as oc

# Prepare list of atomic coordinates of octahedral structure:

coord = [[2.298354000, 5.161785000, 7.971898000],   # <- Metal center atom
         [1.885657000, 4.804777000, 6.183726000],   # Ligand atom 1
         [1.747515000, 6.960963000, 7.932784000],   # Ligand atom 2
         [4.094380000, 5.807257000, 7.588689000],   # Ligand atom 3
         [0.539005000, 4.482809000, 8.460004000],   # Ligand atom 4
         [2.812425000, 3.266553000, 8.131637000],   # Ligand atom 5
         [2.886404000, 5.392925000, 9.848966000]]   # Ligand atom 6

zeta = oc.calc_zeta(coord)             # Zeta
delta = oc.calc_delta(coord)           # Delta
sigma = oc.calc_sigma(coord)           # Sigma
theta = oc.calc_theta(coord)           # Theta

Example output for computed parameters:

Computed parameters
-------------------
Zeta  = 0.228072561
Delta = 0.000476251
Sigma = 47.92652837
Theta = 122.6889727

Other example scripts and octahedral complexes are available at example-py and example-input.

Citation

Please cite this project when you have used OctaDist for scientific publication.

OctaDist: A tool for calculating distortion parameters in coordination complexes.
https://octadist.github.io

Bug report

If you found issues in OctaDist, please report us at here.

Project team

• Rangsiman Ketkaew (Thammasat University, Thailand)
  
  • E-mail: [e-mail]
    
• Yuthana Tantirungrotechai (Thammasat University, Thailand)
  • E-mail: [e-mail]
• David J. Harding (Walailak University, Thailand)
  • E-mail: [e-mail]
• Phimphaka Harding (Walailak University, Thailand)
  • E-mail: [e-mail]
• Mathieu Marchivie (University of Bordeaux, France)
  • E-mail: [e-mail]