OctaDist: A tool for calculating distortion parameters in coordination complexes.
Project description
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: rangsiman1993@gmail.com
- E-mail: rangsiman1993@gmail.com
- Yuthana Tantirungrotechai (Thammasat University, Thailand)
- E-mail: yt203y@gmail.com
- David J. Harding (Walailak University, Thailand)
- E-mail: hdavid@mail.wu.ac.th
- Phimphaka Harding (Walailak University, Thailand)
- E-mail: kphimpha@mail.wu.ac.th
- Mathieu Marchivie (University of Bordeaux, France)
- E-mail: mathieu.marchivie@icmcb.cnrs.fr
Project details
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