PyAR

PyAR stands for "Python program for aggregation and reaction"

Contents

1. Installation
2. Features
3. Interfaced with electronic structure theory programs:
4. Command Line Interface
5. Example usages
6. References
7. Credits
8. License

Installation

Download the file pyar-master.zip. Unzip it. Go the the folder and sudo python3 setup.py install This will create python package in the path /usr/local/lib/python3.6/dist-packages/pyar/ and will create the command line interface pyar-cli in /usr/local/bin

or

Run the following command in the pyar folder sudo -H pip install .

Features:

• Automated prediction of unknown reactions between two reactants (A+B)
• Automated prediction of the geometries of aggregates, atomic clusters etc.
• Automated search for reaction for bond forming between two atoms in two different molecules.

Requirements

• python >= 3.6
• numpy>=1.18.4
• pandas>=1.0.5
• scipy>=1.5.2
• scikit-learn>=0.23.2
• autograd>=1.3

Interfaced with electronic structure theory programmes

• Turbomole
• Mopac
• Xtb
• Orca
• Psi4

Command line usage

The easy usage is by command line. This can also be used as library. The detailed help can be obtained by typing command -h

pyar-cli

The main program can be used as below:

pyar-cli options files

There are other scripts for a few automation tasks.

pyar-tabu

pyar-tabu can be used for

• for making different orientations of two molecules.
• Making a composite molecule containing a seed molecule and N number of monomer molecules.
• Orient two molecules such that i'th atom of one molecule and j 'th atom of second molecule have shortest distance between them

pyar-clustering

• for a clustering analysis of n input molecules to find unique molecules.

pyar-optimiser

• for the bulk optimisation of several molecules

Examples

Reaction

To study the reaction between two reactants A and B using ORCA software interface, with force from 100 to 1000 using N=8 trial orientation, the commandline line argument is,

pyar-cli -r A.xyz B.xyz -N 8 -gmin 100 -gmax 1000 --ssoftware orca

A.xyz and B.xyz are the cartesian coordinate files of the reactants.

Aggregation and clustering

pyar-cli -a A.xyz -N 8 -as 10 --software xtb

This will generate a molecular aggregate/cluster of size upto 10 with XTB package using 8 trial orientations. The A.xyz is a standard cartesian coordinate file. For example the .xyz file for a carbon atom is the following:

1
Comment
C  0.0  0.0   0.0

References

1. "A Global Optimizer for Nanoclusters ", Maya Khatun, Rajat Shubhro Majumdar, Anakuthil Anoop Frontiers in Chemistry 2019, 644
2. "A tabu-search based strategy for modeling molecular aggregates and binary reactions" S Nandi, SR McAnanama-Brereton, MP Waller, A Anoop, Computational and Theoretical Chemistry 2017, 1111, 69-81

Credits

The idea and the initial work started with Dr. Mark P. Waller at University of Muenster in 2011. Mark is currently at pending.ai. Later Dr. Surajit Nandi who as PhD student in AnoopLab made immense contributions. Another major help came from a Masters project student, Deebankur Bhattacharyya.

License

GNU GPL V3