A Python module to analyse the intermolecular interactions across an organic molecular material. This code was written as part of my PhD thesis as a member of the Jelfs Group.
This repository is of scientific relevance, because it takes a crystallographic database file structure, which is provided in periodic coordinates, transforms it to cartesian coordinates and builds a 3x3x3 supercell of the molecular material.
Then the most central molecule is selected and all its surrounding molecules (neighbouring shell) are selected as well, each of them is tested for their interactions with the central molecule.
The major focus is on pi-pi stacking interactions which are relevant to the organic semiconductors industry. Depending on their nature, parallel, perpendicular etc. they behave differently. Thus, if their distance and angle is known and their electron transport has been computed elsewhere it can be related to one another.
The crystack folder contains the script to perform the intermolecular analysis.
This repo is structured as follows:
The main software module is inside the crystack folder. The workflow can be run via
modification of the automation script: run_analysis_for_crystal.sh
There are several Jupyter notebooks for running the analysis interactively (notebooks).
The crystal stacking results are stored in a results.csv file and some results
can be found here: results
Raw Molecular Data: data
A sample polymorph landscape with hundreds of residual (.res) files of molecular crystals: sample-polymorph-landscape
This software package uses the modularity finding ability of pywindow, also developed by the Jelfs Group
pip install pywindow