ellipticbn 1.0.9

Python package for analyzing Cucurbituril crystal structures automatically

ElliptiC - an automated command line tool for visualizing and measuring ellipticity of cucurbituril host/guest structures

How to install

In a terminal, the command for installation is a simple

pip install ElliptiCBn

If you would rather not use pip and prefer installing source, the installation of the package can be done by the following:

• Clone this git repository to your local machine
• In the cloned repository, install the cbn_analysis package through python -m pip install . vv
• Next, install the required dependencies by running pip install -r requirements.txt

How to run the analysis

The ElliptiC package takes a single command line argument: an xyz file containing atom coordinates, or a folder of xyz files containing atom coordinates

To run the analysis package on a single file, navigate to the directory with the ElliptiC script and execute it: (NOTE: if there are spaces in your file name, you will need quotes around the file name)

The same convention can be used to execute the package on a folder of xyz files

How the package works

Below is a diagram of the analysis steps the software completes on any given file

1. In a given XYZ file, extract the coordinates of all carbon atoms (and oxygen atoms used later on in the analysis).

2. Identify strongly connected components to differentiate between host and guest structures.

3. Remove the guest structure since we only care about calculating ellipticity of the host.

4. Using proximity to oxygen atoms, remove the top and bottom rings of the hosts for accurate ellipticity calculation.

5 & 6. Using a Principal Components Analysis, calculate the variance along both major axes of the host ring. The ellipticity is thus (Vax1-Vax2)/Vax1 where Vax1 is the variance on the longest axis (length) and Vax2 is the variance on the second-longest axis (width).

7. Output graphs of both the single ring hosts and the full host-guest structures, as well as a spreadsheet with the calculated ellipticity for each structure.

How to interpret the output

Each xyz file analyzed with this package will produce at least 3 pieces of data:

• 1 interactive 3D scatter plot with all carbons in the CBn structures visualized
• 1 interactive 3D scatter plot with only the central carbon ring of the CBn structures visualized
• 1 spreadsheet with all of the carbons, their positions, distance to the centroid of the structure, and the measured ellipticity

In the case of host CBn structures with an internally situated guest structure, an additional 3D graph will be produced with the guests visualized in the structures (see below)

To see the interactive version of this plot that gets generated from the script, Click Here

The user can visually see the ellipticity in the structues and compare them to the measured values in the spreadsheets:
CB7 structures from above with guests removed

Calculated ellipticity for each structure on a scale of circular (0) to linear (1)

CB10 wide structures with guests removed

Calculated ellipticity for each structure on a scale of circular (0) to linear (1)