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Π-Stacking Toolkit

Armadillo is a Python toolkit which when supplied with a topology and trajectory file is able to produce a list of rings that are π-stacking with one another. From this the toolkit can also be used to plot this data and create .pdb file so that the stacking rings can be visualized. In addition to this the toolkit is highly customisable by the user as the distance and alpha constraints can be altered by the user from the default values that have been set.

armadillo is bound by a Code of Conduct.

Installation

To build armadillo from source, we highly recommend using virtual environments. If possible, we strongly recommend that you use Anaconda as your package manager. Below we provide instructions for conda

With conda

Ensure that you have conda installed.

Create a virtual environment and activate it:

conda create --name armadillo
conda activate armadillo

Install the development and documentation dependencies:

conda env update --name armadillo --file devtools/conda-envs/test_env.yaml
conda env update --name armadillo --file docs/requirements.yaml

If you want to update your dependencies (which can be risky!), run:

conda update --all

And when you are finished, you can exit the virtual environment with:

conda deactivate

Pi-Stacking Definition

Workflow

Example armadillo Pi-Stacking Run Through

Import armadillo and MDanalysis

import armadillo
import MDAnalysis as mda

Loading universe

u = mda.Universe('topology.prmtop', 'trajectory.nc')

Atomgroup containing atoms that make up rings

ag = sum(u.atoms.fragments[:20]) 

Calling the function to find all the rings

ring_list = armadillo.find_all_rings(ag, u)

Looping over the trajectory to produce all the pi-stacking rings

pi_parallel_stacking=[]
pi_t_shaped = []
for ts in u.trajectory[:25:5]:
    parallel_stacking, t_shaped = armadillo.find_pi_stacking_rings(ring_list, ag)

    pi_parallel_stacking.append(parallel_stacking)
    pi_t_shaped.append(t_shaped)

Plotting distrubution of pi-stacking rings

armadillo.pi_stacking_distribution(pi_parallel_stacking[4], pi_t_shaped[4], ring_list, ag, u, frame=20)

Stacked rings can be given tempfactors to be visualized in VMD

First flatten parallel and t-shaped

flat_parallel_pi_stacking = list(armadillo.itertools.chain.from_iterable(pi_parallel_stacking[4]))
flat_t_shaped_pi_stacking = list(armadillo.itertools.chain.from_iterable(pi_t_shaped[4]))

Create atomgroups for the two lists

pi_ag = sum([ring_list[ix] for ix in flat_parallel_pi_stacking])
t_ag = sum([ring_list[ix] for ix in flat_t_shaped_pi_stacking])

Add tempfactors to the universe

u.add_TopologyAttr('tempfactors')

Assign tempfactors to stacking rings

pi_ag.tempfactors=2
t_ag.tempfactors=3

Write pdb file with these tempfactors and visulise in VMD using beta colouring

u.atoms.write('beta_example.pdb')

Red - None Stacking

Light Blue - Parallel/Parallel Displaced Stacking

Dark Blue - T-Shaped Stacking

Copyright

The armadillo source code is hosted at https://github.com/TristanSJones/armadillo and is available under the GNU General Public License, version 3 (see the file LICENSE).

Copyright (c) 2023, Tristan Stephens-Jones

Acknowledgements

armadillo was created by the follow authors

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using armadillo in published work.