ChirPy (chiral python) is a python package for chirality, dynamics, and molecular vibrations.
Main features:
- Computation of vibrational circular dichroism (VCD) from molecular dynamics (MD) and time-correlation functions (TCF)
- Application of the periodic gauge for magnetic moments and crystal symmetry in solid-state
- Interpretation, processing, and creation of molecular topologies and supercells
- Analysis and visualisation of MD results
Furthermore:
- Scientific visualisation
- Interfacing with VMD
- Processing of volumetric data and vector fields
(... work in progress)
Copy or clone the repository into a local directory. Open a bash terminal and change directory to the local copy of the repository.
Make sure you have the following packages installed:
python>= 3.10pip>= 22.3packmol>= 20.0 (optional)
You can also use Anaconda to create a chirpy environment from the delivered conda_env.yml file:
conda env create -f conda_env.ymlIn the parent directory, run:
pip install .ChirPy has now been installed and can be imported within a python environment:
import chirpy as cpCheck that you installation is correct by running from a bash terminal the test suite in tests/:
python run_tests.pyor
./run_tests.py(optional arguments: --verbose, --scripts)
Thank you for reporting bugs and issues to the developers.
Workable binaries can be found in the folder scripts/ with some pre-implemented ChirPy features. Make sure you add this folder to PATH.
Available jupyter notebooks and data sets:
(... under construction)
- S. Jähnigen, A. Zehnacker, and R. Vuilleumier; Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge, J. Phys. Chem. Lett., 2021, 12 (30), 7213-7220.
- S. Jähnigen, D. Sebastiani, R. Vuilleumier; The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution, Phys. Chem. Chem. Phys., 2021, 23, 17232.