Awesome
MoleculeKit
A molecule manipulation library
Getting started
We recommend installing Miniconda on your machine to better manage python packages and environments.
You can install moleculekit either in the "base" conda environment or in a new conda environment. We recommend the second.
Install it into the base conda environment
With conda
With pip
The pip version of moleculekit is VERY limited and not officially supported. Use at your own risk.
(base) user@computer:~$ pip install moleculekit
Optional dependencies of moleculekit
Moleculekit has a small number of optional dependencies which are needed for some of it's functionalities. They were not added to the default dependencies to keep moleculekit a fast and small installation and to avoid unnecessary conflicts with other software. However if you want to leverage all of it's functionality you can install the rest of the dependencies with the following command:
(moleculekit) user@computer:~$ wget https://raw.githubusercontent.com/Acellera/moleculekit/master/extra_requirements.txt
(moleculekit) user@computer:~$ conda install --file extra_requirements.txt -c acellera
Using moleculekit in ipython
Install ipython in the correct conda enviroment using the following command. If you have installed the extra dependencies as above, you can skip this step since it already installs ipython.
(moleculekit) user@computer:~$ conda install ipython
Now you can start an ipython console with
(moleculekit) user@computer:~$ ipython
In the ipython console you can now import any of the modules of moleculekit and use it as normal.
from moleculekit.molecule import Molecule
mol = Molecule('3ptb')
mol.view()
API
For the official documentation of the moleculekit API head over to https://software.acellera.com/moleculekit/index.html
Issues
For any bugs or questions on usage feel free to use the issue tracker of this github repo.
Dev
If you are using moleculekit without installing it by using the PYTHONPATH env var you will need to compile the C++ extensions in-place with the following command:
python setup.py build_ext --inplace
Building for WebAssembly
Install emscripten
https://emscripten.org/docs/getting_started/downloads.html
mamba create -n pyodide-build
mamba activate pyodide-build
mamba install python=3.11
pip install pyodide-build==0.25.1
# Activate the emscripten environment
cd ../emsdk
./emsdk install 3.1.46
./emsdk activate 3.1.46
source emsdk_env.sh
cd -
# Build the package
export PYO3_CROSS_INCLUDE_DIR="HACK"
export PYO3_CROSS_LIB_DIR="HACK"
rm -rf .pyodide-xbuildenv
pyodide build -o dist_pyodide
cp dist_pyodide/*.whl test_wasm/wheels/
cd test_wasm
python3 -m http.server
If you get an error at building about numpy missing, check this issue https://github.com/pyodide/pyodide/issues/4347
Citing MoleculeKit
If you use this software in your publication please cite:
Stefan Doerr, Matthew J. Harvey, Frank Noé, and Gianni De Fabritiis. HTMD: High-throughput molecular dynamics for molecular discovery. Journal of Chemical Theory and Computation, 2016, 12 (4), pp 1845–1852. doi:10.1021/acs.jctc.6b00049