MoleculeKit
A molecule manipulation library
Getting started
Installing moleculekit
With pip
pip install moleculekit
With conda
Using moleculekit in ipython
Install ipython in the correct conda enviroment using the following command.
pip install ipython
Now you can start an ipython console with
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
conda create -n pyodide-build
conda activate pyodide-build
conda 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
Debugging segmentation faults in Cython part
- Put a reproducible script in a file like
segfault.py - Modify setup.py to have
-gas compile flag instead of-O3 - Recompile extensions with
python setup.py build_ext --inplace - Execute script with gdb like
gdb --args python segfault.py - Execute
runand thenbt 10to show the backtrace - Have fun
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
2 maintainers
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