{"id":15018290,"url":"https://github.com/acellera/moleculekit","last_synced_at":"2026-04-28T10:01:08.700Z","repository":{"id":37396611,"uuid":"178184093","full_name":"Acellera/moleculekit","owner":"Acellera","description":"MoleculeKit: Your favorite molecule manipulation 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MoleculeKit\n\n[![Conda](https://anaconda.org/acellera/moleculekit/badges/version.svg)](https://anaconda.org/acellera/moleculekit)\n\nA molecule manipulation library\n\n# Getting started\n\n### Installing moleculekit\n\n#### With pip\n\n```\npip install moleculekit\n```\n\n#### With conda\n\n[Installation Instructions](https://software.acellera.com/moleculekit/installation.html)\n\n### Using moleculekit in ipython\n\nInstall ipython in the correct conda enviroment using the following command.\n\n```\npip install ipython\n```\n\nNow you can start an ipython console with\n\n```\nipython\n```\n\nIn the ipython console you can now import any of the modules of moleculekit and use it as normal.\n\n```python\nfrom moleculekit.molecule import Molecule\n\nmol = Molecule('3ptb')\nmol.view()\n```\n\n### API\n\nFor the official documentation of the moleculekit API head over to https://software.acellera.com/moleculekit/index.html\n\n### Issues\n\nFor any bugs or questions on usage feel free to use the issue tracker of this github repo.\n\n### Dev\n\nIf 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:\n\n```\npython setup.py build_ext --inplace\n```\n\n#### Building for WebAssembly\n\nInstall `emscripten` https://emscripten.org/docs/getting_started/downloads.html\n\n```\nconda create -n pyodide-build\nconda activate pyodide-build\nconda install python=3.11\npip install pyodide-build==0.25.1\n\n# Activate the emscripten environment\ncd ../emsdk\n./emsdk install 3.1.46\n./emsdk activate 3.1.46\nsource emsdk_env.sh\ncd -\n\n# Build the package\nexport PYO3_CROSS_INCLUDE_DIR=\"HACK\"\nexport PYO3_CROSS_LIB_DIR=\"HACK\"\nrm -rf .pyodide-xbuildenv\npyodide build -o dist_pyodide\ncp dist_pyodide/*.whl test_wasm/wheels/\ncd test_wasm\npython3 -m http.server\n```\n\nIf you get an error at building about numpy missing, check this issue https://github.com/pyodide/pyodide/issues/4347\n\n#### Debugging segmentation faults in Cython part\n\n1. Put a reproducible script in a file like `segfault.py`\n2. Modify setup.py to have `-g` as compile flag instead of `-O3`\n3. Recompile extensions with `python setup.py build_ext --inplace`\n4. Execute script with gdb like `gdb --args python segfault.py`\n5. Execute `run` and then `bt 10` to show the backtrace\n6. Have fun\n\n## Citing MoleculeKit\n\nIf you use this software in your publication please cite:\n\nStefan Doerr, Matthew J. Harvey, Frank Noé, and Gianni De Fabritiis.\n**HTMD: High-throughput molecular dynamics for molecular discovery.**\n_Journal of Chemical Theory and Computation_, **2016**, _12_ (4), pp 1845–1852.\n[doi:10.1021/acs.jctc.6b00049](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Facellera%2Fmoleculekit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Facellera%2Fmoleculekit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Facellera%2Fmoleculekit/lists"}