| Name | moleculekit JSON |
| Version |
1.10.4
JSON |
| download |
| home_page | None |
| Summary | A molecule reading/writing and manipulation package. |
| upload_time | 2025-09-10 10:36:28 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | None |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# MoleculeKit
[](https://anaconda.org/acellera/moleculekit)
A molecule manipulation library
# Getting started
### Installing moleculekit
#### With pip
```
pip install moleculekit
```
#### With conda
[Installation Instructions](https://software.acellera.com/moleculekit/installation.html)
### 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.
```python
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
1. Put a reproducible script in a file like `segfault.py`
2. Modify setup.py to have `-g` as compile flag instead of `-O3`
3. Recompile extensions with `python setup.py build_ext --inplace`
4. Execute script with gdb like `gdb --args python segfault.py`
5. Execute `run` and then `bt 10` to show the backtrace
6. 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](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049)
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"description": "# MoleculeKit\n\n[](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 No\u00e9, 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\u20131852.\n[doi:10.1021/acs.jctc.6b00049](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049)\n",
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