| Name | moleculekit JSON |
| Version |
1.8.29
JSON |
| download |
| home_page | None |
| Summary | A molecule reading/writing and manipulation package. |
| upload_time | 2024-03-27 10:02:09 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
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| VCS |
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| bugtrack_url |
|
| requirements |
No requirements were recorded.
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| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
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# MoleculeKit
[](https://anaconda.org/acellera/moleculekit)
[](https://codecov.io/gh/Acellera/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
[Installation Instructions](https://software.acellera.com/moleculekit/installation.html)
#### 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.
```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
```
mamba create -n pyodide-build
mamba activate pyodide-build
mamba install python=3.10
pip install pyodide-build==0.23.2
# Activate the emscripten environment
cd ../emsdk
git checkout 3.1.32
./emsdk install latest
./emsdk activate latest
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
```
## 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[](https://codecov.io/gh/Acellera/moleculekit)\n\nA molecule manipulation library\n\n# Getting started\n\nWe recommend installing Miniconda on your machine to better manage python packages and environments.\n\nYou can install moleculekit either in the \"base\" conda environment or in a new conda environment. We recommend the second.\n\n### Install it into the base conda environment\n\n#### With conda\n\n[Installation Instructions](https://software.acellera.com/moleculekit/installation.html)\n\n#### With pip\n\nThe pip version of moleculekit is VERY limited and not officially supported. Use at your own risk.\n\n```\n(base) user@computer:~$ pip install moleculekit\n```\n\n### Optional dependencies of moleculekit\n\nMoleculekit 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:\n\n```\n(moleculekit) user@computer:~$ wget https://raw.githubusercontent.com/Acellera/moleculekit/master/extra_requirements.txt\n(moleculekit) user@computer:~$ conda install --file extra_requirements.txt -c acellera\n```\n\n### Using moleculekit in ipython\n\nInstall 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.\n\n```\n(moleculekit) user@computer:~$ conda install ipython\n```\n\nNow you can start an ipython console with\n\n```\n(moleculekit) user@computer:~$ ipython\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```\nmamba create -n pyodide-build\nmamba activate pyodide-build\nmamba install python=3.10\npip install pyodide-build==0.23.2\n\n# Activate the emscripten environment\ncd ../emsdk\ngit checkout 3.1.32\n./emsdk install latest\n./emsdk activate latest\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\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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