https://github.com/Acellera/moleculekit
MoleculeKit: Your favorite molecule manipulation kit
https://github.com/Acellera/moleculekit
drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins
Last synced: 5 months ago
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MoleculeKit: Your favorite molecule manipulation kit
- Host: GitHub
- URL: https://github.com/Acellera/moleculekit
- Owner: Acellera
- License: other
- Created: 2019-03-28T10:51:36.000Z (about 6 years ago)
- Default Branch: main
- Last Pushed: 2024-10-23T10:36:51.000Z (6 months ago)
- Last Synced: 2024-10-29T17:36:39.357Z (6 months ago)
- Topics: drug-discovery, machine-learning, molecular-modeling, molecular-simulation, molecule, proteins
- Language: Python
- Homepage:
- Size: 92.4 MB
- Stars: 200
- Watchers: 12
- Forks: 37
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- top-life-sciences - **Acellera/moleculekit** - discovery`, `machine-learning`, `molecular-modeling`, `molecular-simulation`, `molecule`, `proteins`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 193 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 35 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Python <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> Other <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-06-04 13:53:30 | (Ranked by starred repositories)
README
# 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
```
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)