uibcdf / MolSysMT

Open source library to work with molecular systems

https://www.uibcdf.org/MolSysMT/

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Other Python libraries to be checked #12

Open dprada opened 3 years ago

dprada commented 3 years ago

Opened issue to list here other Python libraries to be checked.

dprada commented 3 years ago

ProLIF

From the source: "ProLIF (Protein-Ligand Interaction Fingerprints) is a tool designed to generate interaction fingerprints for protein-ligand and protein-protein interactions extracted from molecular dynamics trajectories and docking simulations."

https://github.com/chemosim-lab/ProLIF

dprada commented 3 years ago

py3Dmol

From the source: "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook. The widget is completely static, which means the viewer doesn't need a running IPython kernel to be useful and web pages and presentations generated from the notebook will work as expected. However, this also means there is only one-way communication between the notebook and the viewer."

https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol
https://birdlet.github.io/2019/10/02/py3dmol_example/

dprada commented 3 years ago

OMMProtocol

From the source: "A command line application to launch molecular dynamics simulations with OpenMM"

https://github.com/insilichem/ommprotocol

dprada commented 3 years ago

IOData

From the source: "IOData is a HORTON 3 module for input/output of quantum chemistry file formats. Documentation is here: https://iodata.readthedocs.io/en/latest/index.html"

https://github.com/theochem/iodata

dprada commented 3 years ago

PypKa

From the source: "A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism DOI: 10.1021/acs.jcim.0c00718"

https://github.com/mms-fcul/PypKa