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2024-04-19 23:37:46 +02:00
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 Awesome Python Chemistry !Awesome (https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg) (https://github.com/sindresorhus/awesome)
 Awesome Python Chemistry !Awesome (https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg) (https://github.com/sindresorhus/awesome)
!License: CC BY 4.0 (https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg) (https://creativecommons.org/licenses/by/4.0/)
A curated list of awesome Python frameworks, libraries, software and resources related to Chemistry.
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 - Learning Resources (#learning-resources)
 - See Also (#see-also)
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General Chemistry
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- AQME (https://github.com/jvalegre/aqme) - Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.
- aizynthfinder (https://github.com/MolecularAI/aizynthfinder) - A tool for retrosynthetic planning.
- batchcalculator (http://lukaszmentel.com/batchcalculator/) - A GUI app based on wxPython for calculating the correct amount of reactants (batch) for a particular composition given by the molar ratio of its 
components.
- batchcalculator (http://lukaszmentel.com/batchcalculator/) - A GUI app based on wxPython for calculating the correct amount of reactants (batch) for a particular composition given by the molar ratio of its components.
- cctbx (https://cctbx.github.io/) - The Computational Crystallography Toolbox.
- ChemFormula (https://github.com/molshape/ChemFormula) - ChemFormula provides a class for working with chemical formulas. It allows parsing chemical formulas, calculating formula weights, and generating 
formatted output strings (e.g. in HTML, LaTeX, or Unicode).
- ChemFormula (https://github.com/molshape/ChemFormula) - ChemFormula provides a class for working with chemical formulas. It allows parsing chemical formulas, calculating formula weights, and generating formatted output strings (e.g. 
in HTML, LaTeX, or Unicode).
- chemlib (https://chemlib.readthedocs.io/en/latest/) - A robust and easy-to-use package that solves a variety of chemistry problems.
- chempy (http://pythonhosted.org/chempy/) - ChemPy is a package useful for chemistry (mainly physical/inorganic/analytical chemistry).
- datamol (https://github.com/datamol-org/datamol): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
@@ -75,8 +74,7 @@
- MORFEUS (https://github.com/kjelljorner/morfeus) - Library for fast calculations of molecular features from 3D structures for machine learning with a focus on steric descriptors.
- olorenchemengine (https://github.com/Oloren-AI/olorenchemengine) - Molecular property prediction with unified API for diverse models and respresentations,
 with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.
- ROBERT (https://github.com/jvalegre/robert) - Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification 
problems.
- ROBERT (https://github.com/jvalegre/robert) - Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification problems.
- schnetpack (https://github.com/atomistic-machine-learning/schnetpack) - Deep Neural Networks for Atomistic Systems.
- selfies (https://github.com/aspuru-guzik-group/selfies) - Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation.
- Summit (https://github.com/sustainable-processes/summit) - Package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).
@@ -99,8 +97,7 @@
- alchemlyb (https://github.com/alchemistry/alchemlyb) - Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.
- atomate2 (https://github.com/materialsproject/atomate2) - atomate2 is a library of computational materials science workflows.
- Atomic Silumation Environment (ASE) (https://wiki.fysik.dtu.dk/ase/index.html) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
- basis_set_exchange (https://github.com/MolSSI-BSE/basis_set_exchange) - A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation 
of basis set data.
- basis_set_exchange (https://github.com/MolSSI-BSE/basis_set_exchange) - A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data.
- CACTVS (https://www.xemistry.com/academic/) - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.
- CalcUS (https://github.com/cyllab/CalcUS) - Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.
- cantera (https://github.com/Cantera/cantera) - A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
@@ -124,8 +121,8 @@
- oddt (https://github.com/oddt/oddt) - Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
- OPEM (https://github.com/ECSIM/opem) - Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.
- openmmtools (https://github.com/choderalab/openmmtools) - A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
- overreact (https://github.com/geem-lab/overreact) - A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for 
quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more.
- overreact (https://github.com/geem-lab/overreact) - A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for quasi-harmonic 
thermochemistry, quantum tunnelling corrections, molecular symmetries and more.
- ParmEd (https://github.com/ParmEd/ParmEd) - Parameter/topology editor and molecular simulator with visualization capability.
- pGrAdd (https://github.com/VlachosGroup/PythonGroupAdditivity) - A library for estimating thermochemical properties of molecules and adsorbates using group additivity.
- phonopy (http://atztogo.github.io/phonopy/) - An open source package for phonon calculations at harmonic and quasi-harmonic levels.
@@ -159,8 +156,8 @@
- FitSNAP (https://github.com/FitSNAP/FitSNAP) - A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package.
- fftool (https://github.com/paduagroup/fftool) - Tool to build force field input files for molecular simulation.
- FLARE (https://github.com/mir-group/flare) - A package for creating fast and accurate interatomic potentials.
- global-chem (https://github.com/Sulstice/global-chem) - A Chemical Knowledge Graph and Toolkit, writting in IUPAC/SMILES/SMARTS, for common small molecules from diverse communities to aid users in selecting 
compounds for forcefield parametirization.
- global-chem (https://github.com/Sulstice/global-chem) - A Chemical Knowledge Graph and Toolkit, writting in IUPAC/SMILES/SMARTS, for common small molecules from diverse communities to aid users in selecting compounds for forcefield 
parametirization.
- matbench-discovery (https://github.com/janosh/matbench-discovery) - A benchmark for ML-guided high-throughput materials discovery.
- NeuralForceField (https://github.com/learningmatter-mit/NeuralForceField) - Neural Network Force Field based on PyTorch.
- openff-toolkit (https://github.com/openforcefield/openff-toolkit) - The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.
@@ -176,8 +173,7 @@
- moleculekit (https://github.com/Acellera/moleculekit) - A molecule manipulation library.
- nglview (https://github.com/arose/nglview) - A Jupyter (https://jupyter.org/) widget to interactively view molecular structures and trajectories.
- PyMOL (https://pymol.org/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
- pymoldyn (https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html) - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais 
lattices.
- pymoldyn (https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html) - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices.
- sumo (http://sumo.readthedocs.io/en/latest/) - A toolkit for plotting and analysis of ab initio solid-state calculation data.
- surfinpy (https://surfinpy.readthedocs.io/en/latest/) - A library for the analysis, plotting and visualisation of ab initio surface calculation data.
- trident-chemwidgets (https://github.com/tridentbio/trident-chemwidgets) - Jupyter Widgets to interact with molecular datasets.
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Resources for learning to apply python to chemistry.
- An Introduction to Applied Bioinformatics (https://github.com/applied-bioinformatics/iab2) - A Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence 
alignment and calculating Hamming distances.
- Computational Thermodynamics (https://kyleniemeyer.github.io/computational-thermo/content/intro.html) - This collection of Jupyter notebooks demonstrates solutions to a range of thermodynamic problems 
including solving chemical equilibria, comparing real versus ideal gas behavior, and calculating the temperature and composition of a combustion reaction.
- SciCompforChemists (https://github.com/weisscharlesj/SciCompforChemists) - Scientific Computing for Chemists with Python is a Jupyter book teaching basic python in chemistry skills, including relevant 
libraries, and applies them to solving chemical problems.
- An Introduction to Applied Bioinformatics (https://github.com/applied-bioinformatics/iab2) - A Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence alignment and calculating 
Hamming distances.
- Computational Thermodynamics (https://kyleniemeyer.github.io/computational-thermo/content/intro.html) - This collection of Jupyter notebooks demonstrates solutions to a range of thermodynamic problems including solving chemical 
equilibria, comparing real versus ideal gas behavior, and calculating the temperature and composition of a combustion reaction.
- SciCompforChemists (https://github.com/weisscharlesj/SciCompforChemists) - Scientific Computing for Chemists with Python is a Jupyter book teaching basic python in chemistry skills, including relevant libraries, and applies them to 
solving chemical problems.
Miscellaneous Awesome
- Colorful Nuclide Chart (https://people.physics.anu.edu.au/~ecs103/chart/) - A beatuful, interactive visualization of nuclides with access to a varirty of nuclear properties and allows saving high quality 
images for publications, presentations and outreach.
- Colorful Nuclide Chart (https://people.physics.anu.edu.au/~ecs103/chart/) - A beatuful, interactive visualization of nuclides with access to a varirty of nuclear properties and allows saving high quality images for publications, 
presentations and outreach.
See Also
- awesome-cheminformatics (https://github.com/hsiaoyi0504/awesome-cheminformatics) Another list focuses on Cheminformatics, including tools not only in Python.
- awesome-small-molecule-ml (https://github.com/benb111/awesome-small-molecule-ml) A collection of papers, datasets, and packages for small-molecule drug discovery. Most links to code are in Python.
- awesome-molecular-docking (https://github.com/yangnianzu0515/awesome-molecular-docking) A curated list of molecular docking software, datasets, and papers.
- jarvis (https://jarvis.nist.gov/) Joint Automated Repository for Various Integrated Simulations is a repository designed to automate materials discovery and optimization using classical force-field, density 
functional theory, machine learning calculations and experiments.
- polypharmacy-ddi-synergy-survey (https://github.com/AstraZeneca/polypharmacy-ddi-synergy-survey) A collection of research papers (with Python implementations) focusing on drug-drug interactions, synergy and 
polypharmacy.
- jarvis (https://jarvis.nist.gov/) Joint Automated Repository for Various Integrated Simulations is a repository designed to automate materials discovery and optimization using classical force-field, density functional theory, machine 
learning calculations and experiments.
- polypharmacy-ddi-synergy-survey (https://github.com/AstraZeneca/polypharmacy-ddi-synergy-survey) A collection of research papers (with Python implementations) focusing on drug-drug interactions, synergy and polypharmacy.