awesome-awesomeness/html/pythonchemistry.html

<h1 id="awesome-python-chemistry-awesome">Awesome Python Chemistry <a
href="https://github.com/sindresorhus/awesome"><img
src="https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg"
alt="Awesome" /></a></h1>
<p><a href="https://creativecommons.org/licenses/by/4.0/"><img
src="https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg"
alt="License: CC BY 4.0" /></a></p>
<p>A curated list of awesome Python frameworks, libraries, software and
resources related to Chemistry.</p>
<p>Inspired by <a
href="https://awesome-python.com">awesome-python</a>.</p>
<h2 id="table-of-contents">Table of contents</h2>
<ul>
<li><a href="#awesome-python-chemistry-">Awesome Python Chemistry <img
src="https://github.com/sindresorhus/awesome" alt="Awesome" /></a>
<ul>
<li><a href="#general-chemistry">General Chemistry</a></li>
<li><a href="#machine-learning">Machine Learning</a></li>
<li><a href="#generative-molecular-design">Generative Molecular
Design</a></li>
<li><a href="#simulations">Simulations</a></li>
<li><a href="#molecular-visualization">Molecular Visualization</a></li>
<li><a href="#database-wrappers">Database Wrappers</a></li>
<li><a href="#learning-resources">Learning Resources</a></li>
<li><a href="#see-also">See Also</a></li>
</ul></li>
</ul>
<hr />
<h2 id="general-chemistry">General Chemistry</h2>
<p><em>Packages and tools for general chemistry.</em></p>
<ul>
<li><a href="https://github.com/jvalegre/aqme">AQME</a> - Ensemble of
automated QM workflows that can be run through jupyter notebooks,
command lines and yaml files.</li>
<li><a
href="https://github.com/MolecularAI/aizynthfinder">aizynthfinder</a> -
A tool for retrosynthetic planning.</li>
<li><a
href="http://lukaszmentel.com/batchcalculator/">batchcalculator</a> - 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.</li>
<li><a href="https://cctbx.github.io/">cctbx</a> - The Computational
Crystallography Toolbox.</li>
<li><a href="https://github.com/molshape/ChemFormula">ChemFormula</a> -
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).</li>
<li><a href="https://chemlib.readthedocs.io/en/latest/">chemlib</a> - A
robust and easy-to-use package that solves a variety of chemistry
problems.</li>
<li><a href="http://pythonhosted.org/chempy/">chempy</a> - ChemPy is a
package useful for chemistry (mainly physical/inorganic/analytical
chemistry).</li>
<li><a href="https://github.com/datamol-org/datamol">datamol</a>: -
Molecular Manipulation Made Easy. A light wrapper build on top of
RDKit.</li>
<li><a href="https://github.com/bobbypaton/GoodVibes">GoodVibes</a> - A
Python program to compute quasi-harmonic thermochemical data from
Gaussian frequency calculations.</li>
<li><a
href="https://github.com/wengong-jin/hgraph2graph">hgraph2graph</a> -
Hierarchical Generation of Molecular Graphs using Structural
Motifs.</li>
<li><a href="http://lewisamarshall.github.io/ionize/">ionize</a> -
Calculates the properties of individual ionic species in aqueous
solution, as well as aqueous solutions containing arbitrary sets of
ions.</li>
<li><a
href="https://lmodea-nano.readthedocs.io/en/latest/">LModeA-nano</a> -
Calculates the intrinsic chemical bond strength based on local
vibrational mode theory in solids and molecules.</li>
<li><a href="http://mendeleev.readthedocs.io/en/stable/">mendeleev</a> -
A package that provides a python API for accessing various properties of
elements from the periodic table of elements.</li>
<li><a href="https://github.com/jjhelmus/nmrglue">nmrglue</a> - A
package for working with nuclear magnetic resonance (NMR) data including
functions for reading common binary file formats and processing NMR
data.</li>
<li><a href="https://github.com/cgohlke/molmass">molmass</a> - Calculate
mass, elemental composition, and mass distribution spectrum of a
molecule given by its chemical formula, relative element weights, or
sequence.</li>
<li><a href="http://openbabel.org/">Open Babel</a> - A chemical toolbox
designed to speak the many languages of chemical data.</li>
<li><a
href="https://github.com/pkienzle/periodictable">periodictable</a> -
This package provides a periodic table of the elements with support for
mass, density and xray/neutron scattering information.</li>
<li><a href="https://github.com/jensengroup/propka">propka</a> -
Predicts the pKa values of ionizable groups in proteins and
protein-ligand complexes based in the 3D structure.</li>
<li><a
href="https://pybaselines.readthedocs.io/en/latest/">pybaselines</a> - A
package for fitting baselines of spectra for baseline correction.</li>
<li><a
href="https://openbabel.org/docs/UseTheLibrary/Python_Pybel.html">pybel</a>
- Pybel provides convenience functions and classes that make it simpler
to use the Open Babel libraries from Python.</li>
<li><a
href="https://pycroscopy.github.io/pycroscopy/index.html">pycroscopy</a>
- Scientific analysis of nanoscale materials imaging data.</li>
<li><a
href="https://pyeql.readthedocs.io/en/latest/index.html">pyEQL</a> - A
set of tools for conventional calculations involving solutions
(mixtures) and electrolytes.</li>
<li><a href="http://pyiron.org/">pyiron</a> - pyiron - an integrated
development environment (IDE) for computational materials science.</li>
<li><a href="http://pymatgen.org">pymatgen</a> - Python Materials
Genomics is a robust, open-source library for materials analysis.</li>
<li><a href="https://github.com/janosh/pymatviz">pymatviz</a> - A
toolkit for visualizations in materials informatics.</li>
<li><a href="https://symfit.readthedocs.io/en/stable/">symfit</a> - a
curve-fitting library ideally suited to chemistry problems, including
fitting experimental kinetics data.</li>
<li><a href="http://pythonhosted.org/symmetry/">symmetry</a> - Symmetry
is a library for materials symmetry analysis.</li>
<li><a href="https://github.com/lukasturcani/stk">stk</a> - A library
for building, manipulating, analyzing and automatic design of molecules,
including a genetic algorithm.</li>
<li><a
href="https://github.com/spectrochempy/spectrochempy">spectrochempy</a>
- A library for processing, analyzing and modeling spectroscopic
data.</li>
</ul>
<h2 id="machine-learning">Machine Learning</h2>
<p><em>Packages and tools for employing machine learning and data
science in chemistry.</em></p>
<ul>
<li><a href="http://amp.readthedocs.io/en/latest/">amp</a> - Is an
open-source package designed to easily bring machine-learning to
atomistic calculations.</li>
<li><a href="https://github.com/drorlab/atom3d">atom3d</a> - Enables
machine learning on three-dimensional molecular structure.</li>
<li><a
href="https://github.com/chainer/chainer-chemistry">chainer-chemistry</a>
- A deep learning framework (based on Chainer) with applications in
Biology and Chemistry.</li>
<li><a href="https://hachmannlab.github.io/chemml/">chemml</a> - A
machine learning and informatics program suite for the analysis, mining,
and modeling of chemical and materials data.</li>
<li><a href="https://github.com/chemprop/chemprop">chemprop</a> -
Message Passing Neural Networks for Molecule Property Prediction .</li>
<li><a href="https://github.com/txie-93/cgcnn">cgcnn</a> - Crystal graph
convolutional neural networks for predicting material properties.</li>
<li><a href="http://deepchem.io/">deepchem</a> - Deep-learning models
for Drug Discovery and Quantum Chemistry.</li>
<li><a
href="https://github.com/kexinhuang12345/DeepPurpose">DeepPurpose</a> -
A Deep Learning Library for Compound and Protein Modeling DTI, Drug
Property, PPI, DDI, Protein Function Prediction.</li>
<li><a
href="https://github.com/bp-kelley/descriptastorus">DescriptaStorus</a>
- Descriptor computation (chemistry) and (optional) storage for machine
learning.</li>
<li><a href="https://github.com/SINGROUP/dscribe">DScribe</a> -
Descriptor library containing a variety of fingerprinting techniques,
including the Smooth Overlap of Atomic Positions (SOAP).</li>
<li><a href="https://github.com/a-r-j/graphein">graphein</a> - Provides
functionality for producing geometric representations of protein and RNA
structures, and biological interaction networks.</li>
<li><a href="https://github.com/hackingmaterials/matminer">Matminer</a>
- Library of descriptors to aid in the data-mining of materials
properties, created by the Lawrence Berkeley National Laboratory.</li>
<li><a href="https://github.com/yangnianzu0515/MoleOOD">MoleOOD</a> - a
robust molecular representation learning framework against distribution
shifts.</li>
<li><a href="https://github.com/materialsvirtuallab/megnet">megnet</a> -
Graph Networks as a Universal Machine Learning Framework for Molecules
and Crystals.</li>
<li><a href="https://github.com/materialsvirtuallab/maml">MAML</a> -
Aims to provide useful high-level interfaces that make ML for materials
science as easy as possible.</li>
<li><a href="https://github.com/kjelljorner/morfeus">MORFEUS</a> -
Library for fast calculations of
<strong>mo</strong>lecula<strong>r</strong>
<strong>fe</strong>at<strong>u</strong>re<strong>s</strong> from 3D
structures for machine learning with a focus on steric descriptors.</li>
<li><a
href="https://github.com/Oloren-AI/olorenchemengine">olorenchemengine</a>
- Molecular property prediction with unified API for diverse models and
respresentations, with integrated uncertainty quantification,
interpretability, and hyperparameter/architecture tuning.</li>
<li><a href="https://github.com/jvalegre/robert">ROBERT</a> - Ensemble
of automated machine learning protocols that can be run sequentially
through a single command line. The program works for regression and
classification problems.</li>
<li><a
href="https://github.com/atomistic-machine-learning/schnetpack">schnetpack</a>
- Deep Neural Networks for Atomistic Systems.</li>
<li><a href="https://github.com/aspuru-guzik-group/selfies">selfies</a>
- Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular
string representation.</li>
<li><a href="https://github.com/sustainable-processes/summit">Summit</a>
- Package for optimizing chemical reactions using machine learning
(contains 10 algorithms + several benchmarks).</li>
<li><a href="https://github.com/mims-harvard/TDC">TDC</a> - Therapeutics
Data Commons (TDC) is the first unifying framework to systematically
access and evaluate machine learning across the entire range of
therapeutics.</li>
<li><a href="https://github.com/yoshida-lab/XenonPy">XenonPy</a> -
Library with several compositional and structural material descriptors,
along with a few pre-trained neural network models of material
properties.</li>
</ul>
<h2 id="generative-molecular-design">Generative Molecular Design</h2>
<p><em>Packages and tools for generating molecular species</em></p>
<ul>
<li><a href="https://github.com/MolecularAI/GraphINVENT">GraphINVENT</a>
- A platform for graph-based molecular generation using graph neural
networks.</li>
<li><a href="https://github.com/BenevolentAI/guacamol">GuacaMol</a> - A
package for benchmarking of models for <em>de novo</em> molecular
design.</li>
<li><a href="https://github.com/molecularsets/moses">moses</a> - A
benchmarking platform for molecular generation models.</li>
<li><a href="https://github.com/choderalab/perses">perses</a> -
Experiments with expanded ensembles to explore chemical space.</li>
</ul>
<h2 id="simulations">Simulations</h2>
<p><em>Packages for atomistic simulations and computational
chemistry.</em></p>
<ul>
<li><a href="https://github.com/alchemistry/alchemlyb">alchemlyb</a> -
Makes alchemical free energy calculations easier by leveraging the full
power and flexibility of the PyData stack.</li>
<li><a href="https://github.com/materialsproject/atomate2">atomate2</a>
- atomate2 is a library of computational materials science
workflows.</li>
<li><a href="https://wiki.fysik.dtu.dk/ase/index.html">Atomic Silumation
Environment (ASE)</a> - Is a set of tools and modules for setting up,
manipulating, running, visualizing and analyzing atomistic
simulations.</li>
<li><a
href="https://github.com/MolSSI-BSE/basis_set_exchange">basis_set_exchange</a>
- A library containing basis sets for use in quantum chemistry
calculations. In addition, this library has functionality for
manipulation of basis set data.</li>
<li><a href="https://www.xemistry.com/academic/">CACTVS</a> - Cactvs is
a universal, scriptable cheminformatics toolkit, with a large collection
of modules for property computation, chemistry data file I/O and other
tasks.</li>
<li><a href="https://github.com/cyllab/CalcUS">CalcUS</a> - Quantum
chemisttry web platform that brings all the necessary tools to perform
quantum chemistry in a user-friendly web interface.</li>
<li><a href="https://github.com/Cantera/cantera">cantera</a> - A
collection of object-oriented software tools for problems involving
chemical kinetics, thermodynamics, and transport processes.</li>
<li><a href="https://github.com/SUNCAT-Center/CatKit">CatKit</a> -
General purpose tools for high-throughput catalysis.</li>
<li><a href="https://github.com/cyllab/ccinput/">ccinput</a> - A tool
and library for creating quantum chemistry input files.</li>
<li><a href="https://cclib.github.io/">cclib</a> - A library for parsing
output files various quantum chemical programs.</li>
<li><a href="https://github.com/ekwan/cctk">cctk</a> - A library for
computational chemistry (DFT) for input file generation, data
extraction, method screening and analysis.<br />
</li>
<li><a href="http://cinfony.github.io/">cinfony</a> - A common API to
several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo,
JChem, OPSIN and cheminformatics webservices).</li>
<li><a
href="http://chemlab.readthedocs.io/en/latest/index.html">chemlab</a> -
Is a library that can help the user with chemistry-relevant
calculations.</li>
<li><a href="https://github.com/materialsproject/emmet">emmet</a> - A
package to ‘build’ collections of materials properties from the output
of computational materials calculations.</li>
<li><a href="https://github.com/Crespo-Otero-group/fromage/">fromage</a>
- The “FRamewOrk for Molecular AGgregate Excitations” enables localised
QM/QM’ excited state calculations in a solid state environment.</li>
<li><a href="https://wiki.fysik.dtu.dk/gpaw/">GPAW</a> - Is a
density-functional theory (DFT) Python code based on the
projector-augmented wave (PAW) method and the atomic simulation
environment (ASE).</li>
<li><a
href="http://theochem.github.io/horton/2.0.1/index.html">horton</a> -
Helpful Open-source Research TOol for N-fermion system, a
quantum-chemistry program that can perform computations involving model
Hamiltonians.</li>
<li><a href="https://github.com/Acellera/htmd">HTMD</a> -
High-Throughput Molecular Dynamics: Programming Environment for
Molecular Discovery.</li>
<li><a href="https://github.com/epam/Indigo">Indigo</a> - Universal
cheminformatics libraries, utilities and database search tools.</li>
<li><a href="https://github.com/theochem/iodata">IoData</a> - File
parser/converter for QM, MD and plane-wave DFT programs.</li>
<li><a href="https://github.com/usnistgov/jarvis">Jarvis-tools</a> - An
open-access software package for atomistic data-driven materials
design</li>
<li><a href="http://mathchem.iam.upr.si/">mathchem</a> - Is a free open
source package for calculating topological indices and other invariants
of molecular graphs.</li>
<li><a href="http://www.mdanalysis.org/">MDAnalysis</a> - Is an
object-oriented library to analyze trajectories from molecular dynamics
(MD) simulations in many popular formats.</li>
<li><a href="http://mdtraj.org">MDTraj</a> - Package for manipulating
molecular dynamics trajectories with support for multiple formats.</li>
<li><a href="http://dirac.cnrs-orleans.fr/MMTK/">MMTK</a> - The
Molecular Modeling Toolkit is an Open Source program library for
molecular simulation applications.</li>
<li><a href="http://molmod.github.io/molmod/index.html">MolMod</a> - A
library with many components that are useful to write molecular modeling
programs.</li>
<li><a
href="https://nmrsim.readthedocs.io/en/latest/index.html">nmrsim</a> - A
library for simulating first- or second-order NMR spectra and dynamic
NMR resonances.</li>
<li><a href="https://github.com/oddt/oddt">oddt</a> - Open Drug
Discovery Toolkit, a modular and comprehensive toolkit for use in
cheminformatics, molecular modeling etc.</li>
<li><a href="https://github.com/ECSIM/opem">OPEM</a> - Open source PEM
(Proton Exchange Membrane) fuel cell simulation tool.</li>
<li><a href="https://github.com/choderalab/openmmtools">openmmtools</a>
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular
simulation engine.</li>
<li><a href="https://github.com/geem-lab/overreact">overreact</a> - 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.</li>
<li><a href="https://github.com/ParmEd/ParmEd">ParmEd</a> -
Parameter/topology editor and molecular simulator with visualization
capability.</li>
<li><a
href="https://github.com/VlachosGroup/PythonGroupAdditivity">pGrAdd</a>
- A library for estimating thermochemical properties of molecules and
adsorbates using group additivity.</li>
<li><a href="http://atztogo.github.io/phonopy/">phonopy</a> - An open
source package for phonon calculations at harmonic and quasi-harmonic
levels.</li>
<li><a href="https://github.com/SCM-NV/PLAMS">PLAMS</a> - Python Library
for Automating Molecular Simulation: input preparation, job execution,
file management, output processing and building data workflows.</li>
<li><a href="https://vlachosgroup.github.io/pMuTT/">pMuTT</a> - A
library for ab-initio thermodynamic and kinetic parameter
estimation.</li>
<li><a href="https://github.com/pmgbergen/porepy">PorePy</a> - A
Simulation Tool for Fractured and Deformable Porous Media.</li>
<li><a href="http://prody.csb.pitt.edu/">ProDy</a> - An open source
package for protein structural dynamics analysis with a flexible and
responsive API.</li>
<li><a href="https://github.com/chemosim-lab/ProLIF">ProLIF</a> -
Interaction Fingerprints for protein-ligand complexes and more.</li>
<li><a href="http://psicode.org">Psi4</a> - A hybrid Python/C++
open-source package for quantum chemistry.</li>
<li><a href="https://github.com/psi4/psi4numpy/">Psi4NumPy</a> -
Psi4-based reference implementations and Jupyter notebook-based
tutorials for foundational quantum chemistry methods.</li>
<li><a href="http://www.emma-project.org/latest/">pyEMMA</a> - Library
for the estimation, validation and analysis Markov models of molecular
kinetics and other kinetic and thermodynamic models from molecular
dynamics data.</li>
<li><a
href="https://pygauss.readthedocs.io/en/stable/index.html">pygauss</a> -
An interactive tool for supporting the life cycle of a computational
molecular chemistry investigations.</li>
<li><a href="http://pyquante.sourceforge.net/">PyQuante</a> - Is an
open-source suite of programs for developing quantum chemistry
methods.</li>
<li><a href="https://github.com/thynnine/pysic">pysic</a> - A calculator
incorporating various empirical pair and many-body potentials.</li>
<li><a href="https://github.com/sunqm/pyscf">Pyscf</a> - A quantum
chemistry package written in Python.</li>
<li><a href="http://pyvib2.sourceforge.net/">pyvib2</a> - A program for
analyzing vibrational motion and vibrational spectra.</li>
<li><a href="http://www.rdkit.org/">RDKit</a> - Open-Source
Cheminformatics Software.</li>
<li><a
href="https://github.com/VlachosGroup/ReNView/wiki/Reaction-Network-Viewer-(ReNView)-Usage-Instructions">ReNView</a>
- A program to visualize reaction networks.</li>
<li><a href="https://github.com/lukasturcani/stk">stk</a> - A library
for building, manipulating, analyzing and automatic design of
molecules.</li>
<li><a
href="https://github.com/quantum-visualizations/qmsolve">QMsolve</a> - A
module for solving and visualizing the Schrödinger equation.</li>
<li><a href="http://libatoms.github.io/QUIP/">QUIP</a> - A collection of
software tools to carry out molecular dynamics simulations.</li>
<li><a href="https://github.com/torchmd/torchmd">torchmd</a> -
End-To-End Molecular Dynamics (MD) Engine using PyTorch.</li>
<li><a href="http://theory.cm.utexas.edu/tsase/">tsase</a> - The library
which depends on ASE to tackle transition state calculations.</li>
<li><a href="https://github.com/choderalab/yank">yank</a> - An open,
extensible Python framework for GPU-accelerated alchemical free energy
calculations.</li>
</ul>
<h3 id="force-fields">Force Fields</h3>
<p><em>Packages related to force fields</em></p>
<ul>
<li><a href="https://github.com/alanwilter/acpype">acpype</a> - Convert
AMBER forcefields from ANTECHAMBER to GROMACS format.</li>
<li><a href="https://github.com/CederGroupHub/chgnet">CHGNet</a> -
Pretrained universal neural network potential for charge-informed
atomistic modeling.</li>
<li><a href="https://github.com/FitSNAP/FitSNAP">FitSNAP</a> - A Package
For Training SNAP Interatomic Potentials for use in the LAMMPS molecular
dynamics package.</li>
<li><a href="https://github.com/paduagroup/fftool">fftool</a> - Tool to
build force field input files for molecular simulation.</li>
<li><a href="https://github.com/mir-group/flare">FLARE</a> - A package
for creating fast and accurate interatomic potentials.</li>
<li><a href="https://github.com/Sulstice/global-chem">global-chem</a> -
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.</li>
<li><a
href="https://github.com/janosh/matbench-discovery">matbench-discovery</a>
- A benchmark for ML-guided high-throughput materials discovery.</li>
<li><a
href="https://github.com/learningmatter-mit/NeuralForceField">NeuralForceField</a>
- Neural Network Force Field based on PyTorch.</li>
<li><a
href="https://github.com/openforcefield/openff-toolkit">openff-toolkit</a>
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF
format, parameterization engine, and other tools.</li>
</ul>
<h2 id="molecular-visualization">Molecular Visualization</h2>
<p><em>Packages for viewing molecular structures.</em></p>
<ul>
<li><a
href="https://wiki.fysik.dtu.dk/ase/ase/gui/gui.html#module-ase.gui">ase-gui</a>
- The graphical user-interface allows users to visualize, manipulate,
and render molecular systems and atoms objects.</li>
<li><a href="https://github.com/lab-cosmo/chemiscope">chemiscope</a> -
An interactive structure/property explorer for materials and
molecules.</li>
<li><a href="http://chemview.readthedocs.io/en/latest/">chemview</a> -
An interactive molecular viewer designed for the IPython notebook.</li>
<li><a href="http://patrickfuller.github.io/imolecule/">imolecule</a> -
An embeddable webGL molecule viewer and file format converter.</li>
<li><a href="https://github.com/Acellera/moleculekit">moleculekit</a> -
A molecule manipulation library.</li>
<li><a href="https://github.com/arose/nglview">nglview</a> - A <a
href="https://jupyter.org/">Jupyter</a> widget to interactively view
molecular structures and trajectories.</li>
<li><a href="https://pymol.org/">PyMOL</a> - A user-sponsored molecular
visualization system on an open-source foundation, maintained and
distributed by Schrödinger.</li>
<li><a
href="https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html">pymoldyn</a>
- A viewer for atomic clusters, crystalline and amorphous materials in a
unit cell corresponding to one of the seven 3D Bravais lattices.</li>
<li><a href="https://github.com/EBjerrum/rdeditor">rdeditor</a> - Simple
RDKit molecule editor GUI using PySide.</li>
<li><a href="http://sumo.readthedocs.io/en/latest/">sumo</a> - A toolkit
for plotting and analysis of ab initio solid-state calculation
data.</li>
<li><a href="https://surfinpy.readthedocs.io/en/latest/">surfinpy</a> -
A library for the analysis, plotting and visualisation of ab initio
surface calculation data.</li>
<li><a
href="https://github.com/tridentbio/trident-chemwidgets">trident-chemwidgets</a>
- Jupyter Widgets to interact with molecular datasets.</li>
</ul>
<h2 id="database-wrappers">Database Wrappers</h2>
<p><em>Providing a python layer for accessing chemical
databases</em></p>
<ul>
<li><a
href="https://downloads.ccdc.cam.ac.uk/documentation/API/index.html">ccdc</a>
- An API for the Cambridge Structural Database System.</li>
<li><a href="http://chemspipy.readthedocs.io/en/latest/">ChemSpiPy</a> -
<a href="http://www.chemspider.com/">ChemSpider</a> wrapper, that allows
chemical searches, chemical file downloads, depiction and retrieval of
chemical properties.</li>
<li><a href="http://cirpy.readthedocs.io/en/latest/">CIRpy</a> - An
interface for the Chemical Identifier Resolver (CIR) by the CADD Group
at the NCI/NIH.</li>
<li><a
href="https://github.com/IvanChernyshov/NistChemPy">NistChemPy</a> - A
package for accessing data from the NIST webbook. API includes access to
thermodynamic properties, molecular structures, IR/MS/UV-Vis spectra and
more.</li>
<li><a href="http://pubchempy.readthedocs.io/en/latest/">pubchempy</a> -
PubChemPy provides a way to interact with PubChem in Python.</li>
<li><a
href="https://github.com/cthoyt/chembl-downloader">chembl-downloader</a>
- Automate downloading and querying the latest (or a given) version of
<a href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></li>
<li><a
href="https://github.com/cthoyt/drugbank_downloader">drugbank-downloader</a>
- Automate downloading, opening, and parsing <a
href="https://www.drugbank.com/">DrugBank</a></li>
</ul>
<h2 id="learning-resources">Learning Resources</h2>
<p><em>Resources for learning to apply python to chemistry.</em></p>
<ul>
<li><a href="https://github.com/applied-bioinformatics/iab2">An
Introduction to Applied Bioinformatics</a> - A Jupyter book
demonstrating working with biochemical data using the scikit-bio library
for tasks such as sequence alignment and calculating Hamming
distances.</li>
<li><a
href="https://kyleniemeyer.github.io/computational-thermo/content/intro.html">Computational
Thermodynamics</a> - 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.</li>
<li><a
href="https://github.com/weisscharlesj/SciCompforChemists">SciCompforChemists</a>
- 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.</li>
</ul>
<h2 id="miscellaneous-awesome">Miscellaneous Awesome</h2>
<ul>
<li><a href="https://people.physics.anu.edu.au/~ecs103/chart/">Colorful
Nuclide Chart</a> - 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.</li>
</ul>
<h2 id="see-also">See Also</h2>
<ul>
<li><a
href="https://github.com/hsiaoyi0504/awesome-cheminformatics">awesome-cheminformatics</a>
Another list focuses on Cheminformatics, including tools not only in
Python.</li>
<li><a
href="https://github.com/benb111/awesome-small-molecule-ml">awesome-small-molecule-ml</a>
A collection of papers, datasets, and packages for small-molecule drug
discovery. Most links to code are in Python.</li>
<li><a
href="https://github.com/yangnianzu0515/awesome-molecular-docking">awesome-molecular-docking</a>
A curated list of molecular docking software, datasets, and papers.</li>
<li><a href="https://jarvis.nist.gov/">jarvis</a> 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.</li>
<li><a
href="https://github.com/AstraZeneca/polypharmacy-ddi-synergy-survey">polypharmacy-ddi-synergy-survey</a>
A collection of research papers (with Python implementations) focusing
on drug-drug interactions, synergy and polypharmacy.</li>
</ul>
<p><a
href="https://github.com/lmmentel/awesome-python-chemistry">pythonchemistry.md
Github</a></p>