Python Libraries for chemistry

July 11, 2024

Python is a powerful programming language widely used in various scientific fields, including chemistry. The versatility and efficiency of Python have led to the development of numerous libraries tailored for chemical data manipulation. These libraries assist in everything from cheminformatics to molecular dynamics and quantum chemistry. Below is an incomplete list of Python libraries that can be used to manipulate different types of chemical data and perform different kinds of operations and calculations.

Cheminformatics

Library	License	Description
RDKit	Open Source	Cheminformatics tools for molecular modeling.
Openeye	Proprietary	Tools for cheminformatics and molecular modeling.
Pybel	Open Source	Python wrapper for the Open Babel toolkit.
MolVS	Open Source	Standardization and validation of chemical structures.
ESPsim	MIT	Shape and electrostatic similarities of molecules.
ScaffoldGraph	MIT	Generation and analysis of molecular scaffold networks.
reaction-network	Open Source	Synthetic planning and reaction pathway prediction.
xyz2graph	MIT	Visualization of XYZ files and reconstruction of the molecular graph.
Matcher	MIT	UI to identify modifications that improved a drug.
FPSim2	MIT	Fast fingerprint-based molecular similarity.
usearch-molecules	Apache2	Molecular similarity and clustering based on fingerprints.
PatentChem	MIT	Searches USPTO for patented molecules.
Metgem	GPL3	Molecular networks generation.
pyADA	GPL3	Compute applicability domain of ML models.

Molecular Dynamics

Library	License	Description
MDAnalysis	Open Source	Analyzing molecular dynamics trajectories.
OpenMM	Open Source	High-performance molecular dynamics simulations.
BioSimSpace	GPL3	Interface to several MD engines.
PyContact	GPL3	Analysis of non-covalent interactions in MD.

Macromolecules

Library	License	Description
Gemmi	Open Source	Macromolecules, 3D structures, molecular dynamics, format conversion.
Biopython	Open Source	Tools for biological computation.
Pyrosetta	Academic License	Interface to Rosetta for macromolecular modeling.
PDBFixer	Open Source	Preparing PDB files for molecular simulations.
ChemLab	GPL3	Macromolecular visualization and system preparation.
QCEngine	BSD3	Standardized interface for several QC and MM engines.
Panel-Chemistry	MIT	Visualization of molecules for building interfaces.

Machine Learning

Library	License	Description
DeepChem	Open Source	Machine learning tools for drug discovery and quantum chemistry.
ChemML	Open Source	Machine learning for chemical research.
Chemprop	Open Source	Machine learning for property prediction.
TorchANI	Open Source	Machine learning potentials for quantum chemistry.
Molfeat	Apache2	Molecular encodings for deep learning.
ASAPDiscovery	MIT	Framework for antiviral drug discovery.
Therapeutics Data Commons	MIT	Datasets and benchmarks for drug discovery AI.
ChemicalX	Apache2	Drug-drug interaction prediction.
Reinvent	Apache2	Molecule generation and scoring framework.
Foundry	MIT	Data preparation for machine learning.
AMPL	MIT	Automatic construction of ML predictive models.
Matbench	MIT	Benchmarking machine learning for materials.
pumml	MIT	Classify molecules with only positive data.

Quantum Chemistry

Library	License	Description
PySCF	Open Source	Quantum chemistry tools.
Psi4	LGPL3	Ab initio quantum chemistry simulations.
VASPy	MIT	Manipulates and visualizes VASP data.
QMFlows	LGPL3	Quantum chemistry workflows.
Quacc	BSD3	Workflow manager for quantum calculations.
GeomeTRIC	BSD3	Geometry optimization of molecules.
Psikit	BSD3	Integrates Psi4 and RDKit.

Format Conversion

Library	License	Description
ParmEd	LGPL	Molecular mechanics parameter file editor.
CDPKit	LGPL	Cheminformatics and format conversion.

Free Energy

Library	License	Description
OpenFE	Open Source	Free energy calculations in molecular dynamics.
Lomap	MIT	Free energy calculations.
Alchemlyb	BSD3	Automate alchemical free energy analysis.

Molecular Mechanics

Library	License	Description
ASE	Open Source	3D structure manipulation and atomistic simulations.
OpenFF	MIT	Molecular mechanics and force fields.
ACPYPE	GPL3	Interface to Antechamber for Amber.
Chemcoord	LGPL3	Manipulate cartesian and internal coordinates.
maml	BSD3	Materials simulations.

Thermodynamics

Library	License	Description
Thermo	MIT	Thermodynamic properties calculation.
Sella	LGPL3	Identify saddle points in thermodynamics.

Analytical Chemistry

Library	License	Description
SpectroChemPy	Free Software	Process and analyze spectrographic data.

Databases

Library	License	Description
Mendeleev	MIT	Periodic table information.
Therapeutics Data Commons	MIT	Datasets and benchmarks for drug discovery AI.
usearch-molecules	Apache2	Molecular similarity and clustering based on fingerprints.
PatentChem	MIT	Searches USPTO for patented molecules.

Automated Design

Library	License	Description
Reinvent	Apache2	Molecule generation and scoring framework.
stk	MIT	Structural data manipulation and molecular design.

Visualization

Library	License	Description
Panel-Chemistry	MIT	Visualization of molecules for building interfaces.
xyz2graph	MIT	Visualization of XYZ files and reconstruction of the molecular graph.

File Format

Library	License	Description
Chemical JSON	Open Source	Chemical JSON file format.

ADMET

Library	License	Description
ChemicalX	Apache2	Drug-drug interaction prediction.