Chemistry Tools
Software libraries and frameworks for cheminformatics and computational chemistry.
Cheminformatics Stack
| Tool | Description | Link |
|---|---|---|
| RDKit | Core cheminformatics toolkit — the foundation of most chemistry ML | rdkit.org |
| OpenBabel | Format conversion, 3D generation | openbabel.org |
| CDK | Java-based cheminformatics toolkit | cdk.github.io |
| Datamol | RDKit wrapper optimized for data science workflows | datamol.io |
| Indigo | Cheminformatics libraries and utilities | github |
| cinfony | Common API to cheminformatics toolkits | github |
General Chemistry
| Tool | Description | Link |
|---|---|---|
| mendeleev | API for periodic table element properties | docs |
| periodictable | Periodic table with mass and scattering information | github |
| chempy | Package for physical/inorganic/analytical chemistry | docs |
| molmass | Calculates mass and composition of molecules | github |
| ChemFormula | Working with chemical formulas and formatted output | github |
| chemlib | Solves a variety of chemistry problems | docs |
| ionize | Calculates properties of ionic species | docs |
| pyEQL | Tools for conventional calculations involving solutions | docs |
| symfit | Curve-fitting library suited to chemistry problems | docs |
| propka | Predicts pKa values of ionizable groups in proteins | github |
Deep Learning for Molecules
| Tool | Description | Link |
|---|---|---|
| DeepChem | Comprehensive ML library for chemistry and life sciences | deepchem.io |
| PyTorch Geometric | Graph neural networks framework | pyg.org |
| DGL-LifeSci | GNN library for life science applications | github |
| Chemprop | Message passing neural networks for molecular property prediction | github |
| SchNetPack | Deep neural networks for atomistic systems | github |
| DScribe | Descriptor library with various fingerprinting techniques | github |
| SELFIES | Self-Referencing Embedded Strings representation | github |
| XenonPy | Material descriptors and neural network models | github |
| TDC | Framework to access ML across therapeutics | github |
| olorenchemengine | Unified API for diverse models with uncertainty quantification | github |
| ROBERT | Ensemble of automated machine learning protocols | github |
| Summit | Package for optimizing chemical reactions using ML | github |
| chemml | ML and informatics for chemical and materials data | docs |
| atom3d | Machine learning on 3D molecular structure | github |
| DeepPurpose | Deep learning for compound and protein modeling | github |
| graphein | Geometric representations of protein/RNA structures | github |
| MORFEUS | Fast calculations of molecular features from 3D structures | github |
Quantum Chemistry & Simulations
| Tool | Description | Link |
|---|---|---|
| Psi4 | Hybrid Python/C++ package for quantum chemistry | psicode.org |
| PySCF | Quantum chemistry package in Python | github |
| GPAW | Density-functional theory Python code | docs |
| cclib | Parsing output files from quantum chemical programs | docs |
| ccinput | Creating quantum chemistry input files | github |
| cctk | DFT input generation and data extraction | github |
| basis_set_exchange | Basis sets for quantum chemistry | github |
| horton | Quantum-chemistry program for model Hamiltonians | docs |
| PyQuante | Suite of programs for quantum chemistry methods | docs |
| Psi4NumPy | Reference implementations for quantum methods | github |
| IoData | QM/MD file parser and converter | github |
| GoodVibes | Computes thermochemical data from Gaussian calculations | github |
| AQME | Ensemble of automated QM workflows | github |
| CalcUS | Quantum chemistry web platform | github |
| QMsolve | Solving and visualizing the Schrödinger equation | github |
Molecular Dynamics
| Tool | Description | Link |
|---|---|---|
| MDAnalysis | Object-oriented library to analyze MD trajectories | mdanalysis.org |
| MDTraj | Molecular dynamics trajectory manipulation | mdtraj.org |
| openmmtools | Toolkit for OpenMM molecular simulation engine | github |
| yank | GPU-accelerated alchemical free energy calculations | github |
| alchemlyb | Alchemical free energy calculations made easier | github |
| HTMD | High-Throughput Molecular Dynamics | github |
| ParmEd | Parameter/topology editor and simulator | github |
| ProDy | Protein structural dynamics analysis | prody.csb.pitt.edu |
| pyEMMA | Markov models of molecular kinetics | docs |
| QUIP | Software tools for molecular dynamics simulations | docs |
| torchmd | Molecular Dynamics Engine using PyTorch | github |
| MolMod | Molecular modeling library components | docs |
Force Fields & Potentials
| Tool | Description | Link |
|---|---|---|
| OpenFF-toolkit | Open Forcefield Toolkit for SMIRNOFF format | github |
| CHGNet | Neural network potential for atomistic modeling | github |
| FLARE | Creating fast and accurate interatomic potentials | github |
| FitSNAP | Training SNAP interatomic potentials | github |
| NeuralForceField | PyTorch-based neural network force field | github |
| acpype | Convert AMBER to GROMACS forcefields | github |
| fftool | Force field input file builder | github |
| global-chem | Chemical Knowledge Graph and Toolkit | github |
Retrosynthesis & Reactions
| Tool | Description | Link |
|---|---|---|
| aizynthfinder | Tool for retrosynthetic planning | github |
| RXNMapper | Atom mapping for reactions | github |
| rxnfp | Reaction fingerprints | github |
| cantera | Software tools for chemical kinetics, thermodynamics, transport | github |
| overreact | Microkinetic models from quantum chemistry calculations | github |
| ReNView | Reaction network visualization | github |
| pMuTT | Ab-initio thermodynamic and kinetic estimation | docs |
| pGrAdd | Thermochemical properties using group additivity | github |
Molecular Design & Generation
Generative Models
| Tool | Description | Link |
|---|---|---|
| GraphINVENT | Graph-based molecular generation | github |
| REINVENT | Reinforcement learning for molecular design | github |
| hgraph2graph | Hierarchical molecular graph generation | github |
| stk | Building, manipulating, analyzing molecules | github |
| perses | Expanded ensembles for chemical space exploration | github |
Diffusion Models
| Tool | Description | Link |
|---|---|---|
| GeoDiff | Geometric diffusion for molecular conformation | Paper |
| EDM | Equivariant diffusion for 3D molecules | Paper |
| DiffSBDD | Structure-based drug design via diffusion | github |
Benchmarks
| Tool | Description | Link |
|---|---|---|
| GuacaMol | Benchmarking for de novo molecular design | github |
| MOSES | Benchmarking platform for molecular generation | github |
Database Wrappers
| Tool | Description | Link |
|---|---|---|
| PubChemPy | Interact with PubChem in Python | docs |
| ChemSpiPy | ChemSpider wrapper for searches | docs |
| CIRpy | Chemical Identifier Resolver interface | docs |
| NistChemPy | NIST webbook data access | github |
| ChemInformant | PubChem client with caching and rate-limit awareness | github |
| chembl-downloader | Automate downloading and querying ChEMBL | github |
| drugbank-downloader | Downloading, opening, and parsing DrugBank | github |
| CCDC API | Cambridge Structural Database API | docs |
Visualization
| Tool | Description | Link |
|---|---|---|
| nglview | Jupyter widget to view molecular structures | github |
| PyMOL | Molecular visualization system | pymol.org |
| py3Dmol | 3D molecular visualization in Jupyter | github |
| chemiscope | Interactive structure/property explorer | github |
| imolecule | WebGL molecule viewer and file format converter | docs |
| chemview | Interactive molecular viewer for IPython notebook | docs |
| moleculekit | Molecule manipulation library | github |
| rdeditor | RDKit molecule editor GUI | github |
| ase-gui | Visualize, manipulate, and render molecular systems | docs |
| mols2grid | Interactive molecule grids | github |
| trident-chemwidgets | Jupyter widgets for molecular datasets | github |
Spectroscopy & Analysis
| Tool | Description | Link |
|---|---|---|
| nmrglue | Working with NMR data | github |
| nmrsim | Simulating NMR spectra and resonances | docs |
| pybaselines | Spectrum baseline fitting and correction | docs |
| spectrochempy | Spectroscopic data processing and modeling | github |
| pyvib2 | Vibrational motion and spectra analysis | docs |
| pycroscopy | Nanoscale materials imaging analysis | docs |
Drug Discovery
| Tool | Description | Link |
|---|---|---|
| oddt | Open Drug Discovery Toolkit | github |
| ProLIF | Interaction fingerprints for protein-ligand | github |
| DescriptaStorus | Descriptor computation for machine learning | github |
| MoleOOD | Robust molecular representation learning framework | github |
| TorchDrug | GNN-based drug discovery library | torchdrug.ai |
| scikit-mol | RDKit and scikit-learn bridge | github |
| MolFeat | Molecular featurization and embeddings | molfeat.datamol.io |
Virtual Screening & Docking
| Tool | Description | Link |
|---|---|---|
| AutoDock Vina | Popular open-source docking software | vina.scripps.edu |
| AutoDock-GPU | GPU-accelerated docking | github |
| DiffDock | Deep learning-based docking | github |
| Smina | Vina fork with extra scoring features | github |
| Gnina | CNN-scoring molecular docking | github |
| HADDOCK | Flexible docking suite | wenmr.science.uu.nl |
| SwissDock | Web docking for beginners | swissdock.ch |
| Meeko | Ligand/receptor preparation for docking | github |
| PLIP | Protein-ligand interaction profiler | plip-tool.biotec.tu-dresden.de |
| ZINCPharmer | Pharmacophore screening | zincpharmer.csb.pitt.edu |
| Pharmit | Interactive pharmacophore modeling | pharmit.csb.pitt.edu |
ADMET Prediction
| Tool | Description | Link |
|---|---|---|
| SwissADME | Drug-likeness and PK properties | swissadme.ch |
| pkCSM | ADMET property prediction | biosig.lab.uq.edu.au |
| ADMETlab 2.0 | PK and toxicity predictions | admetmesh.scbdd.com |
| admetSAR 2.0 | Comprehensive ADMET prediction | lmmd.ecust.edu.cn |
| ProTox-II | Toxicity predictions | tox-new.charite.de |
| ADMET-AI | ADMET prediction based on TDC data | admet.ai |
| DeepPK | DL-based pharmacokinetics | biosig.lab.uq.edu.au |
Network Pharmacology
| Tool | Description | Link |
|---|---|---|
| SwissTargetPrediction | Target prediction via similarity | swisstargetprediction.ch |
| STITCH | Chemical-protein interactions | stitch.embl.de |
| STRING | Protein-protein interaction networks | string-db.org |
| Cytoscape | Molecular interaction network visualization | cytoscape.org |
| Open Targets | Therapeutic target identification | opentargets.org |
| DisGeNET | Gene-disease associations | disgenet.com |
| PharmMapper | Reverse pharmacophore mapping | lilab-ecust.cn |
Protein Structure & Analysis
| Tool | Description | Link |
|---|---|---|
| AlphaFold DB | Predicted protein structures | alphafold.ebi.ac.uk |
| SWISS-MODEL | Homology-modeling server | swissmodel.expasy.org |
| PrankWeb | Pocket prediction and analysis | prankweb.cz |
| CavityPlus | Pocket detection and druggability | pkumdl.cn |
| DynaMut | Predicts mutation-induced stability changes | biosig.lab.uq.edu.au |
| PDBFixer | Repairs PDB files for MD simulations | github |
Molecular Dynamics Engines
| Tool | Description | Link |
|---|---|---|
| GROMACS | Fast, scalable MD engine for biomolecules | gromacs.org |
| OpenMM | GPU-accelerated MD toolkit with Python bindings | openmm.org |
| NAMD | Parallel MD engine for large biomolecular systems | ks.uiuc.edu |
| AMBER | Biomolecular simulations and free energy | ambermd.org |
| LAMMPS | Classical MD simulator for materials science | lammps.org |
Synthesis Planning
| Tool | Description | Link |
|---|---|---|
| Spaya | AI-driven retrosynthesis with route ranking | spaya.ai |
| ASKCOS | Synthesis route prediction with ML | askcos.mit.edu |
| IBM RoboRXN | Automated reaction prediction | rxn.res.ibm.com |
Awesome Lists
| List | Focus |
|---|---|
| awesome-cheminformatics | Tools & libraries |
| awesome-python-chemistry | Python tools |
| awesome-drug-discovery | Drug discovery resources |
| awesome-molecular-generation | Molecular generation papers |
| awesome-small-molecule-ml | Drug discovery papers |
| awesome-molecular-docking | Molecular docking |
Getting Started
# Install core chemistry stack
conda create -n chem python=3.10
conda activate chem
# RDKit (via conda-forge)
conda install -c conda-forge rdkit
# Additional tools
pip install datamol deepchem pubchempy