Python Libraries for Atoms, Molecules, and Chemical Analysis

 

Atomic & Molecular Modeling Libraries

1. ASE (Atomic Simulation Environment)
   Used for atomistic simulations, crystal structures, and molecular modeling.
   ASE
2. PySCF
   Quantum chemistry calculations and electronic structure simulations.
   PySCF
3. Psi4
   Open-source quantum chemistry software.
   Psi4
4. RDKit
   Molecular informatics, cheminformatics, fingerprints, SMILES handling.
   RDKit
5. Open Babel
   Chemical file conversion and molecular data processing.
   Open Babel
6. MDAnalysis
   Molecular dynamics trajectory analysis.
   MDAnalysis
7. ParmEd
   Molecular mechanics parameter editing library.
   ParmEd
8. PyMOL API
   Molecular visualization and protein rendering.
   PyMOL
9. Pybel
   Python wrapper for Open Babel.
   Pybel
10. Atomic Simulation Recipes (ASR)
    Workflow tools for atomistic simulations.
    ASR

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Chemistry & Cheminformatics Libraries

11. PubChemPy
    Access chemical compound data from PubChem.
    PubChemPy
12. mendeleev
    Periodic table data and element properties.
    mendeleev
13. periodictable
    Element/isotope data handling.
    periodictable
14. ChemPy
    Chemical reactions, kinetics, equilibrium calculations.
    ChemPy
15. Cantera
    Thermodynamics, combustion, and chemical kinetics.
    Cantera
16. PyMatGen
    Materials analysis and crystal structure computations.
    pymatgen
17. cclib
    Parses computational chemistry log files.
    cclib
18. Autode
    Automated reaction mechanism calculations.
    Autode
19. DeepChem
    AI + deep learning for chemistry and drug discovery.
    DeepChem
20. PyRx
    Virtual screening and molecular docking.
    PyRx

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Chemical Engineering & Industrial Libraries

21. thermo
    Chemical thermodynamics and property calculations.
    thermo
22. CoolProp
    Thermophysical properties for fluids.
    CoolProp
23. fluids
    Fluid dynamics and pipe flow calculations.
    fluids
24. IDAES-PSE
    Process systems engineering platform.
    IDAES
25. DWSIM Python API
    Chemical process simulation automation.
    DWSIM
26. Pyomo
    Optimization for chemical process engineering.
    Pyomo
27. Biosteam
    Techno-economic simulation for bioprocess industries.
    Biosteam
28. scikit-chem
    Machine learning + cheminformatics utilities.
    scikit-chem
29. PyEQL
    Electrolyte equilibrium calculations.
    PyEQL
30. Reaction Mechanism Generator (RMG)
    Automatically generates chemical reaction mechanisms.
    RMG

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Visualization & Molecular Graphics

31. nglview
    Jupyter molecular visualization widget.
    nglview
32. py3Dmol
    3D molecular visualization in notebooks.
    py3Dmol
33. VMD Python
    Molecular visualization and analysis.
    VMD
34. Mayavi
    Scientific 3D visualization for molecular data.
    Mayavi
35. Plotly Chemistry Visualizations
    Interactive scientific plotting.
    Plotly

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AI, Drug Discovery & Materials Science

36. TorchDrug
    Deep learning framework for molecular graphs.
    TorchDrug
37. DGL-LifeSci
    Graph neural networks for chemistry and biology.
    DGL-LifeSci
38. MolSSI QCArchive
    Quantum chemistry data ecosystem.
    QCArchive
39. Schrodinger Python API
    Drug discovery and molecular simulations.
    Schrodinger
40. OpenMM
    High-performance molecular dynamics simulations.
    OpenMM