Ecosyste.ms: Awesome
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awesome-python-chemistry
https://github.com/2lambda123/awesome-python-chemistry
Last synced: 6 days ago
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Table of contents
- Awesome Python Chemistry ![Awesome - python-chemistry-)
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General Chemistry
- aizynthfinder - A tool for retrosynthetic planning.
- 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).
- 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 - The Computational Crystallography Toolbox.
- chemlib - A robust and easy-to-use package that solves a variety of chemistry problems.
- LModeA-nano - Calculates the intrinsic chemical bond strength based on local vibrational mode theory in solids and molecules.
- Open Babel - A chemical toolbox designed to speak the many languages of chemical data.
- pybel - Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python.
- pycroscopy - Scientific analysis of nanoscale materials imaging data.
- pyEQL - A set of tools for conventional calculations involving solutions (mixtures) and electrolytes.
- symfit - a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data.
- GoodVibes - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.
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Molecular Visualization
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Force Fields
- PyMOL - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
- ase-gui - The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects.
- pymoldyn - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices.
- sumo - A toolkit for plotting and analysis of ab initio solid-state calculation data.
- surfinpy - A library for the analysis, plotting and visualisation of ab initio surface calculation data.
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Simulations
- Atomic Silumation Environment (ASE) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
- CACTVS - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.
- cclib - A library for parsing output files various quantum chemical programs.
- cinfony - A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices).
- GPAW - Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
- horton - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians.
- mathchem - Is a free open source package for calculating topological indices and other invariants of molecular graphs.
- MolMod - A library with many components that are useful to write molecular modeling programs.
- ProDy - An open source package for protein structural dynamics analysis with a flexible and responsive API.
- pyEMMA - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data.
- pygauss - An interactive tool for supporting the life cycle of a computational molecular chemistry investigations.
- phonopy - An open source package for phonon calculations at harmonic and quasi-harmonic levels.
- RDKit - Open-Source Cheminformatics Software.
- tsase - The library which depends on ASE to tackle transition state calculations.
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Learning Resources
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Force Fields
- Computational Thermodynamics - 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.
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Database Wrappers
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Force Fields
- ccdc - An API for the Cambridge Structural Database System.
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Miscellaneous Awesome
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Force Fields
- Colorful Nuclide 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.
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See Also
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Force Fields
- awesome-cheminformatics
- jarvis - field, density functional theory, machine learning calculations and experiments.
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Programming Languages
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Keywords
awesome
2
awesome-list
2
cheminformatics
2
chemistry
2
zero-point-energy
1
vibrational-frequencies
1
lists
1
resources
1
unicorns
1
astrazeneca
1
chemical-reactions
1
thermochemistry
1
monte-carlo-tree-search
1
neural-networks
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reaction-informatics
1
chemical-formulas
1
chemicals
1
quantum-chemistry
1
chemistry-database
1
chemistry-formulas
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python
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python-library
1
python-module
1
bioinformatics
1
gaussian
1
orca
1