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306 search results found

Deepchem ⭐ 4,876

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

Weight Loss ⭐ 3,307

Machine Learning meets ketosis: how to effectively lose weight

Chemprop ⭐ 1,405

Message Passing Neural Networks for Molecule Property Prediction

Pyscf ⭐ 1,061

Python module for quantum chemistry

Awesome Python Chemistry ⭐ 971

A curated list of Python packages related to chemistry

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

Pythonidae ⭐ 810

Curated decibans of scientific programming resources in Python.

Chemicalx ⭐ 657

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

Chainer Chemistry ⭐ 609

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

Qiskit Aqua ⭐ 553

Quantum Algorithms & Applications (**DEPRECATED** since April 2021 - see readme for more info)

Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

⚗ A package useful for chemistry written in Python

Openchem ⭐ 450

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

Python version of the amazing Reaction Mechanism Generator (RMG).

Asciimol ⭐ 341

Curses based ASCII molecule viewer for terminals.

Pubchempy ⭐ 315

Python wrapper for the PubChem PUG REST API.

Awesome Materials Informatics ⭐ 310

Curated list of known efforts in materials informatics = modern materials science

Psi4numpy ⭐ 306

Combining Psi4 and Numpy for education and development.

Chembl_webresource_client ⭐ 303

Official Python client for accessing ChEMBL API

Parsers and algorithms for computational chemistry logfiles

Guacamol ⭐ 265

Benchmarks for generative chemistry

Universal cheminformatics toolkit, utilities and database search tools

Research using Cirq!

Lightdock ⭐ 234

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Manipulating VASP files with Python.

Rxnmapper ⭐ 215

RXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/content/7/15/eabe

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

Geopytool ⭐ 212

An application based on Python and designed as a solution for geology related daily work.

Objective-Reinforced Generative Adversarial Networks (ORGAN) for Sequence Generation Models

Moleculartransformer ⭐ 190

Tensormol ⭐ 190

Tensorflow + Molecules = TensorMol

Torsional Diffusion ⭐ 183

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

Orthopy ⭐ 179

📐 Orthogonal polynomials in all shapes and sizes.

OPEM (Open Source PEM Fuel Cell Simulation Tool)

Chemlab ⭐ 173

The chemistry library you were waiting for

Smiles Transformer ⭐ 154

Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.

Chemics ⭐ 151

A Python package for chemical engineering

Reinvent4 ⭐ 150

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

Scicompforchemists ⭐ 149

Scientific Computing for Chemists text for teaching basic computing skills to chemistry students using Python, Jupyter notebooks, and the SciPy stack. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, NMRglue, SymPy, scikit-image, and scikit-learn.

Rxn4chemistry ⭐ 147

Python wrapper for the IBM RXN for Chemistry API

Software Development ⭐ 145

A primer on software development best practices for computational chemistry

Qcengine ⭐ 141

Quantum chemistry program executor and IO standardizer (QCSchema).

Pyquante2 ⭐ 139

Python Quantum Chemistry Reloaded. This is a rewrite of the standard PyQuante program to clean up things that have been nagging me.

quacc is a flexible platform for computational materials science and quantum chemistry that is built for the big data era.

Basis_set_exchange ⭐ 133

A repository for quantum chemistry basis sets

Molecular Design Toolkit ⭐ 131

Notebook-integrated tools for molecular simulation and visualization

The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

Qcelemental ⭐ 126

Periodic table, physical constants, and molecule parsing for quantum chemistry.

Ase_ani ⭐ 126

ANI-1 neural net potential with python interface (ASE)

Chemdataextractor ⭐ 112

Automatically extract chemical information from scientific documents

Pyrolite ⭐ 109

A set of tools for getting the most from your geochemical data.

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

Panel Chemistry ⭐ 102

🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.

Spectrochempy ⭐ 102

SpectroChemPy is a framework for processing, analyzing and modeling spectroscopic data for chemistry with Python

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

Animation engine for explanatory chemistry videos

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

Rmg Database ⭐ 91

The database of chemical parameters used with Reaction Mechanism Generator

Simple package for fast molecular similarity searches

Matbench ⭐ 88

Matbench: Benchmarks for materials science property prediction

Chemspipy ⭐ 85

Python wrapper for the ChemSpider API

Benchmark Suite for Machine Learning Interatomic Potentials for Materials

Molscribe ⭐ 83

Robust Molecular Structure Recognition with Image-to-Graph Generation

A python package for Abel and inverse Abel transforms

Tools developed for running end-to-end chemistry workflows on quantum computers and simulators.

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

Celescope ⭐ 73

Single Cell Analysis Pipelines

Pysisyphus ⭐ 73

Python suite for optimization of stationary points on ground- and excited states PES and determination of reaction paths.

Qcschema ⭐ 72

A Schema for Quantum Chemistry

Ani1_dataset ⭐ 71

A data set of 20 million calculated off-equilibrium conformations for organic molecules

Simplifying the discovery and usage of machine-learning ready datasets in materials science and chemistry

Yesterday I Learned ⭐ 69

Brainfarts are caused by the rupturing of the cerebral sphincter.

SchNet - a deep learning architecture for quantum chemistry

Reaction Network ⭐ 67

Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by @mattmcdermott (Lawrence Berkeley National Lab).

Periodic_trends ⭐ 67

Python script to plot periodic trends as a heat map over the periodic table of elements

extract and tweak data from electrochemical tests of cells

Pybaselines ⭐ 66

A Python library of algorithms for the baseline correction of experimental data.

ML4Chem: Machine Learning for Chemistry and Materials

Faerun Python ⭐ 64

A python module for generating interactive views of chemical spaces.

Computational_chemistry ⭐ 63

Files used in TMP Chem videos on computational chemistry

MolCalc is a web interface that allows anyone to build molecules and calculate molecular properties online

Chemcoord ⭐ 58

A python module for manipulating cartesian and internal coordinates.

Xyz2graph ⭐ 58

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

Molecule Validation and Standardization

Python wrapper for the NCI Chemical Identifier Resolver (CIR)

Mcmurchie Davidson ⭐ 54

do a simple closed shell Hartree-Fock using McMurchie-Davidson to compute integrals

Py4chemoinformatics ⭐ 53

Python for chemoinformatics

Chemicaljson ⭐ 53

Development of the Chemical JSON data representation

Electronvisualized ⭐ 53

Public Archive: Beautiful and Elegant Quantum Mechanics Visualization.

Kallisto ⭐ 50

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

The SHARC molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.

Bayesgrad ⭐ 48

BayesGrad: Explaining Predictions of Graph Convolutional Networks

Python toolkit for GEOS-Chem. Contains basic plotting scripts, plus the suite of GEOS-Chem benchmarking utilities.

Tencirchem ⭐ 45

Quantum computational chemistry based on TensorCircuit

Document and code of python and PySCF approach XYG3 type of density functional 2nd-derivative realization

Graph Nvp ⭐ 44

GraphNVP: An Invertible Flow Model for Generating Molecular Graphs

Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over searching structure/activity relationships (SAR) derived from large datasets, and takes the form of an accessible web application with simple deployment. Matcher is built around the mmpdb platform.

This library tackles the construction and efficient execution of computational chemistry workflows

Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

Moldqn Pytorch ⭐ 40

A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".

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