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367 search results found

Rdkit ⭐ 2,323

The official sources for the RDKit library

Chemprop ⭐ 1,405

Message Passing Neural Networks for Molecule Property Prediction

Pymatgen ⭐ 1,254

Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.

Coronavirus ⭐ 1,108

Folding@home COVID-19 efforts

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

Molecularnodes ⭐ 729

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Selfies ⭐ 574

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

Dgl Lifesci ⭐ 558

Python package for graph neural networks in chemistry and biology

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

Ansible Node Exporter ⭐ 503

Provision basic metrics exporter for prometheus monitoring tool

Keras Molecules ⭐ 448

Autoencoder network for learning a continuous representation of molecular structures.

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

Datamol ⭐ 423

Molecular Processing Made Easy.

Asciimol ⭐ 341

Curses based ASCII molecule viewer for terminals.

Equibind ⭐ 321

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Graphinvent ⭐ 312

Graph neural networks for molecular design.

Deepqmc ⭐ 308

Deep learning quantum Monte Carlo for electrons in real space

Chembl_webresource_client ⭐ 303

Official Python client for accessing ChEMBL API

Guacamol ⭐ 265

Benchmarks for generative chemistry

ATOM3D: tasks on molecules in three dimensions

Ansible Dockerswarm ⭐ 222

Docker Engine clustering using "Swarm Mode" and Ansible

Rl_graph_generation ⭐ 216

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

Geodiff ⭐ 211

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

Equiformer Pytorch ⭐ 207

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

Constrained Graph Variational Autoencoder ⭐ 203

Sample code for Constrained Graph Variational Autoencoders

Datacollect ⭐ 198

A collection of tools to collect and download various data.

Cctbx_project ⭐ 197

Computational Crystallography Toolbox

Tensormol ⭐ 190

Tensorflow + Molecules = TensorMol

Moleculartransformer ⭐ 190

Grammarvae ⭐ 189

Code for the "Grammar Variational Autoencoder" https://arxiv.org/abs/1703.01925

Moltemplate ⭐ 186

A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies

Ansible Role Bootstrap ⭐ 184

Prepare your system to be managed by Ansible.

Moleculekit ⭐ 183

MoleculeKit: Your favorite molecule manipulation kit

Torsional Diffusion ⭐ 183

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

Openmmforcefields ⭐ 182

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

Multi-View Spectral Graph Convolution with Consistent Edge Attention for Molecular Modeling

Espaloma ⭐ 181

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

Descriptastorus ⭐ 170

Descriptor computation(chemistry) and (optional) storage for machine learning

A hierarchical, component based molecule builder

Hgraph2graph ⭐ 151

Hierarchical Generation of Molecular Graphs using Structural Motifs

Molecule Vagrant ⭐ 145

🚧 Moved to molecule-plugins

Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Fragmenstein ⭐ 139

Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

Qcelemental ⭐ 126

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

band plot using python matplotlib

Molecule Autoencoder ⭐ 119

A project to enable optimization of molecules by transforming them to and from a continuous representation.

Guacamol_baselines ⭐ 117

Baselines models for GuacaMol benchmarks

Pysmiles ⭐ 117

A lightweight python-only library for reading and writing SMILES strings

Mol Instructions ⭐ 116

Mol-Instructions is a Large-Scale Biomolecules Instruction Dataset for Large Language Models.

Crystaltoolkit ⭐ 116

Crystal Toolkit is a framework for building web apps for materials science and is currently powering the new Materials Project website.

Deep Molecular Optimization ⭐ 115

Molecular optimization by capturing chemist’s intuition using the Seq2Seq with attention and the Transformer

Smiles Enumeration ⭐ 115

SMILES enumeration for QSAR modelling using LSTM recurrent neural networks

Gnn Lspe ⭐ 114

Source code for GNN-LSPE (Graph Neural Networks with Learnable Structural and Positional Representations), ICLR 2022

ASAP is a package that can quickly analyze and visualize datasets of crystal or molecular structures.

QML: Quantum Machine Learning

Vmd Python ⭐ 108

Installable VMD as a python module

Polyply_1.0 ⭐ 103

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

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.

Beautiful Atoms ⭐ 102

Python module for drawing and rendering beautiful atoms and molecules using Blender.

G Schnet ⭐ 101

G-SchNet - a generative model for 3d molecular structures

Openshift Applier ⭐ 99

Used to apply OpenShift objects to an OpenShift Cluster

Multiobj Rationale ⭐ 98

Multi-Objective Molecule Generation using Interpretable Substructures (ICML 2020)

Bioblender ⭐ 98

AddOn for Blender to do molecular work

Chatdrug ⭐ 96

LLM for Drug Editing, ICLR 2024

Ansible Role Visual Studio Code ⭐ 96

Ansible role for installing the Visual Studio Code IDE

Nanocar Avogadro ⭐ 95

Nanocar builder Avogadro 2 plug-in

Ansible Later ⭐ 94

Another best practice scanner for Ansible roles and playbooks

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

New ASE compliant Python interface to VASP

Transformer M ⭐ 90

[ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)

Rd_filters ⭐ 89

A script to run structural alerts using the RDKit and ChEMBL

Molecule Ansible Docker Aws ⭐ 88

Example project showing how to test Ansible roles with Molecule using Testinfra and a multiscenario approach with Docker, Vagrant & AWS EC2 as infrastructure providers

Ansible Role Promtail ⭐ 87

🔧 Ansible role for deploying promtail

Quantum Mechanical Bespoke Force Field Derivation Toolkit

Molscribe ⭐ 83

Robust Molecular Structure Recognition with Image-to-Graph Generation

Molecule Design using Monte Carlo Tree Search with Neural Rollout

Pairtools ⭐ 78

CLI tools to process mapped Hi-C data

Protein Science ⭐ 76

A collection of useful tutorials for Protein Science

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

Molecule Docker ⭐ 75

Molecule Docker Driver allows molecule users to test Ansible code using docker containers.

Deep Drug Coder ⭐ 75

A tensorflow.keras generative neural network for de novo drug design, published in Nature Machine Intelligence while working at AstraZeneca.

Implementation of "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyTorch Geometric

Molecule Chef ⭐ 72

Code for our paper "A Model to Search for Synthesizable Molecules" (https://arxiv.org/abs/1906.05221)

Ani1_dataset ⭐ 71

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

Robocrystallographer ⭐ 70

Automatic generation of crystal structure descriptions.

Opencadd ⭐ 70

A Python library for structural cheminformatics

Molecular MHFP fingerprints for cheminformatics applications

The Photoswitch Dataset ⭐ 68

Repository containing a benchmark dataset for machine learning property prediction of photoswitch molecules: https://pubs.rsc.org/en/content/articlehtml/2022/s

Gillespy2 ⭐ 66

Modeling toolkit for biochemical simulation

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

Awesome Deep Learning 4 Life Sciences ⭐ 65

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

3dinfomax ⭐ 64

Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.

Code and pre-trained models for the paper "Domain-Agnostic Molecular Generation with Self-feedback."

Deep Molecular Massspec ⭐ 63

Mass Spectrometry for Small Molecules using Deep Learning

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

Pyfingerprint ⭐ 60

Python tool for generate fingerprints of a molecule

Ansible Blackbox Exporter ⭐ 60

Blackbox prober exporter

Ansible Repertory ⭐ 59

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