The Wayback Machine - https://web.archive.org/web/20220327065615/https://github.com/topics/molecules

#

molecules

Here are 75 public repositories matching this topic...

rasbt / biopandas

Sponsor

Working with molecular structures in pandas DataFrames

bioinformatics pdb molecular-structures pandas-dataframe protein-structure molecule computational-biology drug-discovery molecules mol2 pdb-files

Updated Mar 19, 2022
Python

dewberryants / asciiMol

Curses based ASCII molecule viewer for linux terminals.

visualization chemistry cheminformatics ascii molecules

Updated Mar 23, 2022
Python

jparkhill / TensorMol

Tensorflow + Molecules = TensorMol

machine-learning neural-network chemistry simulation tensorflow monte-carlo molecular-dynamics molecular-simulation force-field molecules meta-dynamics

Updated Feb 11, 2021
Python

gnn-lspe

vijaydwivedi75 / gnn-lspe

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

graphs transformers attention representation-learning molecules message-passing lspe geometric-deep-learning graph-neural-networks graph-representation-learning gnn graph-deep-learning positional-encoding graph-transformer transformer-networks gnn-lspe

Updated Feb 10, 2022
Python

pcko1 / Deep-Drug-Coder

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

neural-network drug-discovery molecules autoencoders lstm-neural-networks denovo-design smiles-strings

Updated Feb 9, 2022
Python

HannesStark / EquiBind

Open

Potential improvement through avoiding DGL TensorDispatcher error

1

PatWalters commented Feb 28, 2022

I encountered this error when running Equibind.

/opt/dgl/src/runtime/tensordispatch.cc:43: TensorDispatcher: dlopen failed: libtorch_cuda.so: cannot open shared object file: No such file or directory

According to this https://discuss.dgl.ai/t/error-tensordispatcher/2468 the error impacts performance but does not impact usage. Equibind appears to run in spite of this error. I thought you m

Read more

good first issue

datamol-org / datamol

Molecular Manipulation Made Easy.

python cheminformatics molecule drug-discovery rdkit drug-design molecules medicinal-chemistry

Updated Mar 23, 2022
Python

ScaffoldGraph

UCLCheminformatics / ScaffoldGraph

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

fragments chemistry cheminformatics networkx computational-chemistry rdkit molecules scaffolds murcko scaffold-networks scaffold-trees hiers

Updated Jan 27, 2022
Python

senya-ashukha / simple-equivariant-gnn

A short and easy PyTorch implementation of E(n) Equivariant Graph Neural Networks

deep-neural-networks deep-learning pytorch neural-networks homo molecules graph-neural-networks gnn equivariance qm9 egnn

Updated Jan 14, 2022
Python

samirelanduk / atomium

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

chemistry biology proteins structural-biology molecules

Updated Mar 11, 2022
Python

HannesStark / 3DInfomax

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

graph molecules 3d graph-neural-networks self-supervised-learning graph-representation-learning pytorch-geometric gnn dgl-graph

Updated Jan 31, 2022
Python

khavernathy / mcmd

Monte Carlo and Molecular Dynamics Simulation Package

crystal chemistry atomic pdb physics monte-carlo molecular-dynamics molecular-simulation molecular-dynamics-simulation monte-carlo-simulation crystal-structure physics-simulation molecules monte-carlo-simulations gas-model gas-dynamics xyz periodicity polarization nvt

Updated Apr 21, 2021
C++

Avogadro / avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

visualization windows linux mac qt chemistry molecules

Updated Sep 11, 2021
C++

PDN

benedekrozemberczki / PDN

Sponsor

The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)

Updated Mar 2, 2022
Python

aimat-lab / gcnn_keras

Graph convolution with tf.keras

machine-learning graph-algorithms graphs neural-networks networks molecules keras-tensorflow graph-networks graph-convolution tensorflow2 ragged-tensors

Updated Mar 4, 2022
Jupyter Notebook

arpitnarechania / d3-molecule

D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.

javascript d3 open-source chemoinformatics molecules interactive-visualizations atoms-in-molecules chemical-bonding

Updated Mar 1, 2018
HTML

lucidrains / molecule-attention-transformer

Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules

deep-learning transformers artificial-intelligence molecules

Updated Dec 2, 2020
Python

lukasturcani / stk-vis

Sponsor

A cross-platform application for visualization of molecular databases.

visualization database mongodb chemistry cheminformatics molecular-structures data-visualization molecules molecular-modeling

Updated Mar 25, 2022
PureScript

wednesday-solutions / react-native-template

An enterprise react-native template application showcasing - Testing strategy, Global state management, middleware support, a network layer, component library integration, localization, navigation configuration and CI

react redux javascript react-native eslint redux-saga es6 architecture atoms molecules scenes saga reduxsauce apisauce

Updated Mar 26, 2022
JavaScript

PanMig / Chemistry-Lab

A 3D first person serious game, aiming to teach player about molecules through an immersive and fun way.

game unity3d molecules serious-game chemistry-lab

Updated Sep 25, 2018
C#

aacgn / atomic

A JavaScript library for building atomic interfaces with vertical and horizontal micro-frontends

javascript virtual-dom vuejs angular reactjs atoms molecules postmessage dom-events micro-frontends single-spa micro-frontend transition-page atomic-template

Updated Jul 26, 2020
JavaScript

allthings / elements

Open

ButtonGroups' view has wrong direction value

janrembold commented Sep 9, 2019

https://github.com/allthings/elements/blob/master/src/molecules/ButtonGroup.jsx#L34
Should be direction="row"...

Read more

bug good first issue

lukasturcani / moldoc

Sponsor

Make better chemistry documentation.

visualization documentation chemistry cheminformatics molecules sphinx-extension

Updated Aug 5, 2021
Python

peterbjorgensen / msgnet

Tensorflow implementation of message passing neural networks for molecules and materials

machine-learning tensorflow graphs materials-science molecules

Updated Mar 9, 2020
Python

duboviy / pymolecule

Molecular viewer [Work in progress]

atom molecular-structures molecule molecular-graphics openbabel molecules pyglet atoms-in-molecules pybel

Updated Apr 26, 2020
Python

icanswim / qchem

An exploration of the state of the art in the application of datascience to quantum chemistry.

machine-learning models quantum-mechanics pytorch datascience quantum-chemistry datasets molecules

Updated Jan 13, 2022
Jupyter Notebook

sbcblab / confid

ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories

molecular-dynamics drug-design molecules conformational-characterization

Updated Dec 20, 2020
Python

urbi-mobility / react-native-urbi-ui

Design system in use by Urbi's React Native app

typescript react-native molecules design-system showcases

Updated Mar 24, 2022
TypeScript

leonardopicchiami / molecular_synthesis_and_reconstruction

Deep Learning And Applied Artificial Intelligence Project 2019/2020 - Molecular Synthesis & Reconstruction

python machine-learning deep-learning pytorch colab vae synthesis reconstruction molecules deep-generative-model molecule-generation vae-pytorch molecular-generation

Updated Aug 31, 2021
Jupyter Notebook

andrewtarzia / mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

chemistry rdkit high-throughput molecules molecular-size

Updated Jan 17, 2022
TeX

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