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Molecule

Molecule is designed to aid in the development and testing of Ansible roles.

Molecule provides support for testing with multiple instances, operating systems and distributions, virtualization providers, test frameworks, and testing scenarios.

Molecule encourages an approach that results in consistently developed roles that are well-written, easily understood and maintained.

https://github.com/awslabs/dgl-lifesci

Python package for graph neural networks in chemistry and biology

bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule

Last synced: 20 Dec 2024

https://github.com/charnley/rmsd

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

alignment assignment atoms kabsch molecule pdb reordering rmsd structure xyz

Last synced: 20 Dec 2024

https://github.com/cloudalchemy/ansible-node-exporter

Provision basic metrics exporter for prometheus monitoring tool

ansible collector metrics metrics-gathering molecule prometheus-exporter tox

Last synced: 26 Sep 2024

https://github.com/ansible/vscode-ansible

vscode/vscodium extension for providing Ansible auto-completion and integrating quality assurance tools like ansible-lint, ansible syntax check, yamllint, molecule and ansible-test.

ansible-dev-tools ansible-language-server ansible-lint hack hacktoberfest lsp molecule taskfile vscode-extension

Last synced: 16 Dec 2024

https://github.com/minkaixu/geodiff

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

computational-biology computational-chemistry conformation diffusion-models generative-models graph-neural-networks iclr iclr2022 molecule score-matching

Last synced: 16 Dec 2024

https://github.com/MinkaiXu/GeoDiff

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

computational-biology computational-chemistry conformation diffusion-models generative-models graph-neural-networks iclr iclr2022 molecule score-matching

Last synced: 28 Nov 2024

https://github.com/lambdacasserole/avogadrio

Worship your favorite molecule by setting it as your wallpaper.

api chemical molecule php wallpaper

Last synced: 17 Dec 2024

https://github.com/atosatto/ansible-dockerswarm

Docker Engine clustering using "Swarm Mode" and Ansible

ansible docker docker-swarm molecule swarm-mode

Last synced: 23 Dec 2024

https://github.com/hicai-zju/scientific-llm-survey

Scientific Large Language Models: A Survey on Biological & Chemical Domains

cell genome large-language-models llms molecule multimodal protein sci-llm science-research scientific-languages survey text

Last synced: 17 Dec 2024

https://github.com/yuyangw/molclr

Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.

deep-learning graph-neural-networks molecule pytorch pytorch-geometric self-supervised-learning

Last synced: 17 Dec 2024

https://github.com/partridgejiang/kekule.js

A Javascript cheminformatics toolkit.

cheminformatics chemistry javascript molecule

Last synced: 22 Dec 2024

https://github.com/mojaie/moleculargraph.jl

Graph-based molecule modeling toolkit for cheminformatics

cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit

Last synced: 23 Dec 2024

https://github.com/lsj2408/transformer-m

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

general-purpose-molecular-model graph-neural-network graph-transformer molecular-modeling molecule transformer

Last synced: 09 Oct 2024

https://github.com/robertdebock/ansible-role-bootstrap

Prepare your system to be managed by Ansible.

ansible bootstrap molecule playbook python sudo system tox

Last synced: 17 Dec 2024

https://github.com/Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins

Last synced: 16 Nov 2024

https://github.com/acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins

Last synced: 21 Dec 2024

https://github.com/mojaie/MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit

Last synced: 30 Oct 2024

https://github.com/chao1224/GraphMVP

Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)

contrastive-learning generative-model geometry graph molecule pretraining self-supervised self-supervised-learning

Last synced: 16 Nov 2024

https://github.com/chao1224/graphmvp

Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)

contrastive-learning generative-model geometry graph molecule pretraining self-supervised self-supervised-learning

Last synced: 09 Oct 2024

https://github.com/rdkit/rdkit-js

A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .

cheminformatics drug-discovery javascript molecule molecule-viewer molecule-visualization node-js npm rdkit react wasm

Last synced: 21 Dec 2024

https://github.com/thomas0809/molscribe

Robust Molecular Structure Recognition with Image-to-Graph Generation

chemistry deep-learning molecule

Last synced: 22 Dec 2024

https://github.com/tsudalab/chemts

Molecule Design using Monte Carlo Tree Search with Neural Rollout

molecule

Last synced: 09 Oct 2024

https://github.com/beautiful-atoms/beautiful-atoms

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

3d ase atomic atoms blender crystal molecule protein pymatgen python rendering ribbon-diagram

Last synced: 17 Dec 2024

https://github.com/grafana/grafana-ansible-collection

grafana.grafana Ansible collection provides modules and roles for managing various resources on Grafana Cloud and roles to manage and deploy Grafana Agent and Grafana

ansible ansible-collection ansible-galaxy ansible-role development devops grafana infrastructure-as-code molecule monitoring observability opentelemetry opentelemetry-collector python scaling yarn

Last synced: 17 Dec 2024

https://github.com/dj-wasabi/ansible-telegraf

Installing and configuring Telegraf via Ansible for RedHat/Debian/Ubuntu/Windows/Suse.

ansible influxdb metrics molecule telegraf tsdb

Last synced: 22 Dec 2024

https://github.com/lab-cosmo/chemiscope

An interactive structure/property explorer for materials and molecules

hacktoberfest materials-science molecule visualization web

Last synced: 21 Dec 2024

https://github.com/sleighzy/ansible-kafka

Ansible role for installing and configuring Apache Kafka on RedHat and Debian platforms.

ansible ansible-galaxy ansible-role centos debian kafka molecule redhat rhel

Last synced: 20 Dec 2024

https://github.com/aamini/chemprop

Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.

active-learning bayesian-optimization chemistry drug-discovery evidential-deep-learning molecule neural-network uncertainty virtual-screening

Last synced: 09 Oct 2024

https://github.com/molstar/vscoding-sequence

VSCode Extension for interactively visualising protein structure data in the editor

molecule molstar pdb pdb-files protein protein-structure structural-biology structure vscode vscode-extension

Last synced: 16 Dec 2024

https://github.com/glambard/molecules_dataset_collection

Collection of data sets of molecules for a validation of properties inference

classification dataset inference machine-learning molecule moleculenet properties rdkit smiles

Last synced: 09 Oct 2024

https://github.com/jonashackt/molecule-ansible-docker-aws

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

amazon-web-services ansible ansible-role ansible-test aws aws-ec2 circleci circleci2 docker docker-installation molecule pytest python testinfra travis-ci vagrant virtualbox

Last synced: 16 Dec 2024

https://github.com/sleighzy/ansible-zookeeper

Ansible role for installing and configuring Apache ZooKeeper

ansible ansible-galaxy ansible-role debian molecule redhat rhel zookeeper

Last synced: 21 Dec 2024

https://github.com/osu-nlp-group/llm4chem

Official code repo for the paper "LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset"

ai4science chemistry llms molecule

Last synced: 18 Dec 2024

https://github.com/geerlingguy/molecule-playbook-testing

This is an example from the Ansible 101 livestream

ansible ansible-101 example github-actions molecule

Last synced: 09 Oct 2024

https://github.com/deepgraphlearning/diffpack

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

deep-learning diffusion-models molecule protein-structure score-based-generative-modeling score-matching

Last synced: 09 Oct 2024

https://github.com/geerlingguy/docker-ubuntu2204-ansible

Ubuntu 22.04 LTS (Jammy Jellyfish) Docker container for Ansible playbook and role testing.

ansible docker jammy-jellyfish molecule testing ubuntu

Last synced: 09 Oct 2024

https://github.com/autodesk/molecule-3d-for-react

3D molecular visualization React component using 3Dmol.js

3d molecule react webgl

Last synced: 01 Nov 2024

https://github.com/robertdebock/ansible-role-fail2ban

Install and configure fail2ban on your system.

ansible fail2ban installer molecule package playbook security tox

Last synced: 16 Dec 2024

https://github.com/mcellteam/cellblender

Create, Simulate, Visualize, and Analyze Realistic 3D Cell Models

blender mcell molecule

Last synced: 09 Oct 2024

https://github.com/robertdebock/ansible-role-dns

Install and configure dns on your system.

ansible bind dns molecule named networking playbook resolving system tox

Last synced: 17 Dec 2024

https://github.com/aromanro/hartreefock

A program implementing the Hartree–Fock (also post-HF: MP2, CCSD(T), CIS and TDHF/RPA)/self-consistent field method (also DIIS) with Gaussian orbitals

atom computational-chemistry computational-physics eigen gaussian gdi-plus hartree-fock mfc molecule orbital physics quantum quantum-chemistry quantum-chemistry-programs quantum-mechanics self-constent-field

Last synced: 18 Dec 2024

https://github.com/gantsign/development-environment

A development environment for Java, Python and Node.js built using Vagrant

ansible intellij java maven molecule nodejs oh-my-zsh vagrant virtualbox vscode

Last synced: 17 Dec 2024

https://github.com/lmdu/dockey

an integrated tool for molecular docking and virtual screening

docking ligand molecular molecule receptor

Last synced: 18 Dec 2024

https://github.com/ansible/tox-ansible

The tox-ansible plugin dynamically creates a full matrix of python interpreter and ansible-core version environments for running integration, sanity, and unit for an ansible collection both locally and in a Github action. tox virtual environments are leveraged for collection building, collection installation, dependency installation, and testing.

ansible ansible-dev-tools ansible-devtools molecule molecule-plugin tox-environment tox-plugin

Last synced: 16 Dec 2024

https://github.com/gofrolist/molecule-action

GitHub Action for running molecule as part of your workflows!

ansible molecule

Last synced: 22 Dec 2024

https://github.com/MinkaiXu/ConfVAE-ICML21

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming (ICML'21)

bilevel-optimization computational-biology computational-chemistry conformation generative-models graph-neural-networks icml-2021 molecule pytorch vae

Last synced: 28 Nov 2024

https://github.com/chem4word/version3

Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word

addin cheminformatics chemistry microsoft-office microsoft-word molecule openxml openxml-sdk structure

Last synced: 09 Oct 2024

https://github.com/ansible-community/molecule-ec2

🚧 Migrated inside molecule-plugins

ansible hacktoberfest molecule molecule-driver

Last synced: 26 Sep 2024

https://github.com/minkaixu/confvae-icml21

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming (ICML'21)

bilevel-optimization computational-biology computational-chemistry conformation generative-models graph-neural-networks icml-2021 molecule pytorch vae

Last synced: 09 Oct 2024

https://github.com/robertdebock/ansible-role-logrotate

Install and configure logrotate on your system.

ansible logrotate molecule monitoring playbook system tox

Last synced: 17 Dec 2024

https://github.com/robertdebock/ansible-role-tomcat

Install and configure tomcat on your system.

ansible molecule playbook system tomcat tox

Last synced: 23 Dec 2024

https://github.com/keiserlab/keras-neural-graph-fingerprint

Keras implementation of Neural Graph Fingerprints as proposed by Duvenaud et al., 2015

atom differentiable-models fingerprint gpu graph graph-algorithms keras molecule morgan-fingerprints neural-networks tensor

Last synced: 09 Oct 2024

https://github.com/makeitworkpress/wp-components

A library of the most common WordPress components, useful for theme and plugin development.

atom components-library molecule php wordpress wordpress-components wordpress-development wordpress-plugin wordpress-theme wp-components

Last synced: 10 Oct 2024

https://github.com/uoi-io/ansible-haproxy

Ansible HAproxy role for Unified OpenStack Installer and others.

ansible ansible-playbook galaxy haproxy load-balancer loadbalancer loadbalancing molecule playbook role

Last synced: 23 Dec 2024

https://github.com/minkaixu/cgcf-confgen

:test_tube: Learning Neural Generative Dynamics for Molecular Conformation Generation (ICLR 2021)

conformation conformation-generation conformer iclr iclr2021 molecule pytorch

Last synced: 09 Oct 2024

https://github.com/robertdebock/ansible-role-users

The purpose of this role is to add users and groups on your system.

ansible molecule playbook server sudo system tox users

Last synced: 17 Dec 2024

https://github.com/chao1224/geossl

GeoSSL: Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching, ICLR'23 (https://openreview.net/forum?id=CjTHVo1dvR)

denoising-diffusion diffusion-models geometry molecular-geometries molecule pretraining self-supervised self-supervised-learning

Last synced: 09 Oct 2024

https://github.com/chao1224/n_gram_graph

N-Gram Graph: Simple Unsupervised Representation for Graphs, NeurIPS'19 (https://arxiv.org/abs/1806.09206)

drug drug-discovery molecular-graph molecule n-gram n-gram-graph pretraining

Last synced: 09 Oct 2024

https://github.com/molecule-js/moleculejs

A library for creating fast and reactive Custom Elements

custom-elements declarative frontend lit-html molecule ui webcomponents

Last synced: 01 Oct 2024

https://github.com/robertdebock/ansible-role-rsyslog

Install and configure rsyslog on your system.

ansible installer molecule monitoring package playbook rsyslog tox

Last synced: 17 Dec 2024

https://github.com/molgw/molgw

Accurate many-body perturbation theory calculations of the electronic structure of molecules and clusters

bethe-salpeter dft fortran greens-functions hartree-fock molecule mpi quantum-mechanics scalapack tddft

Last synced: 09 Oct 2024

https://github.com/graph-0/jodo

Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation

diffusion-models graph-neural-networks molecule

Last synced: 09 Oct 2024

https://github.com/robertdebock/ansible-role-openvpn

Install and configure openvpn server or client on your system.

ansible molecule networking openvpn playbook tox

Last synced: 09 Oct 2024

https://github.com/lean-delivery/ansible-development-kit

Ansible Development Kit (roles development)

ansible ansible-roles cookiecutter development-kit molecule

Last synced: 13 Oct 2024

https://github.com/frankwswang/quiqbox.jl

Exploring the computational power of fermionic quantum systems. Ab initio computation and basis set optimization for electronic structure problems.

automatic-differentiation basis-set computational-chemistry electronic-structure hartree-fock julia many-body-physics molecular-integrals molecule quantum quantum-chemistry

Last synced: 09 Oct 2024

https://github.com/dj-wasabi/ansible-ossec-server

Installing and maintaining the ossec-server for RedHat/Debian/Ubuntu.

ansible-role molecule ossec ossec-server

Last synced: 09 Oct 2024

https://github.com/yunjaechoi/vaemols

Variational Autoencoder for Molecules

molecule rdkit tensorflow variational-autoencoder

Last synced: 12 Oct 2024

https://github.com/yuleicul/obsidian-ketcher

View or draw chemical structures and reactions using Ketcher.

chemistry ketcher molecule obsidian-plugin

Last synced: 09 Oct 2024

https://github.com/chao1224/moleculesde

A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining, ICML'23

conformation diffusion generation geometry group-equivariant-neural-network molecule pretraining reflection-antisymmetric representation sde stochastic-differential-equation

Last synced: 09 Oct 2024

https://github.com/lhm30/pidginv2

PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)

cheminformatics chemoinformatics molecule pubchem random-forest target target-prediction target-predictions weight

Last synced: 09 Oct 2024

https://github.com/tridentbio/trident-chemwidgets

Jupyter Widgets to interact with molecular datasets.

chemistry jupyter jupyter-notebook molecule notebook visualization

Last synced: 09 Oct 2024

https://github.com/chao1224/Loss-Balanced-Task-Weighting

Loss-Balanced Task Weighting to Reduce Negative Transfer in Multi-Task Learning, AAAI-SA'19

molecule multi-task-learning negative-transfer transfer-learning

Last synced: 05 Nov 2024

https://github.com/chao1224/loss-balanced-task-weighting

Loss-Balanced Task Weighting to Reduce Negative Transfer in Multi-Task Learning, AAAI-SA'19

molecule multi-task-learning negative-transfer transfer-learning

Last synced: 09 Oct 2024

Molecule Awesome Lists
awesome-pretrain-on-molecules 242 awesome-AI4Drug-papers 41
Molecule Categories
Papers List 587 Open-Sourced Pretrained Graph Models 68 Molecule 32 Protein 8 Pre-traing Datasets 5 Acknowledgements 3 Gene 1