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Projects in Awesome Lists tagged with molecule
A curated list of projects in awesome lists tagged with molecule .
https://github.com/cloudalchemy/ansible-prometheus
Deploy Prometheus monitoring system
ansible metrics-gathering molecule monitoring prometheus tox
Last synced: 26 Sep 2024
https://github.com/BradyAJohnston/MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
biochemistry blender blender-addon geometry-nodes molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation
Last synced: 02 Aug 2024
https://github.com/bradyajohnston/molecularnodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
biochemistry blender blender-addon geometry-nodes molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation
Last synced: 26 Sep 2024
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: 26 Sep 2024
https://github.com/biopandas/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 26 Sep 2024
https://github.com/BioPandas/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 06 Aug 2024
https://rasbt.github.io/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 08 Sep 2024
https://github.com/CalebBell/thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
chemical-engineering cheminformatics chemistry combustion density environmental-engineering equation-of-state heat-capacity mechanical-engineering molecule physics process-simulation solubility surface-tension thermal-conductivity thermodynamics vapor-pressure viscosity
Last synced: 03 Aug 2024
https://github.com/calebbell/thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
chemical-engineering cheminformatics chemistry combustion density environmental-engineering equation-of-state heat-capacity mechanical-engineering molecule physics process-simulation solubility surface-tension thermal-conductivity thermodynamics vapor-pressure viscosity
Last synced: 26 Sep 2024
https://github.com/cloudalchemy/ansible-grafana
Platform for analytics and monitoring
analytics ansible grafana metrics-visualization molecule monitoring tox
Last synced: 27 Sep 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/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: 26 Sep 2024
https://github.com/datamol-io/datamol
Molecular Processing Made Easy.
cheminformatics drug-design drug-discovery medicinal-chemistry molecule molecules python rdkit
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: 28 Sep 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: 26 Sep 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: 08 Aug 2024
https://github.com/atosatto/ansible-dockerswarm
Docker Engine clustering using "Swarm Mode" and Ansible
ansible docker docker-swarm molecule swarm-mode
Last synced: 26 Sep 2024
https://github.com/partridgejiang/kekule.js
A Javascript cheminformatics toolkit.
cheminformatics chemistry javascript molecule
Last synced: 26 Sep 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: 26 Sep 2024
https://github.com/zjunlp/mol-instructions
[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models
ai-for-science biomedical dataset datasets generation iclr2024 instruction instruction-following instructions large-language-models llama mol-instruction molecule natural-language-processing protein resource science
Last synced: 26 Sep 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: 26 Sep 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: 26 Sep 2024
https://github.com/minkaixu/geoldm
Geometric Latent Diffusion Models for 3D Molecule Generation
deep-generative-model diffusion-models drug-discovery geometric-deep-learning icml-2023 molecule molecule-generation
Last synced: 26 Sep 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: 26 Sep 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: 31 Jul 2024
https://github.com/acellera/moleculekit
MoleculeKit: Your favorite molecule manipulation kit
drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins
Last synced: 26 Sep 2024
https://github.com/Acellera/moleculekit
MoleculeKit: Your favorite molecule manipulation kit
drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins
Last synced: 03 Aug 2024
https://github.com/HICAI-ZJU/Scientific-LLM-Survey?tab=readme-ov-file
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: 02 Aug 2024
https://github.com/tsudalab/chemts
Molecule Design using Monte Carlo Tree Search with Neural Rollout
Last synced: 26 Sep 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: 03 Aug 2024
https://github.com/ansible-community/molecule-vagrant
🚧 Moved to molecule-plugins
ansible hacktoberfest hashicorp molecule molecule-driver vagrant
Last synced: 30 Sep 2024
https://github.com/thomas0809/molscribe
Robust Molecular Structure Recognition with Image-to-Graph Generation
chemistry deep-learning molecule
Last synced: 26 Sep 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: 26 Sep 2024
https://github.com/cloudalchemy/ansible-alertmanager
Deploy Prometheus Alertmanager service
alerting alertmanager ansible molecule prometheus prometheus-alertmanager tox
Last synced: 26 Sep 2024
https://github.com/chao1224/chatdrug
LLM for Drug Editing, ICLR 2024
chatgpt chatgpt3 conversation domain-feedback drug drug-discovery drug-editing editing llm molecule motif peptide protein retrieval secondary-structure small-molecule structure
Last synced: 26 Sep 2024
https://github.com/chao1224/ChatDrug
LLM for Drug Editing, ICLR 2024
chatgpt chatgpt3 conversation domain-feedback drug drug-discovery drug-editing editing llm molecule motif peptide protein retrieval secondary-structure small-molecule structure
Last synced: 03 Aug 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: 27 Sep 2024
https://github.com/zjunlp/molgen
[ICLR 2024] Domain-Agnostic Molecular Generation with Chemical Feedback
generation huggingface iclr2024 language-model molecular-generation molecular-optimization molecule molgen multitask pre-trained-language-models pre-trained-model pre-training pytorch selfies targeted-molecular-generation
Last synced: 26 Sep 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: 29 Sep 2024
https://github.com/lab-cosmo/chemiscope
An interactive structure/property explorer for materials and molecules
hacktoberfest materials-science molecule visualization web
Last synced: 26 Sep 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: 26 Sep 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: 26 Sep 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: 26 Sep 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: 29 Sep 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: 29 Sep 2024
https://github.com/zotko/xyz2graph
Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
3d-plot adjacency-list adjacency-matrix atom atomic-coordinates chemistry chemoinformatics covalent-radii jupyter-notebook molecular-graph molecular-graphs molecule molecule-visualization networkx plotly python visualization xyz xyz-files xyz-reader
Last synced: 26 Sep 2024
https://github.com/aksub99/moldqn-pytorch
A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".
chemistry deep-learning dqn-pytorch drug-discovery inverse-design machine-learning materials-informatics materials-science molecule python pytorch pytorch-implementation pytorch-rl reinforcement-learning
Last synced: 26 Sep 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: 26 Sep 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: 26 Sep 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: 26 Sep 2024
https://github.com/autodesk/molecule-3d-for-react
3D molecular visualization React component using 3Dmol.js
Last synced: 26 Sep 2024
https://github.com/mcellteam/cellblender
Create, Simulate, Visualize, and Analyze Realistic 3D Cell Models
Last synced: 26 Sep 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: 26 Sep 2024
https://github.com/cloudalchemy/ansible-blackbox-exporter
Blackbox prober exporter
ansible blackbox-exporter molecule monitoring prometheus prometheus-exporter tox
Last synced: 26 Sep 2024
https://github.com/gofrolist/molecule-action
GitHub Action for running molecule as part of your workflows!
Last synced: 26 Sep 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: 26 Sep 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: 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: 26 Sep 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/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: 26 Sep 2024
https://github.com/gersteinlab/genai4drug
drug-discovery genai molecule protein
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: 08 Aug 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: 26 Sep 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: 26 Sep 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: 26 Sep 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: 26 Sep 2024
https://github.com/webcyou/apbcss
APB CSS - Atomic Parts Base CSS -
apb-css atomic-parts button-icon css icons molecule oocss oocss-smacss skin smacss
Last synced: 26 Sep 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: 26 Sep 2024
https://github.com/robertdebock/ansible-role-logrotate
Install and configure logrotate on your system.
ansible logrotate molecule monitoring playbook system tox
Last synced: 26 Sep 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: 26 Sep 2024
https://github.com/dylanwal/chemistry_drawer
Draw molecules with plotly!
chemical cheminformatics chemistry molecule plotly rdkit smiles structure
Last synced: 26 Sep 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/graph-0/jodo
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation
diffusion-models graph-neural-networks molecule
Last synced: 26 Sep 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: 26 Sep 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: 26 Sep 2024
https://github.com/ansible-community/molecule-libvirt
Molecule LibVirt Provider
ansible hacktoberfest libvirt molecule molecule-driver
Last synced: 26 Sep 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: 26 Sep 2024
https://github.com/bruneval/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: 30 Jul 2024
https://github.com/qcscine/molassembler
Chemoinformatics toolkit with support for inorganic molecules
chemistry chemoinformatics conformer-generator data-structures graph-algorithms molecule molecule-builder stereochemistry
Last synced: 26 Sep 2024
https://github.com/yunjaechoi/vaemols
Variational Autoencoder for Molecules
molecule rdkit tensorflow variational-autoencoder
Last synced: 28 Sep 2024
https://github.com/lean-delivery/ansible-development-kit
Ansible Development Kit (roles development)
ansible ansible-roles cookiecutter development-kit molecule
Last synced: 29 Sep 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: 26 Sep 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: 26 Sep 2024
https://github.com/yuleicul/obsidian-ketcher
View or draw chemical structures and reactions using Ketcher.
chemistry ketcher molecule obsidian-plugin
Last synced: 26 Sep 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: 26 Sep 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: 26 Sep 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: 01 Aug 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: 26 Sep 2024
https://github.com/tridentbio/trident-chemwidgets
Jupyter Widgets to interact with molecular datasets.
chemistry jupyter jupyter-notebook molecule notebook visualization
Last synced: 26 Sep 2024
