xiaoruiDong/RDMC
Reaction Data and Molecular Conformers (RDMC) is a package dealing with reactions, molecules, conformers, majorly in 3D.
Researcher in cheminformatics, machine learning, quantum chemistry, and scientific modeling. Alumnus of MIT and THU
Repositories
xiaoruiDong/rxntp
RXNTP is a lightweight package for analyzing chemical reaction templates written in Python.
xiaoruiDong/ChemIE
Chemical information extraction
xiaoruiDong/REINVENT4
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
xiaoruiDong/rdkit-mcp-server
xiaoruiDong/rdeditor
Simple RDKit molecule editor GUI using PySide
xiaoruiDong/datamol
Molecular Processing Made Easy.
xiaoruiDong/MolScore
An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular design
xiaoruiDong/ml_scripts
xiaoruiDong/xiaorui-phd-thesis
This repository contains the relevant supplementary information on Xiaorui Dong's PhD thesis.
xiaoruiDong/precomplex_generator
The precomplex generator is a tool for obtaining suitable input structures for automated transition-state (TS) searches (precomplexes) based on single-ended reaction path optimization algorithms.
xiaoruiDong/torsional-diffusion
Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)
xiaoruiDong/OAReactDiff
An object-aware diffusion model for generating chemical reactions
xiaoruiDong/ai-science-training-series
Argonne AI Science Training
xiaoruiDong/chemprop
Message Passing Neural Networks for Molecule Property Prediction
xiaoruiDong/rxnmapper
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/eabe4166).
xiaoruiDong/conformer_generation
A module with expertise in molecular and transition state conformer generation
xiaoruiDong/GeoMol
xiaoruiDong/CCG
A framework to Comprehesive Conformer Generator (CCG)
xiaoruiDong/easy_rmg_model
Contains some of the scripts and APIs to easily build a model by RMG
xiaoruiDong/MESS_tutorial
xiaoruiDong/SciencePlots
Matplotlib styles for scientific plotting
xiaoruiDong/Molssi_workshop
xiaoruiDong/xyz2mol
Converts an xyz file to an RDKit mol object
xiaoruiDong/ACS
Automated Conformer Search for Multi-structural Thermo-Kinetic Calculations
xiaoruiDong/RMG-Py
Python version of the amazing Reaction Mechanism Generator (RMG).
xiaoruiDong/custom-hotword-for-aiy-voicekit
Snowboy API for AIY Voice Kit
xiaoruiDong/RMG-tools
A toolbox providing several handy functions to facilitate RMG and ARC related jobs
xiaoruiDong/ReactionMechanismSimulator.jl
The amazing Reaction Mechanism Simulator for simulating large chemical kinetic mechanisms
xiaoruiDong/ARC
ARC - Automatic Rate Calculator