drmaruyama's repositories
3D-RISM-Tinker
3D-RISM on Tinker
allegro
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
aqme
Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io
cpp_software_design
Code Examples from "C++ Software Design: Design Principles and Patterns for High-Quality Software" (ISBN: 1098113160)
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
fepsuite
Software package for FEP
Hands-On-Transfer-Learning-with-Python
Hands On Transfer Learning with Python, published by Packt
htp_md
Shared repo for trajectory analysis and infrastructure development
ipcsp
Integer Programming encoding for Crystal Structure Prediction with classic and quantum computing bindings
ml4chem
「機械学習による分子最適化」のサポートページ
MLQD
MLQD is a Python Package for Machine Learning-based Quantum Dissipative Dynamics
MoleculeACE
A tool for evaluating the predictive performance on activity cliff compounds of machine learning models
MTL_ChiParameter
Sample code for "Predicting polymer-solvent miscibility using machine-learned Flory-Huggins interaction parameters
mypythonpkg
python packages for HPC
nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
PolymerGNN
Polymer property prediction with GNNs and deep set learning.
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
RadonPy
RadonPy is a Python library to automate physical property calculations for polymer informatics.
rid-kit
Reinforced dynamics
SolvBERT
This is the code for "SolvBERT for solvation free energy and solubility prediction: a demonstration of an NLP model for predicting the properties of molecular complexes" paper. The preprint of this paper can be found in ChemRxiv with https://doi.org/10.26434/chemrxiv-2022-0hl5p
spring_school_2024
repository for sample used in 2024 spring school
torchmd-net
Neural network potentials based on graph neural networks and equivariant transformers