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atomgptlab
jarvis-tools

JARVIS-Tools: an open-source software package for data-driven atomistic materials design. Publications: https://scholar.google.com/citations?user=3w6ej94AAAAJ

169K 10 0
harehare
markdown-query

A jq-like Markdown query language for command-line processing

13K 416 8
AlexanderDokuchaev
md-dead-link-check

A lightweight and fast tool to help you keep your Markdown files free of broken links.

12K 14 2
deepmodeling
reacnetgenerator

an automatic reaction network generator for reactive molecular dynamics simulation

10K 98 47
rdx-lang
rdx-parser

RDX parser for Python — parse .rdx documents at Rust speed

8K 3 0
lennartpollvogt
markdown-to-data

Convert markdown and its elements (tables, lists, code, etc.) into structured, easily processable data formats like lists and hierarchical dictionaries (or JSON), with support for parsing back to markdown.

6K 13 2
codejamninja
sphinx-jekyll-builder

sphinx builder that outputs jekyll compatible markdown files with frontmatter

4K 21 3
tiroq
mdify-cli

MDify is a document-to-Markdown conversion library for extracting structured content from complex PDFs and document images, including tables, charts, and scanned documents.

3K 0 0
FernandoCelmer
mkdocs-simple-blog

Blog Template for Mkdocs

3K 123 13
szn
confluence-md

Markdown to Confluence - upload any .md files to your Confluence cloud page

3K 34 12
hakanu
pervane

Plain text file based note taking and knowledge base building tool, markdown editor, simple browser IDE.

2K 204 14
becksteinlab
imdclient

Streaming analysis from running MD simulations.

2K 12 3
anevis
yaml-to-markdown

A Python utility to take a JSON / YAML file or a python dict / list and create a Markdown file.

1K 2 1
nyelidl
pacs-q

PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transitions in MD and QM/MM MD level.

1K 19 1
tongzhugroup
mddatasetbuilder

A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.

1K 41 11
costrouc
dftfit

Interatomic potential creating using DFT training data.

1K 27 9
yacir
markdown-fenced-code-tabs

Generates tabs for consecutive markdown code blocks

971 47 13
marrink-lab
polyply

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

955 189 34
tboy1337
pr2md

PR2MD is a powerful command-line tool that extracts GitHub Pull Request and Issue data and converts it into comprehensive, well-formatted Markdown documents. Perfect for documentation, archiving, code reviews, or offline analysis of pull requests.

703 1 0
sizmailov
pyxmolpp2

Processing and analysis of MD trajectories

701 7 7
becksteinlab
basicrta

Bayesian nonparametric inference of ligand binding kinetics from molecular dynamics simulations.

417 1 2
webalorn
md2book

Convert markdown files to beautiful books using a simple configuration file

379 11 0
t-0hmura
amber-mlips

MLIP wrapper for AMBER QM/MM (UMA, ORB, MACE, AIMNet2)

335 1 1
BartBruininks
mdvcontainment

Robust characterization of inside and outside in periodic spaces.

322 9 3
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