Md Python Packages

jarvis-tools

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

skills-tree

🌳 A comprehensive collection of all skills available for AI agents and computer-use models — perception, reasoning, memory, code, tool-use, multimodal, orchestration, and more.

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.

md-dead-link-check

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

markdown-query

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

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.

reacnetgenerator

an automatic reaction network generator for reactive molecular dynamics simulation

sphinx-jekyll-builder

sphinx builder that outputs jekyll compatible markdown files with frontmatter

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.

confluence-md

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

imdclient

Streaming analysis from running MD simulations.

rdx-parser

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

mkdocs-simple-blog

Blog Template for Mkdocs

mddatasetbuilder

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

polyply

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

yaml-to-markdown

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

pervane

Plain text backed web based markdown note taking, cloud code editor and knowledge base building app

flexberry-markitdown-mcp

MCP сервер для конвертации файлов в Markdown и из Markdown в PDF.

markdown-fenced-code-tabs

Generates tabs for consecutive markdown code blocks

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.

dftfit

Ab-Initio Molecular Dynamics Potential Development

runxmd

runxmd — add state and execution to your .md files. .xmd is plain Markdown with a run-intent label.

basicrta

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

everythingtohtml

Convert PDF, Office, data, and markup files into clean, self-contained HTML — for humans and for LLMs.