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

markdown-query

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

md-dead-link-check

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

reacnetgenerator

an automatic reaction network generator for reactive molecular dynamics simulation

rdx-parser

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

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.

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

mkdocs-simple-blog

Blog Template for Mkdocs

pervane

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

imdclient

Streaming analysis from running MD simulations.

yaml-to-markdown

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

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.

mddatasetbuilder

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

dftfit

Interatomic potential creating using DFT training data.

markdown-fenced-code-tabs

Generates tabs for consecutive markdown code blocks

polyply

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

pyxmolpp2

Processing and analysis of MD trajectories

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.

basicrta

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

md2book

Convert markdown files to beautiful books using a simple configuration file

amber-mlips

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

mdvcontainment

Robust characterization of inside and outside in periodic spaces.