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Automd Viz

Skill by billwanttobetop

skill-install — Terminal

Install via CLI (Recommended)

clawhub install openclaw/skills/skills/billwanttobetop/automd-viz
Or

AutoMD-Viz - Publication-Quality Visualization for Molecular Dynamics

Version: 1.0.0
Author: Xuan Guo ([email protected])
License: MIT
Repository: https://github.com/Billwanttobetop/automd-viz

📖 Overview

AutoMD-Viz is a standalone visualization toolkit for generating publication-quality figures from molecular dynamics simulation data. It supports multiple visualization types and journal-specific styles (Nature, Science, Cell).

Key Features:

  • 🎨 Molecular structure visualization (PyMOL)
  • 📊 Data plotting (Matplotlib/Seaborn)
  • 🎬 Trajectory visualization (PCA/t-SNE/UMAP)
  • 📦 Automated report generation
  • 🎯 Journal-specific styles (Nature/Science/Cell)
  • 🔧 High-resolution output (300-600 DPI, SVG/PDF/EPS)

🚀 Quick Start

Installation

# Via ClawHub
clawhub install automd-viz

# Or manual installation
git clone https://github.com/Billwanttobetop/automd-viz.git
cd automd-viz
chmod +x automd-viz.sh

Basic Usage

# Generate protein structure figure
./automd-viz.sh --type structure --structure protein.pdb --style nature

# Plot RMSD/RMSF data
./automd-viz.sh --type data --input rmsd.xvg --style science

# Trajectory visualization (PCA)
./automd-viz.sh --type trajectory --structure protein.pdb --trajectory md.xtc

# Generate complete report
./automd-viz.sh --type report --structure protein.pdb --trajectory md.xtc --style nature

📋 Visualization Types

1. Structure Visualization (--type structure)

Generate high-quality molecular structure figures using PyMOL.

Options:

  • --structure <file> - Input structure (PDB/GRO)
  • --style <nature|science|cell> - Journal style
  • --representation <cartoon|surface|sticks> - Display style
  • --color <spectrum|chain|secondary> - Coloring scheme
  • --resolution <300|600> - Output DPI

Example:

./automd-viz.sh --type structure \
  --structure protein.pdb \
  --style nature \
  --representation cartoon \
  --color spectrum \
  --resolution 600

Output:

  • structure_nature.png (high-resolution raster)
  • structure_nature.pse (PyMOL session)

2. Data Plotting (--type data)

Plot time-series data (RMSD, RMSF, energy, etc.) with journal-quality formatting.

Options:

  • --input <file> - Input data file (XVG format)
  • --style <nature|science|cell> - Journal style
  • --xlabel <text> - X-axis label
  • --ylabel <text> - Y-axis label
  • --title <text> - Plot title

Example:

./automd-viz.sh --type data \
  --input rmsd.xvg \
  --style science \
  --xlabel "Time (ns)" \
  --ylabel "RMSD (nm)"

Output:

  • data_plot.pdf (vector graphics)
  • data_plot.png (raster graphics)

3. Trajectory Visualization (--type trajectory)

Visualize trajectory in reduced dimensionality space (PCA/t-SNE/UMAP).

Read Full Documentation on GitHub

Metadata

Author@billwanttobetop
Stars4473
Views0
Updated2026-05-01
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Paste this into your clawhub.json to enable this plugin.

{
  "plugins": {
    "official-billwanttobetop-automd-viz": {
      "enabled": true,
      "auto_update": true
    }
  }
}
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