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molclaw-interaction-visualizer - Analyze and visualize molecular interactions

Analyzes single-structure protein–ligand, peptide, or protein–protein interactions and generates multidimensional visualizations with CSV/JSON exports.

Tags

Updated: 2026-10-16
molecular interactionsprotein-ligand analysisprotein-protein interfacepeptide interfacestructural biologyPyMOL visualizationMCP tool

Capabilities

Analyze single structuresDetect nine interaction typesGenerate 2D diagramsRender PyMOL 3D views

Typical Inputs

Complex structure fileReceptor structure fileLigand structure file

Typical Outputs

2D interaction diagramPyMOL 3D renderingsResidue bar chart

What this skill does

  • Analyze single structures
  • Detect nine interaction types
  • Generate 2D diagrams
  • Render PyMOL 3D views
  • Create interface heatmaps
  • Export CSV and JSON

Inputs

  • Complex structure file
  • Receptor structure file
  • Ligand structure file
  • Partner protein structure file
  • Analysis mode
  • Chain identifiers
  • Ligand residue name
  • Residue numbering offset
  • Residue role annotations
  • Docking score
  • Ligand SMILES
  • Output directory

Outputs

  • 2D interaction diagram
  • PyMOL 3D renderings
  • Residue bar chart
  • Interface heatmap
  • Interface network diagram
  • Partner-site CSV
  • Interaction CSV files
  • Decision-ready JSON

Requirements

  • MolClaw MCP interaction_visualizer tool or local CLI
  • Python and NumPy runtime
  • Server-side input paths for MCP calls
  • molclaw-file-transfer for local uploads
  • PyMOL for 3D rendering

Source

  • Spec: SKILL.md

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