Molaro
Molaro is a next-generation molecular dynamics environment built as a VS Code extension.
Core trick
Claude writes analysis scripts shown for review before execution, and checks radius of gyration against MDTraj and MDAnalysis reference values.
Description
Molaro is a next-generation molecular dynamics environment built as a VS Code extension. Instead of shipping with a fixed set of visualizations and analyses, it provides an extensible agent framework where Claude writes custom Python analysis directly against your trajectory. Every script is shown before execution, can be inspected or edited, and is saved as a reusable Python workflow, allowing your analysis toolkit to grow through conversation rather than waiting for new software releases.
To ensure scientific trust, generated analyses are validated against established molecular dynamics libraries such as MDTraj and MDAnalysis. In our benchmark corpus, Claude-generated radius-of-gyration analysis matched reference implementations to within 1.6 × 10⁻⁸ nm, demonstrating that AI-generated workflows can be both flexible and scientifically reliable.
The long-term vision extends beyond a single viewer. Molaro is designed as an agent platform where researchers can create, publish, and share new analyses, visualizations, and workflows. Rather than relying on a fixed feature roadmap, the community can continuously expand the capabilities of the software by building and distributing new agent-powered tools.
README excerpt
# Molaro Molaro is a VS Code extension for streaming, exploring, and analyzing molecular dynamics trajectories where the data lives, including on remote systems over SSH. It combines a GPU-rendered 3D viewer, a command-driven representation layer, Python analysis mods, and an optional Claude-powered analysis assistant. Molaro was created for the **Build Track of Built with Claude: Life Sciences**, a global virtual hackathon hosted by Anthropic and Cerebral Valley in partnership with Gladstone Institutes. ## What Molaro does - Opens molecular structures and trajectories directly from the VS Code Explorer. - Streams trajectory frames from a Python producer into a CSP-safe Three.js webview instead of copying the full dataset into the editor. - Provides interactive selection, hiding, camera controls, hierarchy navigation, and representations for points, bonds, and backbone traces. - Includes a terminal grammar for selecting, styling, plotting, and composing analysis results. - Runs small Python **mods** beside the trajectory and displays their results as plots, channels, geometry, or viewer commands. - Offers an optional `/claude` assistant that can inspect the loaded system, author and run mods, and operate the viewer through a restricted tool surface with approval gates around writing, running, and deleting mods. Molaro's renderer is deliberately data-neutral. Molecular files are translated by the producer into a typed contract of positions, connectivity, hiera