Moleculix++ takes the same interactive molecule builder you know from Moleculix Junior and connects it to a real scientific backend. Instead of a sketch, your model becomes something you can simulate, analyze, and export.
What it adds over Junior
- Molecular dynamics — hand a built structure to OpenMM and watch it settle, vibrate, and move under a real force field
- Cheminformatics — use RDKit to validate structures, compute molecular descriptors, and check chemical sanity
- Format interoperability — read and write standard structure formats (SDF, MOL, PDB, SMILES) via Indigo, so a model built here works everywhere else
- No mode switching — the same 3D view you build in is the same view you simulate in
- Python bindings — script the whole Moleculix engine directly, with full access to the underlying OpenMM and RDKit calls
Python bindings: the whole engine, scriptable
Moleculix++ isn’t just a GUI in front of OpenMM and RDKit — the same engine that powers the 3D builder is exposed through a Python API. Anything you can do by hand in the interface, you can also drive from a script: build or load a structure, run it through OpenMM for dynamics, hand it to RDKit for validation and descriptors, and get results back as native Python objects.
- Build, load, and edit molecular structures programmatically
- Call OpenMM directly for molecular dynamics, with full control over the simulation
- Call RDKit directly for structure validation, descriptors, and property analysis
- Automate batches of structures instead of clicking through them one at a time
- Combine the interactive builder and scripting freely — build by hand, refine by script, or the reverse
Who it’s for
Moleculix++ is aimed at people who outgrow a pure teaching tool: chemistry students moving into research, hobbyist computational chemists, and anyone who wants to go from “I built a molecule” to “I know how it behaves” without leaving the same application.
Status
Moleculix++ is in active development. The Junior builder you can try today is the same interaction model Moleculix++ is built on — the OpenMM, RDKit, and Indigo integration is what’s being layered underneath it.