Molecular modeling and visualization

Interactive molecular modeling for chemistry education

Moleculix is software for learning chemistry in three dimensions. Students place atoms, form bonds, and watch valence, lone pairs and bond angles appear as they build — then let the molecule relax into the shape it really has.

Moleculix Junior Application Moleculix++ API

Moleculix Junior

A 3D molecule builder for students and teachers. Click atoms into place, form bonds, and turn the structure in your hands to see why molecules bend, or don’t.

Build molecules atom by atom, from a periodic table
See open valences and lone pairs as you build
Fill a structure with hydrogens in one keystroke
Type a SMILES string and get the molecule in 3D
Let the structure relax to its real geometry

Moleculix Junior overview →

Moleculix++

The engine behind Junior, for advanced students, teachers preparing demonstrations, and anyone ready to go past the sketch.

Molecular dynamics via OpenMM, on CPU or NVIDIA GPU
SMILES and HELM peptide notation via RDKit
Protein and structure files in PDB format
Python bindings — build and view molecules from a script

Moleculix++ overview →

Computational foundation

Moleculix is built on established open-source chemistry libraries used in research. Molecular geometries are computed from force fields and chemical rules rather than drawn.

OpenMM

Molecular dynamics: watch a structure move, vibrate and settle under a physical force field.

RDKit

Turns SMILES and HELM notation into 3D structures, and relaxes them to a realistic geometry.

Indigo

A second chemistry engine for reading SMILES notation.

Classroom and institutional use

Moleculix Junior runs on Microsoft Windows. The next release is in preparation. Contact us to be notified when it is available, or to discuss its use in your courses.