AtomModeller

AtomModeller is a software tool for constructing, visualizing, and analyzing atomic- and molecular-scale structures. It provides an interactive environment for building molecules, editing bonds and geometry, and inspecting 3D arrangements. The aim is to support education, basic research, and workflow prototyping in computational chemistry and materials science.

Key features include an intuitive editor for adding atoms and bonds, automatic valence validation, and automated generation of three-dimensional coordinates from two-dimensional representations such as SMILES or InChI. Users can perform rapid conformer generation and geometry optimization using common molecular mechanics force fields (MMFF94, UFF) or lightweight quantum-chemical approximations. Visualization styles include ball-and-stick, space-filling, and wireframe, with options to annotate properties such as partial charges and atom types.

AtomModeller supports interoperability with standard data formats. It can import and export PDB, MOL2, SDF, XYZ, and CIF files, and can exchange structures with other tools through scripting or plugins. Some installations provide scripting interfaces, enabling automation of repetitive tasks, batch processing, and custom workflows.

Typical users include students and educators illustrating structural concepts, researchers building model systems for preliminary analyses, and professionals exploring drug design or materials projects in a low-threshold environment before running more extensive simulations. The software is cross-platform, running on major operating systems and designed to fit into existing computational workflows.

See also: Molecular modelling, Molecular visualization, Computational chemistry, Chemical informatics.