MoloM

A standalone, Python-based molecule viewer/builder skeleton in the spirit of Avogadro: an OpenGL ball-and-stick viewport with the same universal structure import cascade as ORCA Workbench.

Features (skeleton scope)

• Import: native multi-frame .xyz (with JSON-comment metadata), SDF/MOL/MOL2/PDB/CIF/... via OpenBabel (timeout-guarded subprocess) with an RDKit fallback and a last-resort heuristic Label x y z salvage; SMILES → 3D (RDKit ETKDGv3 + MMFF, OpenBabel UFF fallback); paste-XYZ detection.
• Rendering: instanced-OpenGL ball-and-stick using Avogadro 2's element data (Alvarez VdW radii, Pyykkö covalent radii, Jmol-derived colours) and its exact sizing rules; stick / VdW / wireframe presets.
• Bond perception: Avogadro's perceiveBondsSimple rule (covalent radius sum + 0.45 Å tolerance, 0.32 Å minimum, noble gases and H-H excluded).
• Selection & measurement: click / Ctrl+click; 2, 3, 4 selected atoms show distance, angle, dihedral in the status bar.
• Trajectory playback: frame slider + play/pause for multi-frame files.
• Editing (stubs): add/delete atoms, change element, add/remove/cycle bonds — wired UI dispatching into implemented, tested core functions.

Install / run

pip install -e .          # core: numpy, PySide6, PyOpenGL
pip install -e .[chem]    # + rdkit, openbabel-wheel (SMILES + non-xyz formats)
molom [file.xyz]
python -m molom --selftest   # headless check, no GL needed

Architecture

molom/core/ is UI-free and GL-free (unit-testable offline); molom/ui/ is a thin PySide6/OpenGL shell over it. See CLAUDE.md.

Element data transcoded from Avogadro 2 (BSD 3-Clause) — see THIRD_PARTY_NOTICES.md.