Metadata-Version: 2.4
Name: molom
Version: 0.1.0
Summary: Standalone Avogadro-like molecule viewer/builder: ball-and-stick GL viewport with universal structure import
Author: Christian Nelle
License: MIT License
        
        Copyright (c) 2026 Christian Nelle
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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Keywords: chemistry,molecule,viewer,3d,opengl,ball-and-stick,xyz,avogadro,quantum chemistry
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: PySide6
Requires-Dist: PyOpenGL
Provides-Extra: chem
Requires-Dist: rdkit; extra == "chem"
Requires-Dist: openbabel-wheel; extra == "chem"
Dynamic: license-file

# 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](https://github.com/ACH-Repo/ACH-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`.
