PyChem-Pro

Key features:
Chemistry

• SMILES parser with Huckel aromaticity perception, stereochemistry, bracketed atoms, radicals

• PDB / MOL / MOL2 / SDF file readers with automatic bond detection and CONECT parsing

• 3D coordinate generation from molecular topology (BFS + force-field relaxation)

• MMFF94 force field with hydrogen addition, bond stretching, angle bending, torsion, Van der Waals, and BCI partial charge assignment

• L-BFGS and steepest descent optimizers

• Gasteiger partial charges, AM1 and PM3 semi-empirical charge models

• Molecular descriptor calculator (constitutional, topological, electronic, geometric, hybrid, quantum, fingerprints)

• Morgan (ECFP) and topological fingerprints

• Center of Mass and Shrake-Rupley SASA

• 2D-drawing and conversion to SMILES available

Visualization

• Hardware-aware software 3D rendering (QPainter with gradient sphere shading)

• Ball-and-stick, space-fill, wireframe, cartoon, ribbon, and backbone modes

• PyMOL-style protein cartoons with alpha-helix / beta-sheet / coil detection

• Color-by secondary structure, rainbow, chain, B-factor

• 2D chemical structure viewer with single/double/triple/aromatic bond rendering, wedge/hash stereo bonds, atom labels, formal charges

• Natural-language atom selection (sele('organic'), sele('within 5.0 COM'), sele('chain A and helix'))

• High-DPI image export (72 / 150 / 300 / 600 DPI)

• Offline ray-tracer for publication-quality images

• Print (Ctrl+P) — prints 2D and 3D views on a single page

Plugin System

• BasePlugin / PluginWidget API for custom analysis, visualization, I/O, and utility plugins

• Built-in templates for analysis, visualization, and I/O plugin types

• QSAR modeling, Ramachandran, descriptor pruning, docking pose visualization, molecular weight calculator — all shipped as plugins