v0.2.5 — Small Molecule Support

What's New

Small Molecule Support

• Parse HETATM records — ligands rendered as ball-and-stick, ions as spheres
• Water molecules (HOH/WAT) automatically filtered from display
• Classification: multi-atom molecules as Ligands, single-atom metals as Ions
• Works in both HD (3D shaded spheres + sticks) and Braille modes
• Toggle visibility with g key

Ligand Binding Pocket Analysis

• Detects polymer residues within 4.5Å of each ligand
• Shows binding pocket contacts in the interface panel
• Per-ligand summary with closest residues and distances

Extended Element Coloring

• CPK palette expanded: Mg, Zn, Ca, Mn, Co, Cu, Ni, Cl, Br
• Ligands colored magenta (Structure), cyan for ions, or by element (CPK mode)
• Chain mode colors ligands by parent chain

Bug Fix

• NMR multi-model PDB files now load correctly (only first model used)
• Fixes GitHub issue #1: RNA structures like 2KGP no longer crash or show duplicates

Stats

• 65 tests passing
• 18 files changed, 1170 insertions