Chemistry

Protibuild provides accurate molecular visualization using the ball-and-stick model. This section documents the chemical elements and amino acids supported by the application.

Elements

Protibuild supports 5 common elements found in organic molecules and proteins:

CPK Coloring

The application uses standard CPK (Corey-Pauling-Koltun) coloring, which is the industry standard for molecular visualization:

• Hydrogen (H): White - Represented as small white spheres
• Carbon (C): Gray - The backbone of organic molecules
• Nitrogen (N): Blue - Found in amino groups
• Oxygen (O): Red - Found in carbonyl and hydroxyl groups
• Sulfur (S): Yellow - Found in cysteine and methionine

Visualization

• Atoms are rendered as spheres with radii proportional to their covalent radii (scaled by 0.3 for visibility)
• Bonds are rendered as gray cylinders connecting atoms
• Atom size reflects the element type - Hydrogen is smallest, Sulfur is largest

Amino Acids

Protibuild supports all 20 standard amino acids found in proteins. Each amino acid is modeled with accurate atomic positions and bond connectivity.

Amino Acid Reference

Structure

Each amino acid is rendered as a parent entity containing:

1. Atom entities - Individual atoms positioned at their correct 3D coordinates
2. Bond entities - Cylinders connecting bonded atoms
3. Metadata - Amino acid code, residue number, and chain ID

Data Source

Amino acid structures are loaded from a JSON configuration file (amino_acids.json) which contains:

• Atom positions (x, y, z coordinates)
• Atom names (e.g., “CA”, “CB”, “N”, “O”)
• Bond connectivity (pairs of atom indices)

This allows easy extension with additional molecules or modified structures.