Specialized / 3_PROTAC_Analysis.py

PROTAC and Ternary Complex Analysis

Adds dedicated analysis for ternary-complex systems, including component-aware contacts, networks, geometry, quality-control manifests, and optional water bridges.

Why this step matters

PROTAC simulations ask extra questions about a linker, two protein partners, ternary-interface geometry, and contact persistence across components.

Concepts to understand

PROTAC role detection component-specific RMSD/RMSF ligand contacts by protein component ternary interaction networks geometry and water-bridge options QC manifests for figurebook routing

Common outputs

Analysis_Results/PROTAC/QC/protac_figure_manifest.csv Analysis_Results/PROTAC/Contacts/ligand_contacts_detailed.csv Analysis_Results/PROTAC/Networks/protac_interaction_network_all_components.png PROTAC_MD_ANALYSIS_FIGUREBOOK.pdf

Typical commands

python 3_PROTAC_Analysis.py --ligand PTC

python 3_PROTAC_Analysis.py --ligand PTC --quick-test

python 3_PROTAC_Analysis.py --ligand PTC --contacts-only