Topoly

Topoly performs topology analysis of (bio)polymers by computing polynomial invariants and related structures to identify knots, slipknots, links, and spatial graphs for studies of polymer physical properties.

Key Features:

• Topological Polynomial Invariants: Topoly calculates various polynomial invariants to distinguish knots, slipknots, links, and spatial graphs.
• Minimal Spanning Surface Calculation: Topoly computes the minimal spanning surface on loops to detect motifs such as lasso structures and to aid generation of random closed polymers.
• File Format Compatibility: Topoly supports multiple file formats, including PDB.

Scientific Applications:

• Biophysics: Investigating how polymer topology (knots, slipknots, links, spatial graphs) affects biomolecular physical properties.
• Materials Science: Studying topology-dependent material properties and informing design of polymer systems with targeted physical behaviors.

Methodology:

Implemented in Python; computes various polynomial invariants, computes minimal spanning surfaces on loops, and accepts multiple file formats including PDB.