Scoria

Scoria manipulates three-dimensional molecular data to support computational biology analyses.

Key Features:

• Three-dimensional data manipulation: Manipulates three-dimensional molecular structures and trajectory data.
• Dependency-free: Operates without external dependencies, compilers, or complex installation requirements.
• Direct code integration: Allows incorporation of Scoria source code directly into user programs for integration and customization.
• NumPy/SciPy complementarity: Leverages NumPy and SciPy when available to enhance functionality and performance.
• Molecular dynamics trajectory processing: Supports processing and analysis of molecular dynamics trajectories.

Scientific Applications:

• Molecular dynamics trajectory analysis: Applied to analyze molecular dynamics trajectories for structural and temporal investigations.
• FootPrint contact visualization: The FootPrint script uses Scoria to color-code atoms of one molecular chain based on the frequency of their contacts with another chain, enabling inter-chain contact analysis.

Methodology:

Processes and analyzes three-dimensional molecular data and molecular dynamics trajectories; computes per-atom inter-chain contact frequencies for color-coding in the FootPrint script; leverages NumPy and SciPy when available while supporting operation without external dependencies.