API Reference¶
Comprehensive API documentation for all PRISM modules.
Core Modules¶
System Building¶
- PRISMBuilder - Main system builder class
- PRISMSystem - High-level system interface
Analysis¶
- TrajAnalysis - Trajectory analysis tools
- Visualization - Interactive visualizations
Advanced Calculations¶
- PMF Module - PMF alignment and pulling direction optimization
- FEP Module - Free Energy Perturbation calculations and analysis
- Utilities - Helper functions and environment detection
Quick Reference¶
High-Level API¶
import prism
# Build system
system = prism.system("protein.pdb", "ligand.mol2")
system.build()
# Analyze trajectory
analysis = prism.analyze_trajectory("system.gro", "traj.xtc")
# Visualize contacts
prism.visualize_trajectory("md.xtc", "system.gro", "ligand.sdf", output="contacts.html")
Class-Based API¶
from prism import PRISMBuilder, TrajAnalysis
# Builder
builder = PRISMBuilder("protein.pdb", "ligand.mol2", "output")
builder.run()
# Analysis
analyzer = TrajAnalysis("topology.gro", "trajectory.xtc")
analyzer.analyze_all()
Module Index¶
| Module | Purpose | Key Classes |
|---|---|---|
| builder | System construction | PRISMBuilder, PRISMSystem |
| analysis | Trajectory analysis | TrajAnalysis, HTMLGenerator |
| pmf | PMF alignment | PMFAligner |
| fep | FEP calculations | FEPScaffoldBuilder, DistanceAtomMapper, FEPAnalyzer |
| utilities | Helper functions | ConfigurationManager, GromacsEnvironment |
API Stability¶
- Stable: High-level functions (
prism.system,prism.analyze_trajectory,prism.visualize_trajectory) - Evolving: Internal classes (subject to change)
- Experimental: PMF module (API may change in minor versions)