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API Reference Overview

Welcome to the GateWizard API documentation. This reference provides detailed information about all modules, classes, methods, and functions available in GateWizard.

Available Modules

Preparation Module

Module for predicting pKa values and managing protonation states in protein structures.

Key Features: - pKa prediction and analysis - Protonation state assignment based on pH - Disulfide bond detection and application - Protein capping with ACE/NME groups - pH-dependent protein structure preparation

Main Classes: PreparationManager, ProteinCapper

Builder Module

Module for building and preparing molecular dynamics simulation systems.

Key Features: - System configuration and setup - Integration with CHARMM-GUI - Membrane protein system preparation

Main Classes: Builder

MemPrO Module

Module for orienting membrane proteins using MemPrO.

Key Features: - Membrane protein orientation - Ranked orientation results with scoring - Oriented PDB file access by rank - Command-line builder

Main Classes: MemPrO, OrientationResult

Hydration Module

Module for cavity hydration with standalone PACKMOL (AmberTools TIP3P waters).

Key Features: - PACKMOL availability check - Hydrogen status detection (heavy-atom-safe mode) - Cavity volume estimation inside a 3D box - PACKMOL input generation and execution - Custom PACKMOL input support

Main Functions: check_packmol_available, estimate_cavity_volume, hydrate_cavity

Equilibration Module

Module for managing equilibration protocols and workflows for NAMD, GROMACS, OpenMM, and Amber.

Key Features: - NAMD equilibration protocol generation (CHARMM-GUI template integration) - GROMACS equilibration protocol generation - OpenMM equilibration protocol generation - Amber equilibration protocol generation (pmemd / sander mdin + GROUP restraints) - Flexible restraint system (protein backbone/sidechain, lipid head/tail, ligand, ions) - MDAnalysis-based atom selection for restraint files - Progressive force-constant schedule across stages - Custom stage parameters via EquilibrationStage dataclass

Main Classes: NAMDEquilibrationManager, GROMACSEquilibrationManager, OpenMMEquilibrationManager, AmberEquilibrationManager, EquilibrationStage

Analysis Module

Module for analyzing simulation results and monitoring equilibration progress.

Key Features: - NAMD log file parsing and energy analysis - OpenMM StateDataReporter log parsing - MDAnalysis-based trajectory analysis (RMSD, RMSF, distances, radius of gyration) - Lipid bilayer analysis via lipyphilic (area per lipid, membrane thickness) - Dark-theme matplotlib plots - Multi-stage log concatenation with per-file time override - Comprehensive 2×2 energy summary plots

Main Classes: EnergyAnalyzer, TrajectoryAnalyzer, BilayerTrajectoryAnalyzer, OpenMMLogAnalyzer

Getting Help

If you need additional help:

  1. Check the Troubleshooting Guide
  2. Review the User Guide for practical examples
  3. Ask in GitHub Discussions or report bugs via issues
  4. See complete workflow examples in the tests/ example directories

Module Organization

Each module documentation page includes:

  • Import statements - How to import the module
  • Class/Function signatures - Detailed method signatures
  • Parameters - Complete parameter descriptions
  • Returns - Return types and values
  • Examples - Practical code examples
  • Workflows - Complete usage patterns