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¶

Method dictionary¶

A–Z index of public classes and functions. Click a name to jump to its heading.

Structure Manager¶

Load, inspect, edit, and save PDB structures (selections, chain/residue edits, MemPrO orientation).

Key Features:

• Load from disk or PDB ID
• MDAnalysis selections and criteria helpers
• Rename / renumber / delete atoms
• Secondary structure assignment
• Apply a MemPrO orientation to the full system

Main Classes: StructureManager

Structure checker¶

Report missing atoms, gaps, alternate conformations, and chain differences in a PDB or mmCIF file.

Key Features:

• Missing heavy atoms, numbering gaps, SEQRES gaps, and backbone breaks
• Alternate conformations, with the highest occupancy marked as the most likely
• Protein chains that match, differ by a substitution, or differ in length
• Write a PDB that keeps one conformation and leaves the original file unchanged

Biological assembly¶

Expand the oligomer or capsid from operators already stored in a PDB or mmCIF file.

Key Features:

• List biological assemblies and their chain and atom counts
• Build an assembly as mmCIF with chain names such as A1 and A2
• Leave out crystal waters unless requested
• Leave a file that is already the biological unit unchanged

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
• Apply Amber protonation names, then complete missing protein atoms (complete_missing_heavy_atoms, tleap templates including ASH/GLH protons); pdb4amber --reduce can rebuild hydrogens when reduce is installed
• Restore original residue numbers after pdb4amber (preserve_residue_numbers; ACE/NME get N-terminus − 1 / C-terminus + 1)

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: FATSLiM CLI default (apl_method='fatslim'); EVAPL experimental; official lipyphilic AreaPerLipid when apl_method='lipyphilic'; lipyphilic for leaflets and membrane thickness
• Dark-theme matplotlib plots
• Multi-stage log concatenation with per-file time override
• Comprehensive 2×2 energy summary plots

Main Classes: EnergyAnalyzer (namd_analysis), TrajectoryAnalyzer (trajectory_analysis), BilayerTrajectoryAnalyzer (lipid_bilayer_analysis), OpenMMLogAnalyzer

Quick Links¶

• Quick Reference - Common patterns and snippets
• User Guide - Step-by-step tutorials
• Method dictionary - Clickable A–Z of public methods
• Example scripts - tests/<module>_examples/ (included in these pages and run by pytest)

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