API Overview

PolyzyMD is organized into the following modules:

Package Structure

polyzymd/
├── config/           # Configuration and YAML loading
│   ├── schema.py     # Pydantic models for all config sections
│   └── loader.py     # YAML loading utilities
├── builders/         # System building components
│   ├── enzyme.py     # Enzyme/protein preparation
│   ├── substrate.py  # Substrate/ligand handling
│   ├── polymer.py    # Polymer chain generation
│   ├── solvent.py    # Solvation and ion addition
│   └── system_builder.py  # Main system assembly
├── simulation/       # MD simulation execution
│   ├── runner.py     # Simulation runner
│   ├── continuation.py    # Checkpoint continuation
│   ├── progress.py   # Segment progress tracking
│   └── signals.py    # SLURM signal handling
├── workflow/         # HPC workflow management
│   ├── slurm.py      # SLURM script generation
│   └── daisy_chain.py     # Job submission
├── core/             # Core utilities
│   ├── parameters.py # Simulation parameters
│   └── restraints.py # Restraint definitions
├── analysis/         # Post-simulation trajectory analysis
│   ├── rmsf/         # Root Mean Square Fluctuation
│   ├── distances/    # Inter-atomic distance analysis
│   ├── triad/        # Catalytic triad integrity
│   ├── contacts/     # Polymer-protein contacts, binding preference
│   ├── sasa/         # Solvent Accessible Surface Area
│   ├── exposure/     # Chaperone-like exposure dynamics
│   ├── core/         # Statistics, autocorrelation, MetricType
│   └── results/      # Serializable result models
├── compare/          # Multi-condition statistical comparison
│   ├── comparators/  # RMSF, contacts, triad, BFE, affinity, exposure
│   ├── results/      # Comparison result models
│   └── plotters/     # Publication-quality figures
└── cli/              # Command-line interface
    └── main.py       # Click CLI

Key Classes

Configuration

• SimulationConfig - Main configuration container

• EnzymeConfig - Enzyme settings

• PolymerConfig - Polymer settings

• OutputConfig - Output directory settings

Building

• SystemBuilder - Main system builder

• EnzymeBuilder - Enzyme preparation

• PolymerBuilder - Polymer generation

Simulation

• SimulationRunner - Run simulations

• ContinuationManager - Continue from checkpoint

• SimulationProgress - Track segment completion across jobs

Workflow

• DaisyChainSubmitter - Self-resubmitting SLURM job submission

• SlurmConfig - SLURM configuration

Restraints

• RestraintDefinition - Restraint specification

• AtomSelection - Atom selection

• RestraintFactory - Create restraints from config

Analysis

• RMSFCalculator - Per-residue RMSF

• DistanceCalculator - Inter-group distances

• CatalyticTriadAnalyzer - Catalytic triad integrity

• ParallelContactAnalyzer - Polymer-protein contacts

• BaseAnalysisResult - Serializable result base class

Comparison

• BaseComparator - Template Method comparator base

• ExposureDynamicsComparator - Chaperone analysis

• BindingFreeEnergyComparator - Per-contact ΔG_sel

• PolymerAffinityScoreComparator - Total interaction strength

Quick Reference

Load Configuration

from polyzymd.config.schema import SimulationConfig

config = SimulationConfig.from_yaml("config.yaml")
print(config.enzyme.name)

Build System

from polyzymd.builders.system_builder import SystemBuilder

builder = SystemBuilder(config)
interchange = builder.build(replicate=1)

Run Simulation

from polyzymd.simulation.runner import SimulationRunner

runner = SimulationRunner(interchange, working_dir, config)
runner.run_equilibration()
runner.run_production(segment_index=0)

Submit to SLURM

from polyzymd.workflow.daisy_chain import submit_daisy_chain

results = submit_daisy_chain(
    config_path="config.yaml",
    slurm_preset="aa100",
    replicates="1-5",
)