Logo
  • Get Started
    • Start Here
    • What You Will Accomplish
    • Before You Move On
      • Install PolyzyMD with pixi
      • Run Your First PolyzyMD Simulation
  • Tutorials
    • Featured Tutorials
    • What Belongs Here
      • Analyze a Multi-Condition Study
  • How-To Guides
    • Core Simulation Tasks
    • Analysis Tasks
    • Recipe Collections
      • Run PolyzyMD on SLURM Clusters
      • Add Distance Restraints
      • Set Up Equilibration Stages
      • Add Polymers to a Simulation
      • Generate Polymers from SMILES
      • Export a System to GROMACS
      • Troubleshoot Common Problems
      • Run RMSF Analysis
      • Run Distance Analysis
      • Run Contacts Analysis
      • Compare Simulation Conditions
      • Run Catalytic Triad Analysis
      • Experimental: Analyze Binding Preference
      • Experimental: Analyze Binding Free Energy
      • Experimental: Analyze Polymer Affinity
      • Experimental: Analyze Exposure Dynamics
      • Contacts Cookbook
      • Broken Molecule Debugging
  • Reference
    • User-Facing Reference
    • API Reference
    • When Not to Use This Section
      • CLI Reference
      • Configuration Reference
      • Comparison and Plotting Reference
      • Benchmarks
      • API Overview
      • Configuration API
      • Builders API
      • Simulation API
      • Workflow API
      • Core API
      • Analysis API
      • Compare API
  • Explanation
    • Concepts and Design
    • Analysis Interpretation and Best Practices
    • Experimental Analysis Concepts
      • Architecture
      • Residue Assignment and Chain Conventions
      • Colored Logging
      • Statistical Best Practices for Analysis
      • RMSF Best Practices
      • RMSF Reference Selection
      • RMSF Verification
      • Catalytic Triad Best Practices
  • Contributor Guide
    • Start Here
    • Extension Workflows
    • Contributor Mindset
      • Contributing to PolyzyMD
      • Set Up a Contributor Environment
      • Packaging and Distribution Notes
      • Extend Comparison Workflows
      • Extend Plotting Workflows
PolyzyMD
  • Python Module Index

Python Module Index

p
 
p
- polyzymd
    polyzymd.builders.enzyme
    polyzymd.builders.polymer
    polyzymd.builders.solvent
    polyzymd.builders.substrate
    polyzymd.builders.system_builder
    polyzymd.compare.binding_free_energy_formatters
    polyzymd.compare.cli
    polyzymd.compare.comparators.binding_free_energy
    polyzymd.compare.comparators.contacts
    polyzymd.compare.comparators.distances
    polyzymd.compare.comparators.exposure
    polyzymd.compare.comparators.polymer_affinity
    polyzymd.compare.comparators.rmsf
    polyzymd.compare.comparators.triad
    polyzymd.compare.config
    polyzymd.compare.core.base
    polyzymd.compare.core.registry
    polyzymd.compare.plotters.binding_free_energy
    polyzymd.compare.plotters.exposure
    polyzymd.compare.plotters.polymer_affinity
    polyzymd.compare.polymer_affinity_formatters
    polyzymd.compare.results.binding_free_energy
    polyzymd.compare.results.exposure
    polyzymd.compare.results.polymer_affinity
    polyzymd.compare.settings
    polyzymd.compare.statistics
    polyzymd.config.loader
    polyzymd.config.schema
    polyzymd.core.parameters
    polyzymd.core.restraints
    polyzymd.simulation.continuation
    polyzymd.simulation.runner
    polyzymd.workflow.daisy_chain
    polyzymd.workflow.slurm

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