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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

Polychrom is an Open2C polymer simulation library designed to build mechanistic models of chromosomes. It simulates biological processes subject to forces or constraints, which are then compared to Hi-C maps, microscopy, and other data sources.

Development Commands

Installation

pip install cython  # Required dependency
pip install -r requirements.txt
pip install -e .  # Install in development mode

Testing

pytest  # Run all tests

Building Cython Extensions

python setup.py build_ext --inplace

Architecture

Core Components

Simulation Module (polychrom/simulation.py)

  • Central Simulation class manages the entire simulation lifecycle
  • Handles platform setup (CUDA/OpenCL/CPU), integrators, and parameters
  • Methods: set_data() for loading conformations, add_force() for adding forces, doBlock() for running simulation steps

Forces System (polychrom/forces.py, polychrom/forcekits.py)

  • Forces define polymer behavior: connectivity, confinement, crosslinks, tethering
  • Individual forces in forces.py are functions that create OpenMM force objects
  • Complex force combinations are packaged as "forcekits" (e.g., polymer_chains)
  • Legacy forces available in polychrom/legacy/forces.py

Data Storage (polychrom/hdf5_format.py)

  • HDF5Reporter handles simulation output in HDF5 format
  • Backwards compatibility with legacy format via legacy reporter
  • polymerutils.load() function reads both new and old formats

Starting Conformations (polychrom/starting_conformations.py)

  • Functions to generate initial polymer configurations
  • Example: grow_cubic() creates a cubic lattice conformation

Key Design Patterns

  1. Force Architecture: Forces are simple functions that wrap OpenMM force objects, returning the force with a .name attribute
  2. Simulation Flow: Initialize Simulation → Load data → Add forces → Run blocks in loop → Save via reporter
  3. Extensibility: Users can define custom forces in their scripts following the pattern in forces.py

Important Notes

  • OpenMM is the underlying engine (required dependency not in requirements.txt)
  • Cython extensions in _polymer_math.pyx require compilation
  • Main use case is loop extrusion simulations (see examples/loopExtrusion/)
  • Testing uses pytest with configuration in pytest.ini