Welcome to the documentation for the polychrom package

Polychrom is a package for setting up, performing and analyzing polymer simulations of chromosomes. The simulation part is based around VJ Pande’s OpenMM library - a GPU-assisted framework for general molecular dynamics simulations. The analysis part is written by the mirnylab.

Installation

Polychrom requires OpenMM, which can be installed through conda: conda install -c omnia openmm. See http://docs.openmm.org/latest/userguide/application.html#installing-openmm . In our experience, adding -c conda-forge listed in the link above is optional.

CUDA is the fastest GPU-assisted backend to OpenMM. You would need to have the required version of CUDA, or install OpenMM compiled for your version of CUDA.

Other dependencies are simple, and are listed in requirements.txt. All but joblib are installable from either conda/pip, and joblib installs well with pip.

Installation errors and possible fixes

Error: After installation, importing openmm or running polychrom code leads to the error:

version GLIBCXX_3.4.30 not found

Fix:

conda install -c conda-forge libstdcxx-ng=12

Structure

Polychrom is an API, and each simulation has to be set up as a Python script. Simulations are done using a “simulation” module polychrom.simulation. Forces that define the simulation are found in polychrom.forces and polychrom.forcekits modules. Contactmaps from simulated conformations can be generated using polychrom.contactmaps module. Loading and saving individual conformations can be done using polychrom.polymerutils, while loading/saving whole trajetories is done using polychrom.hdf5_format. P(s), R(s), Rg(s) curves and other analyses can be done using polychrom.polymer_analyses.

• polychrom.simulation module
  • Creating a simulation: Simulation class
  • EKExceedsError
  • IntegrationFailError
  • Simulation
• polychrom.polymerutils module
  • Loading and saving individual conformations
  • fetch_block()
  • load()
  • rotation_matrix()
  • save()
• polychrom.hdf5_format module
  • New-style HDF5 trajectories
  • HDF5Reporter
  • list_URIs()
  • load_URI()
  • load_hdf5_file()
  • save_hdf5_file()
• polychrom.polymer_analyses module
  • Analyses of polymer conformations
  • Tools for calculating contacts
  • Tools to calculate P(s) and R(s)
  • R2_scaling()
  • Rg2()
  • Rg2_matrix()
  • Rg2_scaling()
  • calculate_cistrans()
  • calculate_contacts()
  • contact_scaling()
  • generate_bins()
  • getLinkingNumber()
  • kabsch_msd()
  • kabsch_rmsd()
  • mutualSimplify()
  • ndarray_groupby_aggregate()
  • slope_contact_scaling()
  • smart_contacts()
  • streaming_ndarray_agg()
• polychrom.contactmaps module
  • Building contact maps
  • averageContacts()
  • averageContactsSimple()
  • binnedContactMap()
  • chunk()
  • filenameContactMap
  • filenameContactMapRepeat
  • findN()
  • indexing()
  • init()
  • monomerResolutionContactMap()
  • monomerResolutionContactMapSubchains()
  • simple_worker()
  • tonumpyarray()
  • triagToNormal()
  • worker()
• polychrom.forces module
  • Detailed description of forces in polychrom
  • angle_force()
  • constant_force_bonds()
  • cylindrical_confinement()
  • grosberg_angle()
  • grosberg_polymer_bonds()
  • grosberg_repulsive_force()
  • harmonic_bonds()
  • heteropolymer_SSW()
  • polynomial_repulsive()
  • pull_force()
  • selective_SSW()
  • smooth_square_well()
  • spherical_confinement()
  • spherical_well()
  • tether_particles()

Indices and tables

• Index

• Module Index

• Search Page