polychrom package

Submodules

• polychrom.simulation module
  • Creating a simulation: Simulation class
    • Overall parameters
    • Adding forces
    • Defining your own forces
    • Running a simulation
  • EKExceedsError
  • IntegrationFailError
  • Simulation
    • Simulation.RG()
    • Simulation.__init__()
    • Simulation.add_force()
    • Simulation.dist()
    • Simulation.do_block()
    • Simulation.get_data()
    • Simulation.get_scaled_data()
    • Simulation.init_positions()
    • Simulation.init_velocities()
    • Simulation.initialize()
    • Simulation.local_energy_minimization()
    • Simulation.print_stats()
    • Simulation.reinitialize()
    • Simulation.set_data()
    • Simulation.set_velocities()
    • Simulation.show()
• polychrom.forcekits module
  • Forcekits (new in polychrom)
  • polymer_chains()
• polychrom.forces module
  • Detailed description of forces in polychrom
    • Parametrization of bond forces
    • Note on energy equations
  • 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()
• polychrom.contactmaps module
  • Building contact maps
  • averageContacts()
  • averageContactsSimple()
  • binnedContactMap()
  • chunk()
  • filenameContactMap
    • filenameContactMap.__init__()
    • filenameContactMap.next()
  • filenameContactMapRepeat
    • filenameContactMapRepeat.__init__()
    • filenameContactMapRepeat.next()
  • findN()
  • indexing()
  • init()
  • monomerResolutionContactMap()
  • monomerResolutionContactMapSubchains()
  • simple_worker()
  • tonumpyarray()
  • triagToNormal()
  • worker()
• polychrom.hdf5_format module
  • New-style HDF5 trajectories
    • The purpose of the HDF5 reporter
    • one file vs many files vs several files
    • Polychrom storage format
    • Separation of simulation and repoter
    • Multi-stage simulations or loop extrusion
    • URIs to identify individual conformations
  • HDF5Reporter
    • HDF5Reporter.__init__()
    • HDF5Reporter.continue_trajectory()
    • HDF5Reporter.dump_data()
    • HDF5Reporter.report()
  • 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.polymerutils module
  • Loading and saving individual conformations
  • fetch_block()
  • load()
  • rotation_matrix()
  • save()
• polychrom.pymol_show module
  • createRegions()
  • do_coloring()
  • getTmpPath()
  • interpolateData()
  • makeMovie()
  • makeMoviePymol()
  • new_coloring()
  • show_chain()
• polychrom.starting_conformations module
  • create_constrained_random_walk()
  • create_random_walk()
  • create_spiral()
  • grow_cubic()

Module contents

Structure

Polychrom is an API, and each simulation has to be set up as a Python script. Simulations are done using a polychrom.simulation module submodule (polychrom.simulation.simulation)