polychrom
  • 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.polymerutils module
    • Loading and saving individual conformations
    • fetch_block()
    • load()
    • rotation_matrix()
    • save()
  • 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()
    • rotation_matrix()
    • slope_contact_scaling()
    • smart_contacts()
    • streaming_ndarray_agg()
  • 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.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
  • Overview: module code

All modules for which code is available

  • polychrom.contactmaps
  • polychrom.forcekits
  • polychrom.forces
  • polychrom.hdf5_format
  • polychrom.legacy.contactmaps
  • polychrom.legacy.forces
  • polychrom.legacy.legacy_format
  • polychrom.polymer_analyses
  • polychrom.polymerutils
  • polychrom.pymol_show
  • polychrom.simulation
  • polychrom.starting_conformations

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