polychrom
latest
  • polychrom.simulation module
  • polychrom.polymerutils module
    • Loading and saving individual conformations
  • 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
  • polychrom.polymer_analyses module
    • Analyses of polymer conformations
      • Tools for calculating contacts
      • Tools to calculate P(s) and R(s)
  • polychrom.contactmaps module
    • Building contact maps
  • polychrom.forces module
    • Detailed description of forces in polychrom
      • Parametrization of bond forces
      • Note on energy equations
polychrom
  • Docs »
  • 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.starting_conformations

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