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.
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.
Error: After installation, importing openmm or running polychrom code leads to the error:
version GLIBCXX_3.4.30 not foundFix:
conda install -c conda-forge libstdcxx-ng=12Polychrom is an API, and each simulation has to be set up as a Python script. Simulations are done using a "simulation" module :pypolychrom.simulation. Forces that define the simulation are found in :pypolychrom.forces and :pypolychrom.forcekits modules. Contactmaps from simulated conformations can be generated using :pypolychrom.contactmaps module. Loading and saving individual conformations can be done using :pypolychrom.polymerutils, while loading/saving whole trajetories is done using :pypolychrom.hdf5_format. P(s), R(s), Rg(s) curves and other analyses can be done using :pypolychrom.polymer_analyses.
polychrom.simulation polychrom.polymerutils polychrom.hdf5_format polychrom.polymer_analyses polychrom.contactmaps polychrom.forces
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