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polychrom

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Mirny lab polymer simulation library

It keeps improving, but at this point it is as production ready as openmm-polymer ever was. Hence, openmm-polymer is being deprecated in favor of this library. While it is not backwards compatible, the conversion is easy and intuitive. Note that openmm-polymer is not updated anymore, except for critical bugs.

Some autogenerated docs are here (still in development): https://polychrom.readthedocs.io/en/latest/

It has a new storage format that is described here: https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/hdf5_reporter.ipynb and is discussed in the documentation as well.

New loop extrusion example code is here: https://github.com/mirnylab/polychrom/tree/master/examples/loopExtrusion . It is a good starting point for loop extrusion simulations.

Simplest example simulation that does nothing, which is a good starting point for novel simulations: https://github.com/mirnylab/polychrom/blob/master/examples/example/example.py

And for backwards compatibility with analysis routines, we have legacy reporter https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/legacy_reporter.ipynb and polychrom.polymerutils.load function that is backwards compatible with both new and old style format. https://github.com/mirnylab/polychrom/blob/master/polychrom/polymerutils.py#L22

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A draft of a new version of openmm-polymer

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