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Full_pysoftk

This is the full version of pysoftk that includes:

  1. ring ring and all other functions
  2. umap and hbdscan
  3. intrinsic densities (linear and spherical)

How to install it

you need to install first pysoftwhere and then afterwards pysoftk. Using either conda or virtual enviorements, you can use pip install -e . in both cases. In the case of conda, please enable the environment. For a virtual enviorement, please just source the activate file.

To run the test and the pytest inside python

Due to the size of the trajectory file (115MB), I have to split the trajetory into 2 files which are located in the folder test. To join the trajectory just type (cat intrinsic_density_movie_split.aa intrinsic_density_movie_split.ab > intrinsic_density_movie.xtc) this enables to use the file fail.py.

If you want to run all tests within the folder ../pysoftk/test/test_pol , please move the trajectory .xtc to the folder ../pysoftk/test/test_pol/data and then type inside the folder ../pysoftk/test/test_pol the command pytest.