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TTClust : A molecular simulation clustering program

 

TTclust DOI is a python program used to cluster molecular dynamics simulation trajectories. It only requires a trajectory and a topology file (compatible with most molecular dynamic packages such as Amber, Gromacs, Chramm, Namd or trajectory in PDB format thanks to the MDtraj package).

It is available on GitHub https://github.com/tubiana/TTClust.

For Mac user

If you have issues with pip, first try to add to pip the --ignore-installed argument : sudo pip install --ignore-installed -r requirements.txt If it still doesn't work, it's maybe because of the System Integrity Protection (SIP). I suggest you in this case install ANACONDA or MINICONDA and restart your terminal afterwards. Normally, the pip command should work because your default python will be the anaconda (or miniconda) python.

If you have still issues with the GUI or missing packages : install with pip :

pip install wxpython==4.0.0b1
pip install pandas
pip install ttclust

To activate autocompletion for the argpase module, you have to use this command (only once):

sudo activate-global-python-argcomplete

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