pytbc - Tree-based clustering in Python

pytbc contains Python bindings to the tree-based clustering algorithm by Vitalis and Caflisch [Vitalis2012] implemented in Campari.
The Fortran to Python interface is generated with f90wrap to have access to derived types and then compiled with f2py.

Extensions

Campari pytbc bindings are for the moment limited to the tree-based clustering algorithm with dihedral or Euclidean distance (see API reference). More advanced and complete functionalities can be accessed by directly running Campari or by using the CampaRi R package, a complete wrapper of Campari written in R. The user can refer to the documentation of these projects for more in-depth explanations of the algorithm and use cases.

Citations

Please cite [Vitalis2012] if you use pytbc in your work. This project was realized as part of an E-CAM Extended Software Development workshop. Contributions to this project were given by C. Langini, M. Bacci, D. Garolini and A. Vitalis from the Caflisch lab.

Vitalis2012(1,2)

A. Vitalis and A. Caflisch. Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories. J. Chem. Theory Comput. 8 (3), 1108-1120 (2012) DOI

Indices and tables