It is extremely helpful to be able
to partition the thousands of
frames produced in molecular dynamics simulations into a limited number
of most dissimilar conformations. While robust clustering algorithms
are already available to do so, there is a distinct need for an easy-to-use
clustering program with complete user control, taking as input a trajectory
from any molecular dynamics (MD) package and outputting an intuitive
display of results with plots allowing at-a-glance analysis. We present
TTClust (for Trusty Trajectory Clustering), a python program that
uses the MDTraj package to fill this need.
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