Completely rewritten

The program has been rewritten to include the math derived in Chandrasekaran et. al. 2017, which is the latest version of the theory of path. Apart from that the following changes have been made to the program.

• path has been renamed PyPath.

• Several speed and performance enhancements

• Removed the "rock" mode

• Removed use of constraints

• Documentation provided for all functions

Added constraints to the "path" mode

New features

• CA atoms of pairs of aminoacids can now be constrained in the "path" mode

Other

• running-path has been updated to reflect the changes to the program

Added the ability to calculate trajectories along normal modes

New Features

• Compute trajectories along the nth normal mode
• Apply constraints to the normal mode trajectories

Updates

• CA only simulations are computed using Hessian matrices that are mass weighted versions of the Hessian described in Hinsen et.al

Other

• Cleaned up the code to enhance readability