Outputing replica trajectories from simulation output

[covo6734]

The script scan_torsions.py ( foldamers/examples/varying_model_parameters/scan_torsions ) is outputting raw trajectory data (.nc files) into files organized by the angles of sc_bb_bb_sc and sc_bb_bb_bb. PDB files are extracted from these the .nc files and are classified as native or non-native, based on how well they match a determined native structure (I think established before the simulation). The files output into these directories are pdb files from all replicas, but individual replicas are not evident from the native/non-native classification. The values necessary to be considered a native contact and the range of angles used for the sc_bb_bb_sc and sc_bb_bb_bb are both defined in the script.

We want to be able to visualize the individual trajectories of each replica without the extra step of native/non-native classification, so the full of the trajectory of a given replica can be visualized in one file.

Currently, I'm making changes to the file mentioned above and running using the following command.

python scan_torsions.py