DynaBench

DynaBench is an object-oriented Python library to analyze trajectories from molecular dynamics simulations, in pdb and dcd formats. DynaBench offers preprocess step, which includes transforming .dcd files to .pdb, adjusting stride, and time/frame display according to the given time unit and stride.

DynaBench runs 3 types of analysis:

• Quality Control

• Residue Based

• Interaction Based

The complete workflow of DynaBench can be seen in the figure. Visualization functions of DynaBench use outputs of Analysis functions, which can be also provided by the user.

DynaBench returns two .json files: plot_params.json and table_params.json. These files include all the parameters of visualization and analysis runs, respectively. DynaBench can also be run with the .json files.

Availability

DynaBench can be only downloaded from GitHub for now. To download DynaBench from GitHub, please visit https://github.com/Atakanzsn/DynaBench