Main Classes

DynaBench package consists of 2 main classes; dynabench for analysis and Plotter for visualizations.

dynabench

Dynabench.dynabench(trajectory_file, stride=1, split_models=True, chains=None,
 job_name=None, topology_file=None, show_time_as="Frame", timestep=None, time_unit=None)

trajectory_file: string, Path to the trajectory file. The path can be either absolute or relative. Absolute path is recommended.

stride: integer, Stride value for the analysis. Can not be greater than the maximum frame of the trajectory. The default is 1.

split_models: Boolean, Splits all the frames into separate pdb files under the folder named 'models' if True. The default is True.

chains: string, Chains to be analyzed. Chains IDs must be given as comma separated (e.g. 'A,C'). The default is None, which means all chains will be included in the analysis.

job_name: string, Name of the folder where all the outputs will be stored. If None, a random job name with input pdb's name will be created and assigned.

topology_file: string, Path to the topology file. The path can be either absolute or relative. The absolute path is recommended. If the trajectory file is in .dcd format, a topology file is required.

show_time_as: string, 'Frame' or 'Time'. Type of time representation in both analysis outputs and visualizations. The default is 'Frame'.

timestep: float, Timestep between two frames. Recommended if time representation is 'Time'.

time_unit: string, 'ns', or 'nanosecond' for now. Required if time representation is 'Time'.

Plotter

DynaBench.Plotter(job_name)

job_name: string, name or path of the folder where analysis outputs are stored.