Quality Control

Analysis

Quality Control analysis consists of 3 analyses: RMSD, RMSF, and RG. Quality Control is run by run_quality_control function, which creates QualityControl class. run_quality_control gives 3 CSV files:

• QualityControl-overres.csv: Includes RMSF results.

• QualityControl-overtime.csv: Includes RMSD and RG results.

• dockq_results.csv: Includes iRMSD, DockQ Score, lRMSD Fraction of Non-Native Contacts and Fraction of native contacts analysis results for each chain mapping.

DynaBench.dynabench.run_quality_control(rmsd_data={'ref_struc':None, 'ref_frame':0})

• rmsd_data: dict, Dictionary that contains optional variables for RMSD analysis.

  • ref_struc: string, Path to reference structure for RMSD analysis. If None, the structure in the first frame will be set as a reference structure. The default is None.

  • ref_frame: int, Reference frame for RMSD analysis. Can not be greater than the maximum frame number in the trajectory. The default is 0.

Visualization

The visualization of Quality Control analysis is based on the files QualityControl-overres.csv and QualityControl-overtime.csv. Visualization of each analysis is run by 3 different functions. The path of input files can be optionally given by the user.

DynaBench.Plotter.plot_rmsd(path=None)

DynaBench.Plotter.plot_rg(path=None)

• path: string, Path of the input file that includes RMSD, RG, or both analysis data. If None, the function will search the QualityControl-overtime.csv file in the job_name/tables folder. The default is None.

DynaBench.Plotter.plot_irmd(path=None)

DynaBench.Plotter.plot_lrmsd(path=None)

DynaBench.Plotter.plot_dockq(path=None)

DynaBench.Plotter.plot_fnonnat(path=None)

DynaBench.Plotter.plot_fnat(path=None)

• path: string, Path of the input file that includes iRMSD, lRMSD, DockQ Score, FnonNat, Fnat or both analysis data. If None, the function will search the dockq_score.csv file in the job_name/tables folder. The default is None.

DynaBench.Plotter.plot_rmsf(rmsf_path=None, intf_path=None)

The RMSF plot also includes interface residue labeling and skipped frames, if there.

• rmsf_path: string, Path of the file includes RMSF analysis data. If None, the function will search the QualityControl-overres.csv file in the job_name/tables folder. The default is None.

• intf_path: string, Path of the file that includes interface label percentages of residues. The function takes residues that stay as Core, Rim, or Support for at least 50% of the simulation as interface residue. This file is generated after the Residue Based analysis. If there is no such file, interface residues will not be labeled on the plot. If None, the function will search the interface_label_perc.csv file in the job_name/tables folder. The default is None.