Run from script

Complete run (Quality Control, Residue Based and Interaction Based analyses with all visualizations), dcd trajectory file, no stride.

Import the package.

import DynaBench 

Define analysis class, load trajectory .dcd, and topology .pdb file.

mol = DynaBench.dynabench(trajectory_file='your_trajectory_path', topology_file='your_topology_path', 
split_models=True, show_time_as='Frame')

Define plotter class.

draw = DynaBench.Plotter(job_name=mol.job_name)

Quality Control analysis, and RMSD and RG visualizations. RMSF plot can be done after residue-based analysis to mark the interface residues on the plot.

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

draw.plot_rmsd(path=None) 

draw.plot_rg(path=None)

draw.plot_irmsd(path=None)

draw.plot_lrmsd(path=None)

draw.plot_dockq(path=None)

draw.plot_fnonnat(path=None)

draw.plot_fnat(path=None)

Residue Based analysis and Interaction Energy, Biophysical Type-Interface Label, RMSF visualizations.

mol.run_res_based('foldx_path', run_dssp=True)
 
draw.plot_rmsf(rmsf_path=None, intf_path=None)
 
draw.plot_biophys(path=None)

draw.plot_SASA()

draw.plot_dssp(thereshold=50.0, path=None, intf_path=None)

draw.plot_int_energy(thereshold=50.0, res_path=None, intf_path=None) 

Interaction Based analysis and Pairwise Frequency visualizations.

mol.run_inter_based()

draw.plot_pairwise_freq(path=None)

Get JSON files which include all the parameters for analysis and plots, separately.

mol.get_params() 

draw.get_params()