Run from terminal

Arguments

dynabench [-h] [-t TRAJECTORY_FILE] [-c COMMANDS] [-j JOB_NAME] [--remove_water REMOVE_WATER] [--remove_ions REMOVE_IONS] [--foldx_path FOLDX_PATH] [--run_dssp RUN_DSSP] [--time_as TIME_AS] [--timestep TIMESTEP] [--timeunit TIMEUNIT] [--topology_file TOPOLOGY_FILE] [-s STRIDE] [-sm SPLIT_MODELS] [-ch CHAINS] [--rmsd_rs RMSD_RS] [--rmsd_rf RMSD_RF] [--all_hph ALL_HPH] [--rmsd_tpath RMSD_TPATH] [--rg_tpath RG_TPATH] [--rmsf_tpath RMSF_TPATH] [--rmsf_itpath RMSF_ITPATH] [--biophy_tpath BIOPHY_TPATH] [--bondfreq_tpath BONDFREQ_TPATH] [--int_ene_itpath INT_ENE_ITPATH] [--int_ene_tpath INT_ENE_TPATH] [--sasa_tpath SASA_TPATH] [--irmsd_tpath IRMSD_TPATH] [--fnonnat_tpath FNONNAT_TPATH] [--fnat_tpath FNAT_TPATH] [--dssp_tpath DSSP_TPATH] [--dssp_thereshold DSSP_THERESHOLD] [--dssp_intf_tpath DSSP_INTF_TPATH] [--lrmsd_tpath LRMSD_TPATH] [--dockq_tpath DOCKQ_TPATH] [--table_json TABLE_JSON] [--plot_json PLOT_JSON]

Required Arguments

-t , --trajectory_file: Trajectory file in .dcd or .pdb formats. If .dcd, pelase provide topology file with '--topology_file' command.

-c , --commands: Analyses to run. You can provide multiple run commands, in comma seperated form. Choises are: 'all_analysis', 'QualityControl', 'ResidueBased', 'InteractionBased' for analysis and, 'all_plots', 'PlotRMSD', 'PlotRG', 'PlotRMSF', 'PlotPairwiseFreq', 'PlotBiophys', 'PlotResEne' for visualization.

Optional Arguments

-j , --job_name:The name of the job, if null, DynaBench will generate a name from the input file.

--remove_ions:Removes ions if True. Default is True.

--remove_water:Removes water if True. Default is True.

--run_dssp:Runs DSSP analysis within the Residue Based analyses if True. Default is True.

--foldx_path : Absolute path of FoldX executable.

--time_as : 'Frame' or 'Time'. If Time, you should provide time unit with --timeunit command.

--timestep : Timestep value of simulation.

--timeunit : Nanosecond or ns is acceptable for now.

--topology_file : Path of topology file for dcd trajectories.

-s , --stride : Stride value.

-sm , --split_models : Whether models will be split or not.

-ch , --chains : For heteromers, you can decide which two chains to be analyzed. Provide input such as 'A,B'.

--rmsd_rs : Path to reference structure for RMSD analysis.

--rmsd_rf : Reference frame for RMSD analyze.

--all_hph : If True, all possible hydrophobic bonds will be calculated.

--rmsd_tpath : CSV data path for RMSD plot.

--rg_tpath : CSV data path for RG plot.

--rmsf_tpath : CSV data path for RMSF plot.

--rmsf_itpath : CSV data including interface residues path for RMSF plot.

--biophy_tpath : CSV data path of residue based analysis.

--bondfreq_tpath : CSV data of interaction based analysis.

--int_ene_itpath : CSV data path of residue based analysis.

--int_ene_tpath : CSV data including interface residues path for interaction energy plot.

--sasa_tpath : CSV data path for SASA plot.

--irmsd_tpath : CSV data path for iRMSD plot.

--fnonnat_tpath : CSV data path for Fraction of Non-Native Contacts plot.

--fnat_tpath : CSV data path for Fraction of Native Contacts plot.

--dssp_tpath : CSV data path for dssp plot.

--dssp_thereshold : Threshold value for interface residue selection in DSSP analysis. The default is 50.

--dssp_intf_tpath : CSV data of interface residues path for dssp plot.

--lrmsd_tpath : CSV data path for lRMSD plot.

--dockq_tpath : CSV data path for DockQ Score plot.

--table_json : JSON file path for analysis runs.

--plot_json : JSON file path for visualization runs.

Example Runs

Complete run (Quality Control, Residue Based, Interaction Based analyses with all visualizations), pdb input.

dynabench --job_name=job_name --trajectory_file=trajectory_file.pdb --commands=all_analysis,all_plots --foldx_path=foldx_path

or

dynabench --job_name=job_name --trajectory_file= trajectory_file.pdb --commands=QualityControl,ResidueBased,InteractionBased,PlotRMSD,PlotRG,PlotRMSF,'PlotPairwiseFreq', 'PlotBiophys', 'PlotResEne' --foldx_path=foldx_folder_path

All analysis runs, dcd input, stride 20, chains C and D

dynabench --job_name=job_name --trajectory_file=trajectory.dcd --commands=all_analysis --topology_file=topology.pdb --foldx_path=foldx_folder_path --stride=20

Run with .json files

dynabench --table_json=path_to_table_params.json --plot_json=path_to_plot_params.json