This utility parses and extracts data from score files in JSON format

usage: [-h] [-s [SCORETYPES [SCORETYPES ...]]] [-n TOP_N]
                         [--top_n_by_10 TOP_N_BY_10]
                         [--top_n_by_10_scoretype TOP_N_BY_10_SCORETYPE]
                         [--decoy_names [DECOY_NAMES [DECOY_NAMES ...]]]
                         [--list_scoretypes] [--pdb_dir PDB_DIR] [--summary]
                         [--csv] [--make_pdblist] [--pymol_session]
                         [--plot [PLOT [PLOT ...]]] [--copy_top_models]
                         [--prefix PREFIX] [--outdir OUTDIR]
                         [--plot_type {line,scatter,bar,hist,box,kde,area,pie,hexbin}]
                         [--plot_filter PLOT_FILTER] [--native NATIVE]
                         [--ab_structure] [--super SUPER]
                         [scorefiles [scorefiles ...]]

Positional Arguments

scorefiles A list of scorefiles

Named Arguments

-s, --scoretypes

List of score terms to extract

Default: [‘dSASA_int’, ‘delta_unsatHbonds’, ‘hbonds_int’, ‘total_score’, ‘dG_separated’, ‘top_n_by_10’]

-n, --top_n

Only list Top N when doing top scoring decoys or making pymol sessionsDefault is to print all of them.

Default: -1


Top N by 10 percent total score to print out.

Default: 10


Scoretype to use for any top N by 10 printing. If scoretype not present, won’t do anything.

Default: “dG_separated”


Decoy names to use

Default: []


List score term names

Default: False

--pdb_dir, -d Directory for PDBs if different than the directory of the scorefile


General output options.

--summary, -S

Compute stats summarizing data

Default: False

--csv, -c

Output selected columns, top, and decoys as CSV.

Default: False


Output PDBlist file(s)

Default: False


Make pymol session(s) of the scoretypes specified

Default: False


Plot one score type vs another. Save the plot. 2 or 3 Arguments. [X, Y, ‘Title’‘] OR [X, ‘Title’]. If title has spaces, use quotes. Nothing special, just used for quick info.

Default: []


Copy the top -n to the output directory for each scorefile passed.

Default: False

--prefix, -p

Prefix to use for any file output. Do not include any _

Default: “”

--outdir, -o

Output dir. Default is current directory.

Default: “/home/docs/checkouts/”


Options for plot output


Possible choices: line, scatter, bar, hist, box, kde, area, pie, hexbin

The type of plot we are outputting.

Default: “scatter”


Filter X to top Percent of this - useful to remove outliers.

Default: 1.0


Options for pymol session output

--native Native structure to use for pymol sessions.

Specify if the module is a renumbered antibody structure. Will run pymol script for ab-specific selection

Default: False

--super Super this selection instead of align all to.

This program runs Rosetta MPI locally or on a cluster using slurm or qsub. Relative paths are accepted.

usage: [-h]

This program runs Rosetta MPI locally or on a cluster using slurm or qsub. Relative paths are accepted.

usage: [-h]


This extremely simple script checks nstruct of the input files and outputs which nstruct number is missing.

usage: [-h] [-n NSTRUCT]
                                        [--pdb_files [PDB_FILES [PDB_FILES ...]]]
                                        [--pdblist PDBLIST] [--dir DIR]

Named Arguments

-n, --nstruct Default: 1000
--pdb_files Path to PDB files we will be checking.
--pdblist, -l Optional INPUT PDBLIST (without 00s, etc. for which to check
--dir The Directory to check. As opposed to a list of pdb files.

This script creates a Rosetta score file from a set of structures - by parsing the score from them. Pass a directory, a PDBLIST, and/or a list of filenames

usage: [-h] [--prefix PREFIX]
                                               [decoys [decoys ...]]

Positional Arguments


A directory, a PDBLIST, and/or a list of filenames

Default: []

Named Arguments


Any prefix to use.

Default: “”

This script takes a PDBLIST of natives and then adds a new table to the database with struct_id as proper foreign primary key and the native structure based solely on a search of the name tag.

usage: [-h] [--pdblist PDBLIST]
                                               [--db DB]

Named Arguments

--pdblist PDBLIST of native structures used.
--db The database we are working on.