public.rosetta

score_analysis.py

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

usage: score_analysis.py [-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	Top N by 10 percent total score to print out. Default: 10
--top_n_by_10_scoretype
	Scoretype to use for any top N by 10 printing. If scoretype not present, won’t do anything. Default: “dG_separated”
--decoy_names	Decoy names to use Default: []
--list_scoretypes
	List score term names Default: False
--pdb_dir, -d	Directory for PDBs if different than the directory of the scorefile

OUTPUT

General output options.

--summary, -S	Compute stats summarizing data Default: False
--csv, -c	Output selected columns, top, and decoys as CSV. Default: False
--make_pdblist	Output PDBlist file(s) Default: False
--pymol_session
	Make pymol session(s) of the scoretypes specified Default: False
--plot	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_top_models
	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/readthedocs.org/user_builds/bio-jade/checkouts/latest/docs”

PLOTTING

Options for plot output

--plot_type	Possible choices: line, scatter, bar, hist, box, kde, area, pie, hexbin The type of plot we are outputting. Default: “scatter”
--plot_filter	Filter X to top Percent of this - useful to remove outliers. Default: 1.0

PYMOL

Options for pymol session output

--native	Native structure to use for pymol sessions.
--ab_structure	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.

RunRosettaMPI.py

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

usage: RunRosettaMPI.py [-h]

RunRosettaDBMode.py

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

usage: RunRosettaDBMode.py [-h]

util

check_missing_rosetta_nstruct.py

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

usage: check_missing_rosetta_nstruct.py [-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.

create_score_json_from_scored_decoys.py

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: create_score_json_from_scored_decoys.py [-h] [--prefix PREFIX]
                                               [decoys [decoys ...]]

Positional Arguments

decoys

A directory, a PDBLIST, and/or a list of filenames Default: []

Named Arguments

--prefix

Any prefix to use. Default: “”

insert_natives_table_into_features_db.py

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: insert_native_table_into_features_db.py [-h] [--pdblist PDBLIST]
                                               [--db DB]

Named Arguments

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