A repository for modules and applications to aid in the design and analysis of Biological molecules, especially when working with Rosetta or PyRosetta.
- Free software: BSD license
- A suite of modules for working with biological molecules in python.
- A suite of public and pilot applications to make day-to-day tasks easier.
- Commonly used ones include score_analysis.py, get_seq.py, and RunRosettaMPI.py
Used for some applications and the rosetta_jade module.
- Rosetta : [http://www.rosettacommons.org]
- PyRosetta: [http://www.pyrosetta.org]
Simple setup for development (and cluser) purposes.
- Run the
setup.pyscript to copy apps into the bin directory. - Add jade2 to your PythonPath.
- Add the /bin directory to your Path.
This package is still under heavy development, and test code coverage is limited at the moment.
- Jade2
- Application Docs
Created by gh-md-toc
usage: Analyze data output from a glycan_scanning job created using the JADE create_glycan_scanning_job script
[-h] [-s S] [--outdir_prefix OUTDIR_PREFIX] [--get_top] [--get_plots]
[--native_path NATIVE_PATH]
optional arguments:
-h, --help show this help message and exit
-s S Score file with extra metrics.
--outdir_prefix OUTDIR_PREFIX
Prefix for output directories
--get_top Get pymol sessions and top models
--get_plots Get plots for analysis
--native_path NATIVE_PATH
Path to native
usage: convert_fig.py [-h]
Converts images to TIFF figures at 300 DPI for publication using sips.
Arguments: INFILE OUTFILEExample: convert_to.py in_fig.pdf out_fig.tiff
Example: convert_to.py in_fig.png out_fig.eps eps
optional arguments:
-h, --help show this help message and exit
Use: canceljobs.py start end
usage: genscript_to_fasta.py [-h] --format {mutagenesis,GeneSynth} infile
This script outputs fasta files from a genscript format. Pass the --format
option to control which genscript format as input ~~~ Ex: python
genscript_mut_to_fasta.py --format mutagenesis MutagenesisFormatU68 ~~~
positional arguments:
infile The mutagenesis format file.
optional arguments:
-h, --help show this help message and exit
--format {mutagenesis,GeneSynth}
The genscript file format
usage: get_seq.py [-h] [--pdb PDB] [--pdblist PDBLIST]
[--pdblist_input_dir PDBLIST_INPUT_DIR] [--chain CHAIN]
[--cdr CDR]
[--format {basic,fasta,general_order,IgG_order,IgG_order_lambda,IgG_order_kappa,IgG_order_heavy}]
[--outpath OUTPATH] [--prefix PREFIX] [--region REGION]
[--strip_c_term STRIP_C_TERM] [--pad_c_term PAD_C_TERM]
[--output_original_seq]
Uses Biopython to print sequence information. Example: get_seq.py --pdb
2j88_A.pdb --format fasta --outpath test.txt
optional arguments:
-h, --help show this help message and exit
--pdb PDB, -s PDB Input PDB path
--pdblist PDBLIST, -l PDBLIST
Input PDB List
--pdblist_input_dir PDBLIST_INPUT_DIR, -i PDBLIST_INPUT_DIR
Input directory if needed for PDB list
--chain CHAIN, -c CHAIN
A specific chain to output
--cdr CDR Pass a specific CDR to output alignments of.
--format {basic,fasta,general_order,IgG_order,IgG_order_lambda,IgG_order_kappa,IgG_order_heavy}
The output format requried.
--outpath OUTPATH, -o OUTPATH
Output path. If none is specified it will write to
screen.
--prefix PREFIX, -t PREFIX
Tag to add before chain
--region REGION specify a particular region, start:end:chain
--strip_c_term STRIP_C_TERM
Strip this sequence off the C-term of resulting
sequences. (Useful for antibodies
--pad_c_term PAD_C_TERM
Pad this sequence with some C-term (Useful for
antibodies
--output_original_seq
Output the original sequence and the striped seqeunce
if stripped. Default FALSE.
usage: rename_designs.py [-h] -i NEW_NAMES
Renames original files to new names for design ordering. Copy all models going
to be ordered into a single directory first. Run from directory with pdb files
already copied in!
optional arguments:
-h, --help show this help message and exit
-i NEW_NAMES, --new_names NEW_NAMES
File with new to old names. Example line: new_name *
filename. Can have lines that don't have all three.
Will only rename if it has a star in the second
column.
usage: score_analysis.py [-h] -s [SCOREFILES [SCOREFILES ...]]
[--scoretypes [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]
This utility parses and extracts data from score files in JSON format
optional arguments:
-h, --help show this help message and exit
-s [SCOREFILES [SCOREFILES ...]], --scorefiles [SCOREFILES [SCOREFILES ...]]
Scorefiles to use
--scoretypes [SCORETYPES [SCORETYPES ...]]
List of score terms to extract
-n TOP_N, --top_n TOP_N
Only list Top N when doing top scoring decoys or
making pymol sessionsDefault is to print all of them.
--top_n_by_10 TOP_N_BY_10
Top N by 10 percent total score to print out.
--top_n_by_10_scoretype TOP_N_BY_10_SCORETYPE
Scoretype to use for any top N by 10 printing. If
scoretype not present, won't do anything.
--decoy_names [DECOY_NAMES [DECOY_NAMES ...]]
Decoy names to use
--list_scoretypes List score term names
--pdb_dir PDB_DIR, -d PDB_DIR
Directory for PDBs if different than the directory of
the scorefile
OUTPUT:
General output options.
--summary, -S Compute stats summarizing data
--csv, -c Output selected columns, top, and decoys as CSV.
--make_pdblist Output PDBlist file(s)
--pymol_session Make pymol session(s) of the scoretypes specified
--plot [PLOT [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.
--copy_top_models Copy the top -n to the output directory for each
scorefile passed.
--prefix PREFIX, -p PREFIX
Prefix to use for any file output. Do not include any
_
--outdir OUTDIR, -o OUTDIR
Output dir. Default is current directory.
PLOTTING:
Options for plot output
--plot_type {line,scatter,bar,hist,box,kde,area,pie,hexbin}
The type of plot we are outputting.
--plot_filter PLOT_FILTER
Filter X to top Percent of this - useful to remove
outliers.
PYMOL:
Options for pymol session output
--native 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
--super SUPER Super this selection instead of align all to.
usage: This program runs Rosetta MPI locally or on a cluster using slurm or qsub. Relative paths are accepted.
[-h] [-s S] [-l L] [--np NP] [--nstruct NSTRUCT] [--job_name JOB_NAME]
[--outdir OUTDIR] [--json_run JSON_RUN] [--extra_options EXTRA_OPTIONS]
[--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]] [--jd3]
[--program PROGRAM] [--print_only] [--local_test] [--one_file_mpi]
[--job_manager {slurm,qsub,local,local_test}]
[--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]]
[--json_base JSON_BASE] [--compiler {gcc,clang}] [--mpiexec MPIEXEC]
[--machine_file MACHINE_FILE] [--db_mode {sqlite3,mysql,postgres}]
[--db_name DB_NAME] [--db_batch DB_BATCH] [--db_in] [--db_out]
optional arguments:
-h, --help show this help message and exit
Common Options:
-s S Path to a pdb file
-l L Path to a list of pdb files
--np NP Number of processors to use for MPI. Default = 101
--nstruct NSTRUCT The number of structures/parallel runs. Can also set
this in any JSON file.
--job_name JOB_NAME Set the job name used for mpi_tracer_to_file dir and
queue. Default = 'rosetta_run'. (Benchmarking:
Override any set in json_base.)
--outdir OUTDIR, -o OUTDIR
Outpath. Default = 'pwd/decoys'
--json_run JSON_RUN JSON file for specific Rosetta run. Not required. Pre-
Configured JSONS include:
['antibody_designer_even_clus_dock.json',
'relax.json', 'remodel.json', 'cluster_features.json',
'NGK_smooth.json',
'antibody_designer_even_len_clus_dock.json',
'pareto_optimal_relax.json', 'relaxed_design.json',
'antibody_H3.json', 'antibody_features.json',
'antibody_designer_even_len_clus.json',
'glycosylate_relax.json', 'dualspace_relax.json',
'interface_analyzer.json', 'common_flags.json',
'blank.json', 'relaxed_design_ds.json',
'antibody_designer_even_clus.json', 'NGK.json',
'antibody_designer_dock.json', 'snugdock.json',
'antibody_designer.json', 'rosetta_scripts.json',
'glycan_clash_check.json', 'NGK_smooth_shap.json']
--extra_options EXTRA_OPTIONS
Extra Rosetta options. Specify in quotes!
--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]
Any script vars for XML scripts.Specify as you would
in Rosetta. like: glycosylation=137A,136A
--jd3 Is this app JD3? Must build with
extras=mpi,serialization.
--program PROGRAM Define the Rosetta program to use if not set in
json_run
Testing and Debugging:
--print_only Do not actually run anything. Just print setup for
review.
--local_test Is this a local test? Will change nstruct to 1 and run
on 2 processors
--one_file_mpi Output all MPI std::out to a single file instead of
splitting it.
Special Options for controlling execution:
--job_manager {slurm,qsub,local,local_test}
Job Manager to launch job. (Or none if local or
local_test)Default = 'slurm '
--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]
Extra options for the job manager, such as queue or
processor requestsRemove double dashes. Exclusive is
on by default. Specify like: -p imperial exclusive.
--json_base JSON_BASE
JSON file for setting up base paths/etc. for the
cluster.Default =
'database/rosetta/jsons/common_flags.json'
--compiler {gcc,clang}
Set the compiler used. Will set clang automatically
for macos. Default = 'gcc'
--mpiexec MPIEXEC Specify a particular path (or type of) MPI exec.
Default is srun (due to vax). If local or local test,
will use mpiexex
--machine_file MACHINE_FILE
Optional machine file for passing to MPI
Relational Databases:
Options for Rosetta Database input and output. Use for features or for
inputting and output structures as databases
--db_mode {sqlite3,mysql,postgres}
Set the mode for Rosetta to use if using a database.
Features will be output to a database. If not sqlite3,
must build Rosetta with extras. If any post-processing
is required, such as combining sqlite3 dbs, will do
this. Default DB mode for features is sqlite3.
--db_name DB_NAME In or Out database name
--db_batch DB_BATCH Batch of structures.
--db_in Use an input database
--db_out Use an output database
usage: check_missing_rosetta_nstruct.py [-h] [-n NSTRUCT]
[--pdb_files [PDB_FILES [PDB_FILES ...]]]
[--pdblist PDBLIST] [--dir DIR]
This extremely simple script checks nstruct of the input files and outputs
which nstruct number is missing.
optional arguments:
-h, --help show this help message and exit
-n NSTRUCT, --nstruct NSTRUCT
--pdb_files [PDB_FILES [PDB_FILES ...]]
Path to PDB files we will be checking.
--pdblist PDBLIST, -l PDBLIST
Optional INPUT PDBLIST (without 00s, etc. for which to
check
--dir DIR The Directory to check. As opposed to a list of pdb
files.
usage: insert_natives_table_into_features_db.py [-h] [--pdblist PDBLIST]
[--db DB]
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.
optional arguments:
-h, --help show this help message and exit
--pdblist PDBLIST PDBLIST of native structures used.
--db DB The database we are working on.
usage: create_score_json_from_scored_decoys.py [-h] [--prefix PREFIX]
[decoys [decoys ...]]
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
positional arguments:
decoys A directory, a PDBLIST, and/or a list of filenames
optional arguments:
-h, --help show this help message and exit
--prefix PREFIX Any prefix to use.
usage: This program runs Rosetta MPI locally or on a cluster using slurm or qsub. Relative paths are accepted.
[-h] [-s S] [-l L] [--np NP] [--nstruct NSTRUCT] [--job_name JOB_NAME]
[--outdir OUTDIR] [--json_run JSON_RUN] [--extra_options EXTRA_OPTIONS]
[--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]] [--jd3]
[--program PROGRAM] [--print_only] [--local_test] [--one_file_mpi]
[--job_manager {slurm,qsub,local,local_test}]
[--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]]
[--json_base JSON_BASE] [--compiler {gcc,clang}] [--mpiexec MPIEXEC]
[--machine_file MACHINE_FILE]
optional arguments:
-h, --help show this help message and exit
Common Options:
-s S Path to a pdb file
-l L Path to a list of pdb files
--np NP Number of processors to use for MPI. Default = 101
--nstruct NSTRUCT The number of structures/parallel runs. Can also set
this in any JSON file.
--job_name JOB_NAME Set the job name used for mpi_tracer_to_file dir and
queue. Default = 'rosetta_run'. (Benchmarking:
Override any set in json_base.)
--outdir OUTDIR, -o OUTDIR
Outpath. Default = 'pwd/decoys'
--json_run JSON_RUN JSON file for specific Rosetta run. Not required. Pre-
Configured JSONS include:
['antibody_designer_even_clus_dock.json',
'relax.json', 'remodel.json', 'cluster_features.json',
'NGK_smooth.json',
'antibody_designer_even_len_clus_dock.json',
'pareto_optimal_relax.json', 'relaxed_design.json',
'antibody_H3.json', 'antibody_features.json',
'antibody_designer_even_len_clus.json',
'glycosylate_relax.json', 'dualspace_relax.json',
'interface_analyzer.json', 'common_flags.json',
'blank.json', 'relaxed_design_ds.json',
'antibody_designer_even_clus.json', 'NGK.json',
'antibody_designer_dock.json', 'snugdock.json',
'antibody_designer.json', 'rosetta_scripts.json',
'glycan_clash_check.json', 'NGK_smooth_shap.json']
--extra_options EXTRA_OPTIONS
Extra Rosetta options. Specify in quotes!
--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]
Any script vars for XML scripts.Specify as you would
in Rosetta. like: glycosylation=137A,136A
--jd3 Is this app JD3? Must build with
extras=mpi,serialization.
--program PROGRAM Define the Rosetta program to use if not set in
json_run
Testing and Debugging:
--print_only Do not actually run anything. Just print setup for
review.
--local_test Is this a local test? Will change nstruct to 1 and run
on 2 processors
--one_file_mpi Output all MPI std::out to a single file instead of
splitting it.
Special Options for controlling execution:
--job_manager {slurm,qsub,local,local_test}
Job Manager to launch job. (Or none if local or
local_test)Default = 'slurm '
--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]
Extra options for the job manager, such as queue or
processor requestsRemove double dashes. Exclusive is
on by default. Specify like: -p imperial exclusive.
--json_base JSON_BASE
JSON file for setting up base paths/etc. for the
cluster.Default =
'database/rosetta/jsons/common_flags.json'
--compiler {gcc,clang}
Set the compiler used. Will set clang automatically
for macos. Default = 'gcc'
--mpiexec MPIEXEC Specify a particular path (or type of) MPI exec.
Default is srun (due to vax). If local or local test,
will use mpiexex
--machine_file MACHINE_FILE
Optional machine file for passing to MPI
Simple app to scan a PDB file and print PDB info and Rosetta understood chains
and resnums.
positional arguments:
pdb_file The PDB file to scan.
optional arguments:
-h, --help show this help message and exit
--chain CHAIN, -c CHAIN
Specify only a single chain to scan.
--echo_input, -e Echo the input structure as output. This is to check
how Rosettta worked reading it.
This simple script aims to identify glycosylated positions in a PDB and thier associated rosetta Resnums.
Please specifiy a PDB as the only argument to this script.
usage: Get Phi/Psi of all residues in protein or a range of residues
[-h] -s S [--start START] [--span SPAN]
optional arguments:
-h, --help show this help message and exit
-s S Input Structure
--start START Starting resnum (pose/PDB - EX:24L)
--span SPAN Number of residues to print from start
usage: Create a JD3 Job Definition file to scan compatible surface residues and do denovo glycosylation and modeling. This is for IDEAL sequons only
[-h] [--selections SELECTIONS] [--selector SELECTOR] -s S
[--include_prolines] [--include_glycines_if_D] [--design_plus_1]
[--enable_T_and_S] [--design_sequon_regardless_of_plus_two_layer]
[--include_boundary_buried]
[--include_boundary_hydrophobics INCLUDE_BOUNDARY_HYDROPHOBICS]
[--glycan_relax_rounds GLYCAN_RELAX_ROUNDS]
[--skip_functional_sites SKIP_FUNCTIONAL_SITES]
optional arguments:
-h, --help show this help message and exit
--selections SELECTIONS, -x SELECTIONS
Input XML to pull ResidueSelections to limit scan.
--selector SELECTOR Name of a residue selector from input xml to limit
search to. Loops, regions, etc. This will be combined
as AND logic
-s S Input PDB we will be scanning.
--include_prolines
--include_glycines_if_D
Include glycines? Glycines can either be D/L
conformation. Set this option to only include glycines
if they are D. Otherwise, skip them at +2
--design_plus_1 Design the +1 position?
--enable_T_and_S Enable Threonine and Serine at +2? By default we use
only threonine as this has been shown to havehigher
occupancy at the glycan site in general.
--design_sequon_regardless_of_plus_two_layer
Enable design of the primary sequon if the +2 residue
is part of the core (and not already ser/thr)?
--include_boundary_buried
Only use the LayerSelector to define the core for the
+2 residues. Otherwise, we use the SC sasa measured in
addition for the boundary residues and do not include
these if not designing
--include_boundary_hydrophobics INCLUDE_BOUNDARY_HYDROPHOBICS
Include hydrophobic boundary residues (for +2 design)?
By default we leave these out to maintain foldability
--glycan_relax_rounds GLYCAN_RELAX_ROUNDS
Number of glycan relax rounds (which is multiplied by
n glycans. Default is 100 (25 in app), but since this
is per-position, 100 is reasonable.
--skip_functional_sites SKIP_FUNCTIONAL_SITES
Comma-separated List of residues (PDBnumbering -ex
286A) to skip as including as a potential sequon. This
means we skip any potential sequon that includes these
residues.
usage: get_mutation_energy.py [-h] [--pdb PDB] [--outpath OUTPATH]
[--filename FILENAME] [--region REGION]
[--relax_whole_structure] [--alanine_scan]
Basic app to get mutation energy of each residue in a particular region using
PyRosetta
optional arguments:
-h, --help show this help message and exit
--pdb PDB, -s PDB Path to PDB file. Required.
--outpath OUTPATH, -o OUTPATH
Full output directory path. Default is pwd/RESULTS
--filename FILENAME, -n FILENAME
The filename of the results file
--region REGION, -r REGION
(region designated as start:end:chain) If none is
given, will use whole PDB
--relax_whole_structure, -m
Relax the whole structure? Default is to only relax
chain under question. If no region is set, will
default to true
--alanine_scan, -a Trigger the script to do an alanine scan of the
mutations instead of a full mutational scan.
usage: build_loop_pyrosetta.py [-h] --start START --stop STOP --sequence
SEQUENCE [--out_prefix OUT_PREFIX]
[--retain_aligned_roots] --pdb PDB [--kic]
[--dump_midpoints]
This script builds a loop between two places in a structure with the given
sequence, and closes the loop.It is not meant to be the last modeling step,
just to create missing density or to prepare for loop modeling.
optional arguments:
-h, --help show this help message and exit
--start START Starting resnum. Ex: 24L
--stop STOP Ending resnum. Ex. 42L.
--sequence SEQUENCE Sequence of the loop
--out_prefix OUT_PREFIX
Any prefix to give results.
--retain_aligned_roots
Attempt to keep any aligned root residues during the
build
--pdb PDB, -s PDB Input model
--kic Run KIC peruturber after closing the loop?
--dump_midpoints Dump midpoint PDBs?
usage: split_antibody_components.py [-h] [--any_structure] --ab_dir AB_DIR
--output_dir OUTPUT_DIR
Script for splitting AHO renumbered antibodies into Fv, Fc, and linker regions
optional arguments:
-h, --help show this help message and exit
--any_structure Be default, we only output structures with both L/H.
Pass this option to split structures that are L or H
only.
--ab_dir AB_DIR, -a AB_DIR
Antibody Directory with AHO-renumbered structures to
split. Can be .pdb, or .pdb.gz
--output_dir OUTPUT_DIR, -o OUTPUT_DIR
Output Directory for antibody structures.
usage: Creates Features Databases for antibody design using MPI. This uses RunRosettaMPI, so that it can be run locally or on a cluster.
[-h] [--indir INDIR]
[--analysis {all,cluster_features,antibody_features}]
[--use_present_dbs] --db_prefix DB_PREFIX [--native] [-s S] [-l L]
[--np NP] [--nstruct NSTRUCT] [--job_name JOB_NAME] [--outdir OUTDIR]
[--json_run JSON_RUN] [--extra_options EXTRA_OPTIONS]
[--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]] [--jd3] [--print_only]
[--local_test] [--one_file_mpi]
[--job_manager {slurm,qsub,local,local_test}]
[--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]]
[--json_base JSON_BASE] [--compiler {gcc,clang}] [--mpiexec MPIEXEC]
[--machine_file MACHINE_FILE] [--db_mode {sqlite3,mysql,postgres}]
[--db_name DB_NAME] [--db_batch DB_BATCH] [--db_in] [--db_out]
optional arguments:
-h, --help show this help message and exit
RAbD Analyze:
Options specific for Analysis of RAbD Output Structures
--indir INDIR Input directory used for either PDBLIST path (if
PDBLIST and this is given) or a path full of PDBs to
analyze
--analysis {all,cluster_features,antibody_features}
Analysis to run on PDBs
--use_present_dbs Do not attempt to delete features databases present
--db_prefix DB_PREFIX
Prefix to use for output databases. Recommended to use
the design and strategy name
--native Indicate that this is a set of native structures
Common Options:
-s S Path to a pdb file
-l L Path to a list of pdb files
--np NP Number of processors to use for MPI. Default = 101
--nstruct NSTRUCT The number of structures/parallel runs. Can also set
this in any JSON file.
--job_name JOB_NAME Set the job name used for mpi_tracer_to_file dir and
queue. Default = 'rosetta_run'. (Benchmarking:
Override any set in json_base.)
--outdir OUTDIR, -o OUTDIR
Outpath. Default = 'pwd/decoys'
--json_run JSON_RUN JSON file for specific Rosetta run. Not required. Pre-
Configured JSONS include:
['antibody_designer_even_clus_dock.json',
'relax.json', 'remodel.json', 'cluster_features.json',
'NGK_smooth.json',
'antibody_designer_even_len_clus_dock.json',
'pareto_optimal_relax.json', 'relaxed_design.json',
'antibody_H3.json', 'antibody_features.json',
'antibody_designer_even_len_clus.json',
'glycosylate_relax.json', 'dualspace_relax.json',
'interface_analyzer.json', 'common_flags.json',
'blank.json', 'relaxed_design_ds.json',
'antibody_designer_even_clus.json', 'NGK.json',
'antibody_designer_dock.json', 'snugdock.json',
'antibody_designer.json', 'rosetta_scripts.json',
'glycan_clash_check.json', 'NGK_smooth_shap.json']
--extra_options EXTRA_OPTIONS
Extra Rosetta options. Specify in quotes!
--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]
Any script vars for XML scripts.Specify as you would
in Rosetta. like: glycosylation=137A,136A
--jd3 Is this app JD3? Must build with
extras=mpi,serialization.
Testing and Debugging:
--print_only Do not actually run anything. Just print setup for
review.
--local_test Is this a local test? Will change nstruct to 1 and run
on 2 processors
--one_file_mpi Output all MPI std::out to a single file instead of
splitting it.
Special Options for controlling execution:
--job_manager {slurm,qsub,local,local_test}
Job Manager to launch job. (Or none if local or
local_test)Default = 'slurm '
--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]
Extra options for the job manager, such as queue or
processor requestsRemove double dashes. Exclusive is
on by default. Specify like: -p imperial exclusive.
--json_base JSON_BASE
JSON file for setting up base paths/etc. for the
cluster.Default =
'database/rosetta/jsons/common_flags.json'
--compiler {gcc,clang}
Set the compiler used. Will set clang automatically
for macos. Default = 'gcc'
--mpiexec MPIEXEC Specify a particular path (or type of) MPI exec.
Default is srun (due to vax). If local or local test,
will use mpiexex
--machine_file MACHINE_FILE
Optional machine file for passing to MPI
Relational Databases:
Options for Rosetta Database input and output. Use for features or for
inputting and output structures as databases
--db_mode {sqlite3,mysql,postgres}
Set the mode for Rosetta to use if using a database.
Features will be output to a database. If not sqlite3,
must build Rosetta with extras. If any post-processing
is required, such as combining sqlite3 dbs, will do
this. Default DB mode for features is sqlite3.
--db_name DB_NAME In or Out database name
--db_batch DB_BATCH Batch of structures.
--db_in Use an input database
--db_out Use an output database
usage: RAbD_Jade.py [-h] [--db_dir DB_DIR] [--analysis_name ANALYSIS_NAME]
[--native NATIVE] [--root_dir ROOT_DIR]
[--cdrs [{L1,H1,L1,H2,L3,H3} [{L1,H1,L1,H2,L3,H3} ...]]]
[--pyigclassify_dir PYIGCLASSIFY_DIR]
[--jsons [JSONS [JSONS ...]]]
GUI application to analyze designs output by RosettaAntibodyDesign. Designs
should first be analyzed by both the AntibodyFeatures and CDRClusterFeatures
reporters into sqlite3 databases.
optional arguments:
-h, --help show this help message and exit
--db_dir DB_DIR Directory with databases to compare. DEFAULT =
databases
--analysis_name ANALYSIS_NAME
Main directory to complete analysis. DEFAULT =
prelim_analysis
--native NATIVE Any native structure to compare to
--root_dir ROOT_DIR Root directory to run analysis from
--cdrs [{L1,H1,L1,H2,L3,H3} [{L1,H1,L1,H2,L3,H3} ...]]
A list of CDRs for the analysis (Not used for Features
Reporters)
--pyigclassify_dir PYIGCLASSIFY_DIR
Optional PyIgClassify Root Directory with DBOUT. Used
for debugging.
--jsons [JSONS [JSONS ...]], -j [JSONS [JSONS ...]]
Analysis JSONs to use. See RAbD_MB.AnalysisInfo for
more on what is in the JSON.The JSON allows us to
specify the final name, decoy directory, and features
db associated with the benchmark as well as all
options that went into it.
usage: convert_IMGT_to_fasta.py [-h] --inpath INPATH --outpath OUTPATH
This script converts an IMGT output file (5_AA-seqs.csv) to a FASTA. All
Framework and CDRs are concatonated. * is skipped. The FASTA file can then be
used by PyIgClassify.
optional arguments:
-h, --help show this help message and exit
--inpath INPATH, -i INPATH
Input IMGT file path
--outpath OUTPATH, -o OUTPATH
Output Fasta outfile path.
usage: order_ab_chains.py [-h] [--in_dir IN_DIR] [--in_pdblist IN_PDBLIST]
[--in_single IN_SINGLE] [--out_dir OUT_DIR]
[--reverse]
Reorders PDBFiles in a dirctory according to A_LH in order for Rosetta
Antibody Design benchmarking. Removes HetAtm
optional arguments:
-h, --help show this help message and exit
--in_dir IN_DIR, -i IN_DIR
Input Directory of PDB files listed in any passed
PDBLIST. Default=PWD
--in_pdblist IN_PDBLIST, -l IN_PDBLIST
Input PDBList file. Assumes PDBList has no paths and
requires an input directory as if we run Rosetta.
--in_single IN_SINGLE, -s IN_SINGLE
Path to Input PDB File, instead of list.
--out_dir OUT_DIR, -d OUT_DIR
Output Directory. Resultant PDB files will go here.
--reverse, -r Reverse order (LH_A instead of A_LH). Used for
snugdock
usage: match_antibody_structures.py [-h] --db DB --ab_dir AB_DIR --where WHERE
[--outdir OUTDIR] [--prefix PREFIX]
[--cdr CDR] [--native NATIVE]
This App aims to make pymol alignments using the PyIgClassify database and
structures, matching specific criterion.
optional arguments:
-h, --help show this help message and exit
Required Arguments:
--db DB, -d DB Database to use from PyIgClassify.
--ab_dir AB_DIR, -b AB_DIR
Directory with renumbered antibody PDBs (Full or CDRs-
only)
--where WHERE, -w WHERE
Your where clause for the db in quotes. Not including
WHERE. Use ' ' for string matches
Other Arguments:
--outdir OUTDIR, -o OUTDIR
Output directory.
--prefix PREFIX, -p PREFIX
Output prefix
--cdr CDR, -c CDR Optionally load the CDR PDBs of the given type in the
ab_dir. If this option is set, the ab_dir should be of
CDRs only from PyIgClassify.
--native NATIVE, -n NATIVE
Align everything to this PDB, the native or something
you are interested in.
usage: create_features_json.py [-h] [--databases [DATABASES [DATABASES ...]]]
[--script {cluster,antibody,interface,antibody_minimal}]
[--db_path DB_PATH] [--outdir OUTDIR]
[--outname OUTNAME]
[--add_comparison_to_this_json ADD_COMPARISON_TO_THIS_JSON]
[--run]
This script will create either cluster features or antibody features json for
use in Features R script. Example Cmd-line: python create_features_json.py
--database databases/baseline_comparison.txt --scripts cluster
optional arguments:
-h, --help show this help message and exit
--databases [DATABASES [DATABASES ...]], -l [DATABASES [DATABASES ...]]
List of dbs: db_name,short_name,ref keyword if the
reference databaseSeparated by white space.
--script {cluster,antibody,interface,antibody_minimal}, -s {cluster,antibody,interface,antibody_minimal}
Script type. Will setup the appropriate output formats
and R scripts
--db_path DB_PATH, -p DB_PATH
Path to databases. Default is pwd/databases
--outdir OUTDIR, -o OUTDIR
Where to put the result of the analysis scripts.
Currently unsupported by the features framework.
--outname OUTNAME, -n OUTNAME
Output file name of json file
--add_comparison_to_this_json ADD_COMPARISON_TO_THIS_JSON, -a ADD_COMPARISON_TO_THIS_JSON
Add all this data to this json as more sample sources.
--run, -r Go ahead and run compare_sample_sources.R. Must be in
path!!
usage: Delete chains from a PDB (not cif) file. Only works with ATOM records.
[-h] -s S [-c CHAINS] [-k KEEP_CHAINS] [--suffix SUFFIX]
optional arguments:
-h, --help show this help message and exit
-s S PDB file
-c CHAINS, --chains CHAINS
Comma-separated list of chains to remove
-k KEEP_CHAINS, --keep_chains KEEP_CHAINS
Chains to keep. Use this instead of the chains option
--suffix SUFFIX Suffix to add to output file
usage: place_TERs.py [-h] [pdb_files [pdb_files ...]]
This script places ters between ATOM/HETATM columns. This is currently needed
to reload symmetrized glycan posescreated by the god aweful make_symm_file.pl
Rosetta script. USE: place_TERs.py my_pdb - Does it in place.
positional arguments:
pdb_files Path to PDB files we will be stripping.
optional arguments:
-h, --help show this help message and exit
usage: strip_ANISOU.py [-h] [pdb_files [pdb_files ...]]
Strips ANISOU lines out of PDBs.
positional arguments:
pdb_files Path to PDB file we will be stripping.
optional arguments:
-h, --help show this help message and exit
usage: bm-RAbD_Jade.py [-h] [--main_dir MAIN_DIR] [--out_dir OUT_DIR] --jsons
[JSONS [JSONS ...]]
This program is a GUI used for benchmarking Rosetta Antibody Design.Before
running this application, you will probably want to run
'run_rabd_features_for_benchmarks.py to create the databases required.
optional arguments:
-h, --help show this help message and exit
--main_dir MAIN_DIR Main working directory. Not Required. Default = PWD
--out_dir OUT_DIR Output data directory. Not Required. Default =
pooled_data
--jsons [JSONS [JSONS ...]], -j [JSONS [JSONS ...]]
Analysis JSONs to use. See RAbD_MB.AnalysisInfo for
more on what is in the JSON.The JSON allows us to
specify the final name, decoy directory, and features
db associated with the benchmark as well as all
options that went into it.
usage: bm-calculate_plot_mc_acceptance_rabd.py [-h] --jsons
[JSONS [JSONS ...]]
[--data_outdir DATA_OUTDIR]
[--plot_outdir PLOT_OUTDIR]
[--root_dataset_dir ROOT_DATASET_DIR]
Calculates and plots monte carlo acceptance values for antibody design
benchmarking.
optional arguments:
-h, --help show this help message and exit
--jsons [JSONS [JSONS ...]], -j [JSONS [JSONS ...]]
Analysis JSONs to use. See RAbD_MB.AnalysisInfo for
more on what is in the JSON.The JSON allows us to
specify the final name, decoy directory, and features
db associated with the benchmark as well as all
options that went into it.
--data_outdir DATA_OUTDIR, -o DATA_OUTDIR
Path to outfile. DEFAULT = data
--plot_outdir PLOT_OUTDIR, -p PLOT_OUTDIR
DIR for plots. DEFAULT = plots/mc_benchmarks
--root_dataset_dir ROOT_DATASET_DIR
List of PDBIds to use for individual PDB output.
DEFAULT = datasets/pdblists
usage: bm-output_all_clusters.py [-h] --jsons [JSONS [JSONS ...]]
[--data_outdir DATA_OUTDIR]
Calculates and plots monte carlo acceptance values for antibody design
benchmarking.
optional arguments:
-h, --help show this help message and exit
--jsons [JSONS [JSONS ...]], -j [JSONS [JSONS ...]]
Analysis JSONs to use. See RAbD_MB.AnalysisInfo for
more on what is in the JSON.The JSON allows us to
specify the final name, decoy directory, and features
db associated with the benchmark as well as all
options that went into it.
--data_outdir DATA_OUTDIR, -o DATA_OUTDIR
Path to outfile. DEFAULT = data
usage: This program runs Rosetta MPI locally or on a cluster using slurm or qsub. Relative paths are accepted.
[-h] [-s S] [-l L] [--np NP] [--nstruct NSTRUCT] [--job_name JOB_NAME]
[--outdir OUTDIR] [--json_run JSON_RUN] [--extra_options EXTRA_OPTIONS]
[--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]] [--jd3]
[--program PROGRAM] [--print_only] [--local_test] [--one_file_mpi]
[--job_manager {slurm,qsub,local,local_test}]
[--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]]
[--json_base JSON_BASE] [--compiler {gcc,clang}] [--mpiexec MPIEXEC]
[--machine_file MACHINE_FILE] [--json_benchmark JSON_BENCHMARK]
[--separate_job_per_pdb]
optional arguments:
-h, --help show this help message and exit
Common Options:
-s S Path to a pdb file
-l L Path to a list of pdb files
--np NP Number of processors to use for MPI. Default = 101
--nstruct NSTRUCT The number of structures/parallel runs. Can also set
this in any JSON file.
--job_name JOB_NAME Set the job name used for mpi_tracer_to_file dir and
queue. Default = 'rosetta_run'. (Benchmarking:
Override any set in json_base.)
--outdir OUTDIR, -o OUTDIR
Outpath. Default = 'pwd/decoys'
--json_run JSON_RUN JSON file for specific Rosetta run. Not required. Pre-
Configured JSONS include:
['antibody_designer_even_clus_dock.json',
'relax.json', 'remodel.json', 'cluster_features.json',
'NGK_smooth.json',
'antibody_designer_even_len_clus_dock.json',
'pareto_optimal_relax.json', 'relaxed_design.json',
'antibody_H3.json', 'antibody_features.json',
'antibody_designer_even_len_clus.json',
'glycosylate_relax.json', 'dualspace_relax.json',
'interface_analyzer.json', 'common_flags.json',
'blank.json', 'relaxed_design_ds.json',
'antibody_designer_even_clus.json', 'NGK.json',
'antibody_designer_dock.json', 'snugdock.json',
'antibody_designer.json', 'rosetta_scripts.json',
'glycan_clash_check.json', 'NGK_smooth_shap.json']
--extra_options EXTRA_OPTIONS
Extra Rosetta options. Specify in quotes!
--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]
Any script vars for XML scripts.Specify as you would
in Rosetta. like: glycosylation=137A,136A
--jd3 Is this app JD3? Must build with
extras=mpi,serialization.
--program PROGRAM Define the Rosetta program to use if not set in
json_run
Testing and Debugging:
--print_only Do not actually run anything. Just print setup for
review.
--local_test Is this a local test? Will change nstruct to 1 and run
on 2 processors
--one_file_mpi Output all MPI std::out to a single file instead of
splitting it.
Special Options for controlling execution:
--job_manager {slurm,qsub,local,local_test}
Job Manager to launch job. (Or none if local or
local_test)Default = 'slurm '
--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]
Extra options for the job manager, such as queue or
processor requestsRemove double dashes. Exclusive is
on by default. Specify like: -p imperial exclusive.
--json_base JSON_BASE
JSON file for setting up base paths/etc. for the
cluster.Default =
'database/rosetta/jsons/common_flags.json'
--compiler {gcc,clang}
Set the compiler used. Will set clang automatically
for macos. Default = 'gcc'
--mpiexec MPIEXEC Specify a particular path (or type of) MPI exec.
Default is srun (due to vax). If local or local test,
will use mpiexex
--machine_file MACHINE_FILE
Optional machine file for passing to MPI
Benchmark Options:
Options specific for Benchmarking
--json_benchmark JSON_BENCHMARK
JSON file for setting up specific benchmark
--separate_job_per_pdb
Separate each PDB in any PDB list given (to python
app) into a separate Job and Directory
usage: bm-calculate_recoveries_and_risk_ratios.py [-h] --jsons
[JSONS [JSONS ...]]
[--data_outdir DATA_OUTDIR]
Calculates and plots monte carlo acceptance values for antibody design
benchmarking.
optional arguments:
-h, --help show this help message and exit
--jsons [JSONS [JSONS ...]], -j [JSONS [JSONS ...]]
Analysis JSONs to use. See RAbD_MB.AnalysisInfo for
more on what is in the JSON.The JSON allows us to
specify the final name, decoy directory, and features
db associated with the benchmark as well as all
options that went into it.
--data_outdir DATA_OUTDIR, -o DATA_OUTDIR
Path to outfile. DEFAULT = data
usage: bm-calculate_graft_closure_rabd.py [-h] [--dir DIR] [--outfile OUTFILE]
[--use_ensemble]
[--match_name MATCH_NAME]
Calculate the frequence of graft closures.
optional arguments:
-h, --help show this help message and exit
--dir DIR, -i DIR Input directory
--outfile OUTFILE, -o OUTFILE
Path to outfile
--use_ensemble Use ensembles in calculation
--match_name MATCH_NAME
Match a subexperiment in the file name such as relax
usage: This program runs Rosetta MPI locally or on a cluster using slurm or qsub. Relative paths are accepted.
[-h] [-s S] [-l L] [--np NP] [--nstruct NSTRUCT] [--job_name JOB_NAME]
[--outdir OUTDIR] [--json_run JSON_RUN] [--extra_options EXTRA_OPTIONS]
[--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]] [--jd3] [--print_only]
[--local_test] [--one_file_mpi]
[--job_manager {slurm,qsub,local,local_test}]
[--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]]
[--json_base JSON_BASE] [--compiler {gcc,clang}] [--mpiexec MPIEXEC]
[--machine_file MACHINE_FILE] [--json_benchmark JSON_BENCHMARK]
[--separate_job_per_pdb]
optional arguments:
-h, --help show this help message and exit
Common Options:
-s S Path to a pdb file
-l L Path to a list of pdb files
--np NP Number of processors to use for MPI. Default = 101
--nstruct NSTRUCT The number of structures/parallel runs. Can also set
this in any JSON file.
--job_name JOB_NAME Set the job name used for mpi_tracer_to_file dir and
queue. Default = 'rosetta_run'. (Benchmarking:
Override any set in json_base.)
--outdir OUTDIR, -o OUTDIR
Outpath. Default = 'pwd/decoys'
--json_run JSON_RUN JSON file for specific Rosetta run. Not required. Pre-
Configured JSONS include:
['antibody_designer_even_clus_dock.json',
'relax.json', 'remodel.json', 'cluster_features.json',
'NGK_smooth.json',
'antibody_designer_even_len_clus_dock.json',
'pareto_optimal_relax.json', 'relaxed_design.json',
'antibody_H3.json', 'antibody_features.json',
'antibody_designer_even_len_clus.json',
'glycosylate_relax.json', 'dualspace_relax.json',
'interface_analyzer.json', 'common_flags.json',
'blank.json', 'relaxed_design_ds.json',
'antibody_designer_even_clus.json', 'NGK.json',
'antibody_designer_dock.json', 'snugdock.json',
'antibody_designer.json', 'rosetta_scripts.json',
'glycan_clash_check.json', 'NGK_smooth_shap.json']
--extra_options EXTRA_OPTIONS
Extra Rosetta options. Specify in quotes!
--script_vars [SCRIPT_VARS [SCRIPT_VARS ...]]
Any script vars for XML scripts.Specify as you would
in Rosetta. like: glycosylation=137A,136A
--jd3 Is this app JD3? Must build with
extras=mpi,serialization.
Testing and Debugging:
--print_only Do not actually run anything. Just print setup for
review.
--local_test Is this a local test? Will change nstruct to 1 and run
on 2 processors
--one_file_mpi Output all MPI std::out to a single file instead of
splitting it.
Special Options for controlling execution:
--job_manager {slurm,qsub,local,local_test}
Job Manager to launch job. (Or none if local or
local_test)Default = 'slurm '
--job_manager_opts [JOB_MANAGER_OPTS [JOB_MANAGER_OPTS ...]]
Extra options for the job manager, such as queue or
processor requestsRemove double dashes. Exclusive is
on by default. Specify like: -p imperial exclusive.
--json_base JSON_BASE
JSON file for setting up base paths/etc. for the
cluster.Default =
'database/rosetta/jsons/common_flags.json'
--compiler {gcc,clang}
Set the compiler used. Will set clang automatically
for macos. Default = 'gcc'
--mpiexec MPIEXEC Specify a particular path (or type of) MPI exec.
Default is srun (due to vax). If local or local test,
will use mpiexex
--machine_file MACHINE_FILE
Optional machine file for passing to MPI
Benchmark Options:
Options specific for Benchmarking
--json_benchmark JSON_BENCHMARK
JSON file for setting up specific benchmark
--separate_job_per_pdb
Separate each PDB in any PDB list given (to python
app) into a separate Job and Directory