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