This page is a list of accessory scripts which are helpful in working with Rosetta input/output and job running.

Many of these scripts have further help options. Try running them without any arguments or with the '-h' flag to get further information.

General Rosetta Tools

Input Preparation

PDB

tools/protein_tools/scripts/clean_pdb.py
  - Prepare PDBs for Rosetta by cleaning and renumbering residues.

tools/renumber_pdb.py
  - Renumber PDB such that PDB numbering matches pose numbering.

tools/protein_tools/scripts/pdb_renumber.py
  - Renumber PDB such that PDB numbering matches pose numbering.

tools/convert_hatm_names.py
  - Convert the hydrogen naming convention of all PDBs in a directory to Rosetta conventions.

tools/protein_tools/scripts/remove_loop_coords.py
  - Zero out coordinates of atoms marked as loop in a loop file.

Ligands

main/source/scripts/python/public/molfile_to_params.py
  - Make Rosetta *.params files.

main/source/scripts/python/public/rename_params.py
  - Rename params files so that none conflict with each other.

main/source/scripts/python/public/batch_molfile_to_params.py
  - Make Rosetta *.params files for a large number of inputs.

main/source/src/apps/public/ligand_docking/assign_charges.py
  - Assign AM1-BCC charges to ligands.

tools/protein_tools/scripts/calculate_ligand_rmsd.py   - Pymol based script for calculating small molecule RMSDs

tools/protein_tools/scripts/visualize_ligand.py   - Generate Pymol session for visualizing ligand binding pocket

Symmetry

main/source/src/apps/public/symmetry/make_symmdef_file_denovo.py
  - Make a symmetry file.

main/source/src/apps/public/symmetry/make_symmdef_file.pl
  - Make a symmetry file for an existing PDB.

Membrane

main/source/src/apps/public/membrane_abinitio/octopus2span.pl
  - Convert an Octopus topology file to a Rosetta span file.

main/source/src/apps/public/membrane_abinitio/run_lips.pl
  - Run lipophilicity predictions.

main/source/src/apps/public/membrane_abinitio/alignblast.pl
  - Extract a multiple alignment of hits from Blast or PsiBlast output.

RosettaMembrane Framework

tools/membrane_tools/prep_mpdb.py
  - Prep all required datafiles for the RosettaMembrane Framework.

tools/membrane_tools/octopus2span.pl
  - Convert an Octopus topology file to a Rosetta span file.

tools/membrane_tools/run_lips.pl
  - Generate a lipid accessibility file.

tools/membrane_tools/alignblast.pl
  - Generate multiple alignent file from Blast output - dependancy of run_lips.pl.

tools/membrane_tools/write_mp_xml.py
  - Write a resource definition file template for membrane framework protocols.

tools/membrane_tools/mptest_ut.py
  - Run unit test for RosettaMembrane Framework code.

tools/membrane_tools/check_spanfile_in_pymol.pl
  - Color PDB model by residue range regions as defined in membrane spanfile.

Electron Density

main/source/src/apps/public/electron_density/prepare_template_for_MR.pl
  -

Contact Maps

tools/analysis/contactMapTools.py
  -

Fragments

tools/fragment_tools/make_fragments.pl
  - Generate fragments from a fasta file.

tools/fragment_tools/install_dependencies.pl
  - Install dependancies for fragment picking.

tools/fragment_tools/ss_pred_converter.py
  - Convert secondary structure predictions to PsiPred-SS2 format.

tools/fragment_tools/update_revdat.pl
  - Update revdat file for benchmarking cutoffs.

Constraint files

tools/protein_tools/scripts/generate_atom_pair_constraint_file.py   - Generate a Rosetta constraint file to restrain atom pair distances based on a PDB file.

tools/analysis/constraints/calc_exp_viol.pl
  - Creates a printout of the actual distance and violation for every atom pair constraint given a PDB file and constraint file.

tools/analysis/constraints/calc_exp_viol_spline.pl
  - Creates a printout of the actual distances and violations for a set of EPR distance constraints given a PDB file and a constraint file.

Job Running

main/source/scripts/python/public/parallel.py
  - Utility for running a large number of command lines in parallel.

Output Manipulation

Silent files

main/source/scripts/python/public/pymol_silent.py
  - A pymol plugin to read silent files.

tools/analysis/extract_pdbs_from_pdbsilent_by_tags.py
  - Extract particular structures from a silent file by their tags.

Score files

main/source/scripts/python/public/column.sh
  - Select only certain columns from a file.

main/source/scripts/python/public/sd.py
  - Extract data from silent files.

main/source/tools/scorefile.py
  - Parse and extract data from score files in JSON format.

main/source/src/apps/public/enzdes/DesignSelect.pl
  - Select only those rows of a tabular format which have columns matching requirements.

PDBs

main/source/scripts/python/public/pdb2fasta.py
  - Extract a FASTA formatted sequence from a PDB.

tools/protein_tools/scripts/get_fasta_from_pdb.py
  - Extract a FASTA formatted sequence from a PDB.

Analysis of Multiple Structures

tools/protein_tools/scripts/SequenceProfile.py
  - Create a sequence profile from a list of PDBs.

Plotting Utilities

main/source/scripts/python/public/rmsd_score_pymol_plotter/rmsd_score_pymol_plotter.py
  - Create score vs. rmsd (funnel) plots.

main/source/scripts/python/public/rmsd_score_pymol_plotter/rmsd_score_pymol_plotter_generator.pl
  - Create score vs. rmsd (funnel) plots.

tools/protein_tools/scripts/score_vs_rmsd_full.py
  - Create score vs. rmsd (funnel) plots.

tools/protein_tools/scripts/score_vs_rmsd.py
  - Create score vs. rmsd (funnel) plots.

tools/protein_tools/scripts/score_scatter_plot.py
  - Create score term vs. score term scatter plots.

tools/protein_tools/scripts/score_vs_rmsCore.R
  - Create a score vs. RMSD scatter plot from a score file. The RMSD is calculated for the protein core region and the scorefile must contain a 'rms_core' column.

tools/protein_tools/scripts/score_vs_rmsTM.R
  - Create a score vs. RMSD scatter plot from a score file. The RMSD is calculated for the protein transmembrane region and the scorefile must contain a 'rms_TM' column.

tools/analysis/numeric/MultiDimensionalHistogram.R
  -

tools/analysis/protocols/moves/DOFHistogramRecorder.R
  -

tools/analysis/constraints/score_vs_atom_pair_constraint.R
  - Make a total score vs. atom_pair_constraint scatter plot.

Clustering Utilities

tools/protein_tools/scripts/clustering.py
  - Run and parse the Rosetta clustering.

Unclassified

main/source/scripts/python/public/color_pdb.py
  -

main/source/scripts/python/public/color_pdb_byatom.py
  -

main/source/scripts/python/public/get_pdb.py
  -

main/source/src/utility/make_static_database.py
  -

tools/protein_tools/scripts/best_models.py
  -

tools/protein_tools/scripts/sequence_recovery.py
  -

tools/protein_tools/scripts/small_molecule_rmsd_table.py
  -

tools/protein_tools/scripts/tabbed_to_bcl.py
  -

tools/protein_tools/scripts/thread_pdb_from_alignment.py
  -

tools/protein_tools/scripts/top_n_percent.py
  -

tools/protein_tools/setup.py
  -

tools/perl_tools/addChain.pl
  -

tools/perl_tools/cleanPdbCA.pl
  -

tools/perl_tools/createTemplate.pl
  -

tools/perl_tools/getCAcoords.pl
  -

tools/perl_tools/getFastaFromCoords.pl
  -

tools/perl_tools/getFirstChain.pl
  -

tools/perl_tools/getPdb.pl
  -

tools/perl_tools/removeChain.pl
  -

tools/perl_tools/removeExtendedChain.pl
  -

tools/perl_tools/removeTERs.pl
  -

tools/python_pdb_structure/compare_sequences.py
  -

tools/python_pdb_structure/create_matcher_gridlig.py
  -

tools/python_pdb_structure/find_neighbors.py
  -

tools/python_pdb_structure/hist.py
  -

tools/python_pdb_structure/intdef_basics.py
  -

tools/python_pdb_structure/pdb_structure.py
  -

tools/python_pdb_structure/sequence_profile.py
  -

tools/python_pdb_structure/test_compare_sequences.py
  -

tools/python_pdb_structure/test_sequence_profile.py
  -

tools/python_pdb_structure/vector3d.py
  -

Application Specific Scripts

Ligand Docking

main/source/src/apps/public/ligand_docking/arls.py
  - Automatic RosettaLigand setup.

main/source/src/apps/public/ligand_docking/best_ifaceE.py
  - Prints the tags of the 'best' structures from a ligand docking run.

main/source/src/apps/public/ligand_docking/pdb_to_molfile.py
  - Extracts coordinates from PDB file to regenerate mol/sdf/mol2 files.

main/source/src/apps/public/ligand_docking/prune_atdiff_top5pct.py
  - Extract the top 5% by total score from an AtomTreeDiff file.

main/source/src/apps/public/ligand_docking/get_scores.py
  - Extract the SCORES line of an AtomTreeDiff file into tabular format.

main/source/src/apps/public/ligand_docking/plot_funnels.R
  -

Antibody

tools/antibody/antibody.py
  - Pre-processing script for antibody protocol.

tools/antibody/antibody_repertoire.py
  - Processes a fasta file of an antibody repertoire to create a dB of structures.

tools/antibody/convert_pdb_to_antibody_numbering_scheme.py
  - Script to change a PDB sequence into a cannonical antibody numbering scheme.

tools/antibody/chothia_mapping_v2.pl
  - Script to map the given PDB sequence to the Chothia numbering.

tools/antibody/chothia_renumber_v2.pl
  - Script to re-number PDB files according to the Chothia scheme.

tools/antibody/classification_H3.pl
  -

tools/antibody/colorcdr.pml
  -

tools/antibody/kink_constraints.py
  - Output kink constraint files for a set of antibodies.

tools/antibody/kink_geom.py
  - Calculate kink geometry for a set of antibodies.

tools/antibody/kink_plots.R
  - Plot geometry of the H3 kink.

tools/antibody/make_angle_distances.py
  - Calculates orientational distance between all antibodies in database.

tools/antibody/superimpose_interface.py
  -

Constrained Relax

main/source/src/apps/public/relax_w_allatom_cst/clean_pdb_keep_ligand.py
  - Clean the PDB, keeping the ligand

main/source/src/apps/public/relax_w_allatom_cst/sidechain_cst_3.py
  - Create a constraint file for the sidechain heavy atoms.

main/source/src/apps/public/relax_w_allatom_cst/amino_acids.py
  - Utility data script.

RosettaCM

tools/protein_tools/scripts/setup_RosettaCM.py
  -

RNA

tools/rna_tools/bin/amino_acids.py
  -

tools/rna_tools/bin/biox3_jobsub.py
  -

tools/rna_tools/bin/cat_outfiles.py
  -

tools/rna_tools/bin/check_cutpoints.py
  -

tools/rna_tools/bin/cluster_info.py
  -

tools/rna_tools/bin/easy_cat.py
  -

tools/rna_tools/bin/extract_chain.py
  -

tools/rna_tools/bin/extract_lowscore_decoys_outfile.py
  -

tools/rna_tools/bin/extract_lowscore_decoys.py
  -

tools/rna_tools/bin/fetch_pdb.py
  -

tools/rna_tools/bin/fields.py
  -

tools/rna_tools/bin/fix_chainbreaks_with_erraser.py
  -

tools/rna_tools/bin/get_res_num.py
  -

tools/rna_tools/bin/get_sequence.py
  -

tools/rna_tools/bin/get_surrounding_res.py
  -

tools/rna_tools/bin/helix_preassemble_setup.py
  -

tools/rna_tools/bin/make_rna_rosetta_ready.py
  - rna-denovo

tools/rna_tools/bin/make_tag.py
  -

tools/rna_tools/bin/mpi4py_jobsub.py
  -

tools/rna_tools/bin/parallel_min_setup.py
  -

tools/rna_tools/bin/parse_options.py
  -

tools/rna_tools/bin/parse_tag.py
  -

tools/rna_tools/bin/pdb2fasta.py
  -

tools/rna_tools/bin/pdbslice.py
  - rna-denovo-setup

tools/rna_tools/bin/pdbsubset.py
  -

tools/rna_tools/bin/pp_jobsub.py
  -

tools/rna_tools/bin/pp_util.py
  -

tools/rna_tools/bin/prepare_rna_puzzle_submissions.py
  -

tools/rna_tools/bin/qsub_torque.py
  -

tools/rna_tools/bin/read_pdb.py
  -

tools/rna_tools/bin/renumber_pdb_in_place.py
  - rna-denovo-setup

tools/rna_tools/bin/reorder_pdb.py
  -

tools/rna_tools/bin/reorder_to_standard_pdb.py
  -

tools/rna_tools/bin/replace_chain_inplace.py
  - rna-denovo-setup

tools/rna_tools/bin/replace_chain.py
  -

tools/rna_tools/bin/rna_denovo_jobscript.py
  -

tools/rna_tools/bin/rna_denovo_setup.py
  - rna-denovo-setup

tools/rna_tools/bin/rna_helix.py
  - rna-denovo-setup

tools/rna_tools/bin/rna_server_conversions.py
  -

tools/rna_tools/bin/rosetta_exe.py
  -

tools/rna_tools/bin/rosetta_submit.py
  -

tools/rna_tools/bin/rsync_from_cluster.py
  -

tools/rna_tools/bin/rsync_to_cluster.py
  -

tools/rna_tools/bin/silent_file_sort_and_select.py
  -

tools/rna_tools/cluster_setup/biox3_jobsub.py
  -

tools/rna_tools/cluster_setup/cluster_info.py
  -

tools/rna_tools/cluster_setup/easy_cat.py
  -

tools/rna_tools/cluster_setup/mpi4py_jobsub.py
  -

tools/rna_tools/cluster_setup/pp_jobsub.py
  -

tools/rna_tools/cluster_setup/pp_util.py
  -

tools/rna_tools/cluster_setup/qsub_torque.py
  -

tools/rna_tools/cluster_setup/rosetta_submit.py
  -

tools/rna_tools/cluster_setup/rsync_from_cluster.py
  -

tools/rna_tools/cluster_setup/rsync_to_cluster.py
  -

tools/rna_tools/job_setup/helix_preassemble_setup.py
  -

tools/rna_tools/job_setup/make_tag.py
  -

tools/rna_tools/job_setup/parallel_min_setup.py
  -

tools/rna_tools/job_setup/parse_options.py
  -

tools/rna_tools/job_setup/parse_tag.py
  -

tools/rna_tools/job_setup/rna_denovo_jobscript.py
  -

tools/rna_tools/job_setup/rna_denovo_setup.py
  - rna-denovo-setup

tools/rna_tools/job_setup/rna_server_conversions.py
  -

tools/rna_tools/job_setup/rosetta_exe.py
  -

tools/rna_tools/pdb_util/amino_acids.py
  -

tools/rna_tools/pdb_util/check_cutpoints.py
  -

tools/rna_tools/pdb_util/extract_chain.py
  -

tools/rna_tools/pdb_util/fetch_pdb.py
  -

tools/rna_tools/pdb_util/fix_chainbreaks_with_erraser.py
  -

tools/rna_tools/pdb_util/get_res_num.py
  -

tools/rna_tools/pdb_util/get_sequence.py
  -

tools/rna_tools/pdb_util/get_surrounding_res.py
  -

tools/rna_tools/pdb_util/make_rna_rosetta_ready.py
  -

tools/rna_tools/pdb_util/pdb2fasta.py
  -

tools/rna_tools/pdb_util/pdbslice.py
  - rna-denovo-setup

tools/rna_tools/pdb_util/pdbsubset.py
  -

tools/rna_tools/pdb_util/plot_contour.py
  - Sample-around-nucleobase

tools/rna_tools/pdb_util/prepare_rna_puzzle_submissions.py
  -

tools/rna_tools/pdb_util/read_pdb.py
  -

tools/rna_tools/pdb_util/renumber_pdb_in_place.py
  - rna-denovo-setup

tools/rna_tools/pdb_util/reorder_pdb.py
  -

tools/rna_tools/pdb_util/reorder_to_standard_pdb.py
  -

tools/rna_tools/pdb_util/replace_chain_inplace.py
  - rna-denovo-setup

tools/rna_tools/pdb_util/replace_chain.py
  -

tools/rna_tools/pdb_util/rna_helix.py
  - rna-denovo-setup

tools/rna_tools/silent_util/cat_outfiles.py
  -

tools/rna_tools/silent_util/extract_lowscore_decoys_outfile.py
  -

tools/rna_tools/silent_util/extract_lowscore_decoys.py
  -

tools/rna_tools/silent_util/fields.py
  -

tools/rna_tools/silent_util/silent_file_sort_and_select.py
  -

tools/rna_tools/sym_link.py
  -

Stepwise assembly

tools/SWA_protein_python/generate_dag/generate_CA_constraints.py
  - swa-protein-main swa-protein-long-loop

tools/SWA_protein_python/generate_dag/generate_constraints.py
  -

tools/SWA_protein_python/generate_dag/generate_swa_protein_dag.py
  - swa-protein-long-loop

tools/SWA_protein_python/generate_dag/get_sequence.py
  -

tools/SWA_protein_python/generate_dag/make_tag.py
  -

tools/SWA_protein_python/generate_dag/parse_options.py
  -

tools/SWA_protein_python/run_dag_on_cluster/extract_lowscore_decoys_outfile.py
  -

tools/SWA_protein_python/run_dag_on_cluster/parse_options.py
  -

tools/SWA_protein_python/run_dag_on_cluster/stepwise_post_process_cluster.py
  -

tools/SWA_protein_python/run_dag_on_cluster/stepwise_post_process_combine_and_filter_outfiles.py
  -

tools/SWA_protein_python/run_dag_on_cluster/stepwise_pre_process_setup_dirs.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_condor_test.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_dagman_LSF_continuous.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_dagman_slave.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_kick_off_slave_jobs.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_parse_options.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_pseudo_dagman_continuous.py
  - swa-protein-long-loop

tools/SWA_protein_python/run_dag_on_cluster/SWA_sampling_post_process.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_sampling_pre_process.py
  -

tools/SWA_protein_python/run_dag_on_cluster/SWA_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/benchmark_command.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/benchmark_command_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_continuous.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_continuous_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_general_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_generic_silent_file_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_slave.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/generic_empty_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/dagman/submit_DAG_job.py
  -

tools/SWA_RNA_python/SWA_dagman_python/database/SWA_amino_acids.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_dag_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_easy_cat.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_filterer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_final_filter_dag.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_pre_process.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_rna_build_dagman.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_rna_build_dagman_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/setup_FARFAR_job_files_parse_options.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/setup_FARFAR_job_files.py
  -

tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/setup_FARFAR_job_files_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/calculate_pairwise_RMSD.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/calculate_RMSD.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/check_mapper_files_exist.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/cluster_rotamers.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/combine_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/count_molprobity_clash_atoms.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_benchmark_job_files.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_benchmark_table.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_benchmark_table_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_gnuplot_script.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_idealize_helix_general.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_idealize_helix.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_local_dag.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_RNA_primer_simple.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_score_vs_rmsd_plot.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_torsion_database_check_length.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/create_torsion_database.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/ensure_rna_rosetta_ready.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/extend_silent_struct_with_idealized_helix.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/extract_C1_P_atom_from_PDB.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/extract_FR3D_data.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/extract_hbond_stat.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/extract_MC_annotate_data.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/extract_torsions_from_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/fields.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/find_sequence.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/fix_pymol_output_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/get_OLLM_chain_closure_only_regions.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/invert_chain_sequence.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/line_counts.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/lower_sequence.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/minimize_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/path_check_gnuplot.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/pdb2seqlist.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/pdb_to_silent_file.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/remove_columns.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/remove_duplicate_sequence_line_in_silent_file.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/remove_hydrogen_from_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/renumber_pdb_in_place.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/replace_chain_inplace.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/replace_silent_scoreline.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/Reposition_pdb_atom_name.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/reweight_chem_shift_score.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/reweight_silent_file_SCORE.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/Rosetta_all_atom_derivative_check.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/Rosetta_import_and_dump_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/Rosetta_to_standard_PDB.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/select_models_silentfile.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/slice_pdb_list.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/slice_sample_res_and_surrounding.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_add_hydrogen.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_align_pdb.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_all_rna_rosetta_ready.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_cat_outfiles.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_cat_outfiles_wrapper.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_cluster.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_copy_non_full_length_regions.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_extract_pdb.py
  - swa-rna-loop

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_filter_outfile_wrapper.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_filter_silent_file.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_make_rna_rosetta_ready.py
  - swa-rna-loop

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_mutate_residues.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_pdb2fasta.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_pdbslice.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_pdb_slice_wrapper.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_plot_region_FINALs.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_SS_LOOP_create_benchmark_table.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_SS_LOOP_create_benchmark_table_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_trace_pathway.py
  -

tools/SWA_RNA_python/SWA_dagman_python/misc/SWA_trace_pathway_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/benchmark_command.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/benchmark_command_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_continuous_MPI_wrapper.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_continuous.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_continuous_qsub.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_continuous_qsub_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_continuous_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_generic_silent_file_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/DAG_slave.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/generic_empty_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/old_dagman_works_with_condor/submit_DAG_job.py
  -

tools/SWA_RNA_python/SWA_dagman_python/parser/SWA_parse_benchmark.py
  -

tools/SWA_RNA_python/SWA_dagman_python/parser/SWA_parse_internal_arguments.py
  -

tools/SWA_RNA_python/SWA_dagman_python/parser/SWA_parse_options.py
  -

tools/SWA_RNA_python/SWA_dagman_python/parser/SWA_parse_rosetta_options.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/infinite_loop.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/kill_all_slave_jobs.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/LSF_scheduler.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/MPI_helloword.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/MPI_PBS_scheduler.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/MPI_SGE_scheduler.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/PBS_scheduler.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/print_queued_jobs.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/scheduler_build_test.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/scheduler_common.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/scheduler_queue_job.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/scheduler_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/scheduler/simple_test_script.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/create_dag_job_files.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/DAG_rebuild_bulge_pre_process.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/DAG_rebuild_bulge.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/DAG_rebuild_bulge_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/DAG_rebuild_bulge_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/setup_SWA_RNA_dag_job_files.py
  - swa-rna-loop

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/submit_SWA_rna_minimize_benchmark.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_DAG_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_rna_build_dagman.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_rna_build_dagman_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_rna_minimize.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_rna_minimize_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_sample_virt_ribose_reducer.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_sampling_combine_long_loop_pre_process.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_sampling_post_process.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_sampling_post_process_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/SWA_DAG/SWA_sampling_pre_process.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/plot_silent_file_scores.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/SWA_rna_build_commands_from_dagman.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/SWA_rna_build_dag_parse.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/SWA_rna_serial_hack.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/SWA_rna_setup_inputs.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/SWA_setup_benchmark.py
  -

tools/SWA_RNA_python/SWA_dagman_python/swa_revival/SWA_setup_benchmark_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/chemical_shift_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/DAGMAN_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/error_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/extract_FR3D_data_functions.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/extract_MC_annotate_data_functions.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/list_operations.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/master_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/PATHS.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/PDB_operations.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/RNA_BP_and_BS_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/RNA_sequence.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/Rosetta_to_standard_PDB_functions.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/silent_file_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/SWA_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/torsion_database_util.py
  -

tools/SWA_RNA_python/SWA_dagman_python/utility/USER_PATHS.py
  -

RECCES

  • See RECCES for more information.

tools/recces/data.py
  -

tools/recces/min_func.py
  -

tools/recces/util.py
  -

Remodel

See also the Remodel and RosettaRemodel documentation.

tools/remodel/getBluePrintFromCoords.pl
  -

ddG monomer

main/source/src/apps/public/ddg/convert_to_cst_file.sh
  - Convert ddG logfile to a constraint file.

Pepspec

tools/analysis/apps/gen_pepspec_pwm.py
  - Generate a position weight matrix from PepSpec output.

Beta peptides

tools/beta-peptide/create_beta_peptide_params.py
  -

tools/beta-peptide/make_beta_peptide_bbdep.py
  -

High Throughput Docking

tools/hts_tools/add_activity_tags_to_database.py
  -

tools/hts_tools/add_hydrogens.py
  -

tools/hts_tools/add_ligands_to_job_file.py
  -

tools/hts_tools/clean_pdb.py
  -

tools/hts_tools/compress_ligands.py
  -

tools/hts_tools/get_descriptor_data.py
  -

tools/hts_tools/hts_util.py
  -

tools/hts_tools/ligand_database.py
  -

tools/hts_tools/make_evenly_grouped_jobs.py
  -

tools/hts_tools/make_ligand_centroid_pdb.py
  -

tools/hts_tools/make_params.py
  -

tools/hts_tools/make_startfom_files.py
  -

tools/hts_tools/prepare_sdfs_for_bcl.py
  -

tools/hts_tools/sdf_parser/MolFile.py
  -

tools/hts_tools/sdf_parser/MolFileTests.py
  -

tools/hts_tools/sdf_parser/SdfFile.py
  -

tools/hts_tools/sdf_parser/SdfTest.py
  -

tools/hts_tools/sdf_split_organize.py
  -

tools/hts_tools/setup_screening_project.py
  -

Fiber Difraction

tools/fragment_tools/pdb2vall/pdb2vall.py
  -

tools/fiber_diffraction/layer_line_pruner.py
  - Remove neighboring points from free or working sets.

tools/fiber_diffraction/make_helix_denovo_cnsm.py
  - Helix denovo symmetry definition file generator.

tools/fiber_diffraction/make_helix_denovo.py
  - Helix denovo symmetry definition file generator.

Vall generation

tools/fragment_tools/pdb2vall/amino_acids.py
  -

tools/fragment_tools/pdb2vall/database/rcsb_data/get_ss_dis.sh
  -

tools/fragment_tools/pdb2vall/database/rcsb_data/rsyncPDB.sh
  -

tools/fragment_tools/pdb2vall/database/rcsb_data/update_rcsb_data.pl
  -

tools/fragment_tools/pdb2vall/get_missing_den_from_disss.py
  -

tools/fragment_tools/pdb2vall/jump_over_missing_density.py
  -

tools/fragment_tools/pdb2vall/numbering_back_to_pdbseqres.py
  -

tools/fragment_tools/pdb2vall/parse_dssp_results.py
  -

tools/fragment_tools/pdb2vall/pdb_scripts/amino_acids.py
  -

tools/fragment_tools/pdb2vall/pdb_scripts/clean_pdb.py
  -

tools/fragment_tools/pdb2vall/pdb_scripts/fetch_raw_pdb.py
  -

tools/fragment_tools/pdb2vall/pdb_scripts/get_pdb_new.py
  -

tools/fragment_tools/pdb2vall/pdb_scripts/maxsprout/test/runmaxsprout.pl
  -

tools/fragment_tools/pdb2vall/pdb_scripts/pdb2fasta.py
  -

tools/fragment_tools/pdb2vall/pdb_scripts/rebuild_pdb_from_CA.sh
  -

tools/fragment_tools/pdb2vall/renumber_structure_profile_checkpoint_back_to_seqres.py
  -

tools/fragment_tools/pdb2vall/sequence_profile_scripts/run_psiblast_filtnr_tight.pl
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/create_checkpoint_from_fasta_alignment.pl
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7/doc/example.sh
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7/par/background-map.py
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7/src/pdb_T_modifier.py
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/dssp2threestateSS.pl
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/generate_struct_profile.rb
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/get_structure_profile_checkpoint.py
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/make_alignment_from_fragfile.pl
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/make_alignment_from_fragfile_rmsCutoff.pl
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/make_depthfile.py
  -

tools/fragment_tools/pdb2vall/structure_profile_scripts/make_sequence_fragments.pl
  -

Design Analysis Tools

tools/protein_tools/scripts/design_analysis/analysis_tools.py
  -

tools/protein_tools/scripts/design_analysis/argument_parsing.py
  -

tools/protein_tools/scripts/design_analysis/design_analysis.py
  -

tools/protein_tools/scripts/design_analysis/scoretable.py
  -

tools/protein_tools/scripts/design_analysis/sequence_analysis.py
  -

Small Molecule Artificial Neural Networks

tools/ann_tools/cat_sdfs.py
  -

tools/ann_tools/compute_csv_tables.py
  -

tools/ann_tools/make_bcl_inputs_for_plotting.py
  -

tools/ann_tools/make_bcl_roc_plots.py
  -

tools/ann_tools/make_datasets.py
  -

tools/ann_tools/score_sdf.py
  -

tools/ann_tools/sort_sdfs.py
  -

Epitope Prediction Tools

We have provided tools to predict epitopes using Propred matrices or NetMHCII, and also to create databases to allow sequences to be evaluated quickly in Rosetta. See MHCEpitopeEnergy for more details on immunogenicity scoring in Rosetta. See the tools documentation for details on how to use the mhc_energy_tools.

tools/mhc_energy_tools/mhc_score.py to perform epitope scoring on FASTA, PDB, or raw peptides, with basic reporting and plotting capabilities. tools/mhc_energy_tools/mhc_gen_db.py to generate SQL databases from FASTA or PDB files, with design space being specified from a CSV file or a PSSM.

Unclassified

main/source/external/R/BranchAngleOptimizer.R
  -

main/source/scripts/python/public/orbitals_pretty.pml

main/tests/integration/tests/inv_kin_lig_loop_design/showme.pml

tools/analysis/apps/sequence_tolerance.R
  -

Build scripts

main/source/scons.py
  - Main script for Rosetta compilation.

main/source/ninja_build.py
  - Script for the alternative CMake+ninja build system.

Test scripts

main/source/test/run.py
  - Run the unit tests.

main/tests/integration/integration.py
  - Run the integration tests.

main/tests/benchmark/benchmark.py
  - Run the benchmark server tests locally.

main/tests/sfxn_fingerprint/sfxn_fingerprint.py
  - Run the scorefunction fingerprint test.

main/tests/profile/profile.py
  - Run the profile tests.

main/tests/profile/compare_results.py
  - Compare the results of the profile tests.

main/tests/FeatureExtraction/features.py
  -

Scripting Utilities

main/source/scripts/python/public/amino_acids.py
  - Data about amino acids and their properties.

tools/protein_tools/scripts/amino_acids.py
  - Data about amino acids and their properties.

tools/python_pdb_structure/amino_acids.py
  - Data about amino acids and their properties.

main/source/scripts/python/public/param_utils.py
  - Functions for manipulating params files.

main/source/scripts/python/public/rosetta_py/io/pdb.py
  - Utilities for reading PDB files.

main/source/scripts/python/public/rosetta_py/io/mdl_molfile.py
  - Utilities for reading sdf/mol/mol2 files.

main/source/scripts/python/public/rosetta_py/utility/rankorder.py
  - Functions for sorting data.

main/source/scripts/python/public/rosetta_py/utility/ForkManager.py
  - Utilities for handling multiprocessing.

main/source/scripts/python/public/rosetta_py/utility/r3.py
  - A 3D vector class for python.

tools/protein_tools/rosettautil/bcl/file_formats.py
  -

tools/protein_tools/rosettautil/graphics/plotting.py
  -

tools/protein_tools/rosettautil/protein/alignment.py
  -

tools/protein_tools/rosettautil/protein/naccess.py
  -

tools/protein_tools/rosettautil/protein/pdbStat.py
  -

tools/protein_tools/rosettautil/protein/PSSM.py
  -

tools/protein_tools/rosettautil/protein/util.py
  -

tools/protein_tools/rosettautil/rosetta/loops.py
  -

tools/protein_tools/rosettautil/rosetta/map_pdb_residues.py
  -

tools/protein_tools/rosettautil/rosetta/params.py
  -

tools/protein_tools/rosettautil/rosetta/resfile.py
  -

tools/protein_tools/rosettautil/rosetta/rosettaScore_beta.py
  -

tools/protein_tools/rosettautil/rosetta/rosettaScore.py
  -

tools/protein_tools/rosettautil/rosetta/weights.py
  -

tools/protein_tools/rosettautil/util/fileutil.py
  -

Coding Tools

main/source/make_ctags.sh
  - Make a ctag file for code editors.

tools/Check_header_guards_and_copyright.py
  - Check that the copyright header on each Rosetta file is correct.

tools/coding_util/remove_dead_code.py
  - Remove files which are not needed for the compile.

tools/code_coverage.py
  - Calculate code coverage over integration and unit test.

tools/git_revision_parser.py
  - Attempt to find relevant revision designations from a git commit.

tools/coding_util/generate_warnings_list.py
  - Find compiler warnings in Rosetta code.

main/source/src/utility/tools/make_templates.py
  -

tools/perl_util/compiler.pl
  -

tools/perl_util/diff_int.pl
  -

tools/perl_util/find_includes.pl
  -

tools/perl_util/grep_source.pl
  -

tools/perl_util/hack_replace.pl
  -

tools/perl_util/include_guard.pl
  -

tools/perl_util/promote_lib.pl
  -

tools/perl_util/ralph-build.pl
  -

tools/perl_util/remove_trailing_whitespace.pl
  -

tools/perl_util/scons_to_makefile.pl
  -

tools/perl_util/spaces2tabs.pl
  -

tools/perl_util/suggest_compilation_fixes.pl
  -

tools/coding_util/artistic_spacing.py
  -

tools/coding_util/create_rosetta_class.py
  -

tools/coding_util/create_rosetta_mover.py
  -

tools/coding_util/create_variables_for_class.py
  -

tools/coding_util/fix_AUTO_REMOVE.py
  -

tools/coding_util/fixes/DNA_RNA_atom_rename.sh
  -

tools/coding_util/fixes/DNA_RNA_residue_rename_pdb.py
  -

tools/coding_util/fixes/DNA_RNA_residue_rename.sh
  -

tools/coding_util/fixes/fix_general_to_align.py
  -

tools/coding_util/fixes/fix_namespace_scopes.py
  -

tools/coding_util/fixes/fix_swa_rna_Output.py
  -

tools/coding_util/fixes/fix_tracer_names.py
  -

tools/coding_util/fixes/func_fixup.sh
  -

tools/coding_util/fixes/remove_Contain_seq_num.py
  -

tools/coding_util/fixes/remove_VIRT.py
  -

tools/coding_util/fixes/rename_rU.sh
  -

tools/coding_util/fixes/swa_rna_add_tracer_to_output.py
  -

tools/coding_util/fixes/swa_rna_fix_underscores.sh
  -

tools/coding_util/fixes/switch_DNA_hydrogens.sh
  -

tools/coding_util/fixes/switch_OP1_OP2.sh
  -

tools/coding_util/fixes/switch_RNA_hydrogens_H2.sh
  -

tools/coding_util/fixes/switch_RNA_hydrogens_H4.sh
  -

tools/coding_util/fixes/switch_RNA_hydrogens.sh
  -

tools/coding_util/fixes/update_swm_options2.sh
  -

tools/coding_util/fixes/update_swm_options.sh
  -

Unclassified

main/source/GUIs/rosetta_flag_file_builder/*
  -

main/source/src/python/packaged_bindings/*
  -

main/source/src/python/bindings/*
  -

tools/clang/clang.py
  -

tools/clang_ast_transform/*
  -

tools/PyRosetta.develop/DeployPyRosetta.py
  -

tools/python_cc_reader/*
  -

tools/willclang/*

See Also