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.
NOTE TO DEVELOPERS:
The tools repository is intended to be used for general-purpose scripts for development purposes (generating/processing input files, etc.). Python scripts for scientific purposes should be placed in the main repository so that they remain in sync with the Rosetta code base. Scientific python scripts for public use should be placed in main/source/scripts/python/public/ and should have accompanying integration tests. Private scripts should be placed in main/source/scripts/python/pilot/<user_name>.
Scripts in all of these categories should be listed and briefly described on this page. Public scientific scripts intended to be used as standalone applications should also have a separate application documentation page (see the How to write documentation page for notes on formatting application documentation).
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.
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
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.
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.
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.
main/source/src/apps/public/electron_density/prepare_template_for_MR.pl
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tools/analysis/contactMapTools.py
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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.
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.
main/source/scripts/python/public/parallel.py
- Utility for running a large number of command lines in parallel.
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.
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.
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.
tools/protein_tools/scripts/SequenceProfile.py
- Create a sequence profile from a list of PDBs.
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
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tools/analysis/protocols/moves/DOFHistogramRecorder.R
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tools/analysis/constraints/score_vs_atom_pair_constraint.R
- Make a total score vs. atom_pair_constraint scatter plot.
tools/protein_tools/scripts/clustering.py
- Run and parse the Rosetta clustering.
main/source/scripts/python/public/color_pdb.py
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main/source/scripts/python/public/color_pdb_byatom.py
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main/source/scripts/python/public/get_pdb.py
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main/source/src/utility/make_static_database.py
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tools/protein_tools/scripts/best_models.py
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tools/protein_tools/scripts/sequence_recovery.py
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tools/protein_tools/scripts/small_molecule_rmsd_table.py
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tools/protein_tools/scripts/tabbed_to_bcl.py
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tools/protein_tools/scripts/thread_pdb_from_alignment.py
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tools/protein_tools/scripts/top_n_percent.py
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tools/protein_tools/setup.py
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tools/perl_tools/addChain.pl
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tools/perl_tools/cleanPdbCA.pl
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tools/perl_tools/createTemplate.pl
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tools/perl_tools/getCAcoords.pl
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tools/perl_tools/getFastaFromCoords.pl
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tools/perl_tools/getFirstChain.pl
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tools/perl_tools/getPdb.pl
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tools/perl_tools/removeChain.pl
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tools/perl_tools/removeExtendedChain.pl
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tools/perl_tools/removeTERs.pl
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tools/python_pdb_structure/compare_sequences.py
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tools/python_pdb_structure/create_matcher_gridlig.py
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tools/python_pdb_structure/find_neighbors.py
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tools/python_pdb_structure/hist.py
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tools/python_pdb_structure/intdef_basics.py
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tools/python_pdb_structure/pdb_structure.py
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tools/python_pdb_structure/sequence_profile.py
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tools/python_pdb_structure/test_compare_sequences.py
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tools/python_pdb_structure/test_sequence_profile.py
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tools/python_pdb_structure/vector3d.py
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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
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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
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tools/antibody/colorcdr.pml
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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
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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.
tools/protein_tools/scripts/setup_RosettaCM.py
- A script to setup RosettaCM modeling.
tools/protein_tools/scripts/RosettaEnzCM.py
- Generates atomic distance constraints for predicted catalytic residues from known template residues.
tools/rna_tools/bin/amino_acids.py
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tools/rna_tools/bin/biox3_jobsub.py
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tools/rna_tools/bin/cat_outfiles.py
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tools/rna_tools/bin/check_cutpoints.py
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tools/rna_tools/bin/cluster_info.py
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tools/rna_tools/bin/easy_cat.py
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tools/rna_tools/bin/extract_chain.py
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tools/rna_tools/bin/extract_lowscore_decoys_outfile.py
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tools/rna_tools/bin/extract_lowscore_decoys.py
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tools/rna_tools/bin/fetch_pdb.py
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tools/rna_tools/bin/fields.py
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tools/rna_tools/bin/fix_chainbreaks_with_erraser.py
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tools/rna_tools/bin/get_res_num.py
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tools/rna_tools/bin/get_sequence.py
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tools/rna_tools/bin/get_surrounding_res.py
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tools/rna_tools/bin/helix_preassemble_setup.py
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tools/rna_tools/bin/make_rna_rosetta_ready.py
- rna-denovo
tools/rna_tools/bin/make_tag.py
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tools/rna_tools/bin/mpi4py_jobsub.py
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tools/rna_tools/bin/parallel_min_setup.py
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tools/rna_tools/bin/parse_options.py
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tools/rna_tools/bin/parse_tag.py
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tools/rna_tools/bin/pdb2fasta.py
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tools/rna_tools/bin/pdbslice.py
- rna-denovo-setup
tools/rna_tools/bin/pdbsubset.py
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tools/rna_tools/bin/pp_jobsub.py
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tools/rna_tools/bin/pp_util.py
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tools/rna_tools/bin/prepare_rna_puzzle_submissions.py
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tools/rna_tools/bin/qsub_torque.py
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tools/rna_tools/bin/read_pdb.py
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tools/rna_tools/bin/renumber_pdb_in_place.py
- rna-denovo-setup
tools/rna_tools/bin/reorder_pdb.py
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tools/rna_tools/bin/reorder_to_standard_pdb.py
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tools/rna_tools/bin/replace_chain_inplace.py
- rna-denovo-setup
tools/rna_tools/bin/replace_chain.py
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tools/rna_tools/bin/rna_denovo_jobscript.py
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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
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tools/rna_tools/bin/rosetta_exe.py
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tools/rna_tools/bin/rosetta_submit.py
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tools/rna_tools/bin/rsync_from_cluster.py
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tools/rna_tools/bin/rsync_to_cluster.py
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tools/rna_tools/bin/silent_file_sort_and_select.py
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tools/rna_tools/cluster_setup/biox3_jobsub.py
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tools/rna_tools/cluster_setup/cluster_info.py
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tools/rna_tools/cluster_setup/easy_cat.py
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tools/rna_tools/cluster_setup/mpi4py_jobsub.py
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tools/rna_tools/cluster_setup/pp_jobsub.py
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tools/rna_tools/cluster_setup/pp_util.py
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tools/rna_tools/cluster_setup/qsub_torque.py
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tools/rna_tools/cluster_setup/rosetta_submit.py
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tools/rna_tools/cluster_setup/rsync_from_cluster.py
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tools/rna_tools/cluster_setup/rsync_to_cluster.py
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tools/rna_tools/job_setup/helix_preassemble_setup.py
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tools/rna_tools/job_setup/make_tag.py
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tools/rna_tools/job_setup/parallel_min_setup.py
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tools/rna_tools/job_setup/parse_options.py
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tools/rna_tools/job_setup/parse_tag.py
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tools/rna_tools/job_setup/rna_denovo_jobscript.py
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tools/rna_tools/job_setup/rna_denovo_setup.py
- rna-denovo-setup
tools/rna_tools/job_setup/rna_server_conversions.py
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tools/rna_tools/job_setup/rosetta_exe.py
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tools/rna_tools/pdb_util/amino_acids.py
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tools/rna_tools/pdb_util/check_cutpoints.py
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tools/rna_tools/pdb_util/extract_chain.py
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tools/rna_tools/pdb_util/fetch_pdb.py
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tools/rna_tools/pdb_util/fix_chainbreaks_with_erraser.py
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tools/rna_tools/pdb_util/get_res_num.py
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tools/rna_tools/pdb_util/get_sequence.py
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tools/rna_tools/pdb_util/get_surrounding_res.py
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tools/rna_tools/pdb_util/make_rna_rosetta_ready.py
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tools/rna_tools/pdb_util/pdb2fasta.py
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tools/rna_tools/pdb_util/pdbslice.py
- rna-denovo-setup
tools/rna_tools/pdb_util/pdbsubset.py
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tools/rna_tools/pdb_util/plot_contour.py
- Sample-around-nucleobase
tools/rna_tools/pdb_util/prepare_rna_puzzle_submissions.py
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tools/rna_tools/pdb_util/read_pdb.py
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tools/rna_tools/pdb_util/renumber_pdb_in_place.py
- rna-denovo-setup
tools/rna_tools/pdb_util/reorder_pdb.py
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tools/rna_tools/pdb_util/reorder_to_standard_pdb.py
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tools/rna_tools/pdb_util/replace_chain_inplace.py
- rna-denovo-setup
tools/rna_tools/pdb_util/replace_chain.py
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tools/rna_tools/pdb_util/rna_helix.py
- rna-denovo-setup
tools/rna_tools/silent_util/cat_outfiles.py
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tools/rna_tools/silent_util/extract_lowscore_decoys_outfile.py
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tools/rna_tools/silent_util/extract_lowscore_decoys.py
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tools/rna_tools/silent_util/fields.py
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tools/rna_tools/silent_util/silent_file_sort_and_select.py
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tools/rna_tools/sym_link.py
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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
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tools/SWA_protein_python/generate_dag/generate_swa_protein_dag.py
- swa-protein-long-loop
tools/SWA_protein_python/generate_dag/get_sequence.py
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tools/SWA_protein_python/generate_dag/make_tag.py
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tools/SWA_protein_python/generate_dag/parse_options.py
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tools/SWA_protein_python/run_dag_on_cluster/extract_lowscore_decoys_outfile.py
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tools/SWA_protein_python/run_dag_on_cluster/parse_options.py
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tools/SWA_protein_python/run_dag_on_cluster/stepwise_post_process_cluster.py
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tools/SWA_protein_python/run_dag_on_cluster/stepwise_post_process_combine_and_filter_outfiles.py
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tools/SWA_protein_python/run_dag_on_cluster/stepwise_pre_process_setup_dirs.py
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tools/SWA_protein_python/run_dag_on_cluster/SWA_condor_test.py
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tools/SWA_protein_python/run_dag_on_cluster/SWA_dagman_LSF_continuous.py
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tools/SWA_protein_python/run_dag_on_cluster/SWA_dagman_slave.py
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tools/SWA_protein_python/run_dag_on_cluster/SWA_kick_off_slave_jobs.py
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tools/SWA_protein_python/run_dag_on_cluster/SWA_parse_options.py
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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
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tools/SWA_protein_python/run_dag_on_cluster/SWA_sampling_pre_process.py
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tools/SWA_protein_python/run_dag_on_cluster/SWA_util.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/benchmark_command.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/benchmark_command_util.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_continuous.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_continuous_util.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_general_util.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_generic_silent_file_reducer.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_reducer.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/DAG_slave.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/generic_empty_reducer.py
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tools/SWA_RNA_python/SWA_dagman_python/dagman/submit_DAG_job.py
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tools/SWA_RNA_python/SWA_dagman_python/database/SWA_amino_acids.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_dag_util.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_easy_cat.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_filterer.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_final_filter_dag.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_pre_process.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_rna_build_dagman.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/FARFAR_rna_build_dagman_util.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/setup_FARFAR_job_files_parse_options.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/setup_FARFAR_job_files.py
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tools/SWA_RNA_python/SWA_dagman_python/FARFAR_DAG/setup_FARFAR_job_files_util.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/calculate_pairwise_RMSD.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/calculate_RMSD.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/check_mapper_files_exist.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/cluster_rotamers.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/combine_pdb.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/count_molprobity_clash_atoms.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_benchmark_job_files.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_benchmark_table.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_benchmark_table_util.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_gnuplot_script.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_idealize_helix_general.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_idealize_helix.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_local_dag.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_RNA_primer_simple.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_score_vs_rmsd_plot.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_torsion_database_check_length.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/create_torsion_database.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/ensure_rna_rosetta_ready.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/extend_silent_struct_with_idealized_helix.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/extract_C1_P_atom_from_PDB.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/extract_FR3D_data.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/extract_hbond_stat.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/extract_MC_annotate_data.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/extract_torsions_from_pdb.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/fields.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/find_sequence.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/fix_pymol_output_pdb.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/get_OLLM_chain_closure_only_regions.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/invert_chain_sequence.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/line_counts.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/lower_sequence.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/minimize_pdb.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/path_check_gnuplot.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/pdb2seqlist.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/pdb_to_silent_file.py
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tools/SWA_RNA_python/SWA_dagman_python/misc/remove_columns.py
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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
-
tools/recces/data.py
-
tools/recces/min_func.py
-
tools/recces/util.py
-
See also the Remodel and RosettaRemodel documentation.
tools/remodel/getBluePrintFromCoords.pl
-
main/source/src/apps/public/ddg/convert_to_cst_file.sh
- Convert ddG logfile to a constraint file.
tools/analysis/apps/gen_pepspec_pwm.py
- Generate a position weight matrix from PepSpec output.
tools/beta-peptide/create_beta_peptide_params.py
-
tools/beta-peptide/make_beta_peptide_bbdep.py
-
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
-
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.
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
-
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
-
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
-
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.
AMBRose is a PyRosetta package for easily working with AMBER. Its documentation can be found here, and the package itself is found at tools/AmbRose/ambrose.
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
-
main/source/scons.py
- Main script for Rosetta compilation.
main/source/ninja_build.py
- Script for the alternative CMake+ninja build system.
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
-
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
-
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
-
main/source/GUIs/rosetta_flag_file_builder/*
-
main/source/src/python/packaged_bindings/*
-
main/source/src/python/bindings/*
-
tools/AmbRose/AmbRose.py
- Python module for the interconversion between Rosetta and Amber poses
tools/clang/clang.py
-
tools/clang_ast_transform/*
-
tools/PyRosetta.develop/DeployPyRosetta.py
-
tools/python_cc_reader/*
-
tools/willclang/*