pyrosetta_help package

Subpackages

• pyrosetta_help.alphafold package
  • Submodules
  • pyrosetta_help.alphafold.constraints module
    • add_interchain_pae_constraints()
    • add_pae_constraints()
    • add_stretch_constraint()
    • make_pae_constraint()
  • pyrosetta_help.alphafold.multimodel module
    • AF2NotebookAnalyser
      • AF2NotebookAnalyser.__init__()
      • AF2NotebookAnalyser.calculate_interface()
      • AF2NotebookAnalyser.constrain()
      • AF2NotebookAnalyser.constrain_and_relax()
      • AF2NotebookAnalyser.dump()
      • AF2NotebookAnalyser.dump_pdbs()
      • AF2NotebookAnalyser.find_interface_residues()
      • AF2NotebookAnalyser.get_errors()
      • AF2NotebookAnalyser.get_interactions()
      • AF2NotebookAnalyser.get_median_interface_bfactors()
      • AF2NotebookAnalyser.get_poses()
      • AF2NotebookAnalyser.load()
      • AF2NotebookAnalyser.make_AF2_dataframe()
      • AF2NotebookAnalyser.make_phosphorylated()
      • AF2NotebookAnalyser.parse_phosphosite()
      • AF2NotebookAnalyser.poses
      • AF2NotebookAnalyser.relax()
      • AF2NotebookAnalyser.sidechain_relax()
  • pyrosetta_help.alphafold.plot module
    • make_pae_plot()
  • pyrosetta_help.alphafold.retrieval module
    • get_alphafold2_error()
    • pose_from_alphafold2()
    • reshape_errors()
  • pyrosetta_help.alphafold.superimpose module
    • superimpose_by_pLDDT()
  • Module contents
• pyrosetta_help.blueprint_maker package
  • Module contents
    • Blueprinter
      • Blueprinter.ResInfo
• pyrosetta_help.chain_ops package
  • Submodules
  • pyrosetta_help.chain_ops.chain_ops module
    • ChainOps
      • ChainOps.__init__()
      • ChainOps.dump()
      • ChainOps.get_entry()
      • ChainOps.get_entry_of_key()
      • ChainOps.get_pose_of_chain()
      • ChainOps.load()
  • pyrosetta_help.chain_ops.transmogrifier module
    • Murinizer
      • Murinizer.__init__()
    • Transmogrifier
      • Transmogrifier.__init__()
      • Transmogrifier.align_seqs()
      • Transmogrifier.covert_A2B()
      • Transmogrifier.from_chain_ops()
      • Transmogrifier.transmogrify()
  • Module contents
• pyrosetta_help.common_ops package
  • Submodules
  • pyrosetta_help.common_ops.constraints module
    • constraints2pandas()
    • get_AtomID()
    • get_AtomID_by_NGL_sele()
    • get_AtomID_from_pymol_line()
    • get_NGL_selection_from_AtomID()
    • make_constraint_from_pymol_line()
    • print_bad_constraint_scores()
    • print_constraint_score()
    • print_constraint_scores()
  • pyrosetta_help.common_ops.distances module
    • measure_distance_matrix()
    • measure_inter_residue_distance()
    • measure_ligand_distances()
  • pyrosetta_help.common_ops.downloads module
    • download_cif()
    • download_map()
    • download_opm()
    • download_pdb()
  • pyrosetta_help.common_ops.faux_selectors module
    • AlteredSelector
      • AlteredSelector.__init__()
      • AlteredSelector.apply()
    • OrListSelector()
    • RingSelector
      • RingSelector.__init__()
      • RingSelector.apply()
    • UnalteredSelector
      • UnalteredSelector.__init__()
      • UnalteredSelector.apply()
    • get_bfactor_vector()
  • pyrosetta_help.common_ops.minimize module
    • do_chainwise_relax()
    • do_local_relax()
    • get_local_relax()
    • get_local_scorefxn()
    • prep_ED()
  • pyrosetta_help.common_ops.nglview module
  • pyrosetta_help.common_ops.ss_changes module
    • make_310_helical()
    • make_alpha_helical()
    • make_pi_helical()
    • make_sheet()
    • make_ss()
  • pyrosetta_help.common_ops.utils module
    • add_bfactor_from_score()
    • assign_chain_letter()
    • clarify_selector()
    • correct_numbering()
    • count_ligands()
    • fix_offset()
    • get_last_res_in_chain()
    • get_pdbstr()
    • make_blank_pose()
    • pose2pandas()
    • pose_from_file()
    • pose_range()
    • what_is_chain()
  • Module contents
• pyrosetta_help.init_ops package
  • Submodules
  • pyrosetta_help.init_ops.log module
    • configure_logger()
    • get_all_log_entries()
    • get_log_entries()
  • pyrosetta_help.init_ops.make_options module
    • make_option_string()
  • Module contents
• pyrosetta_help.installer package
  • Module contents
    • check_pyrosetta()
    • download_pyrosetta()
    • get_latest_release_url()
    • get_os_name()
    • install_pyrosetta()
    • parse()
• pyrosetta_help.ligands package
  • Submodules
  • pyrosetta_help.ligands.hunter module
    • LigandHunter
      • LigandHunter.__init__()
      • LigandHunter.candidate_ligands
      • LigandHunter.cofactor_codes
      • LigandHunter.cofactor_reference
      • LigandHunter.get_most_common_ligands()
      • LigandHunter.get_pdb_entry_by_ligand()
      • LigandHunter.ligand_data
      • LigandHunter.missing_codes
      • LigandHunter.to_dataframe()
  • pyrosetta_help.ligands.load module
    • get_smiles()
    • parameterized_pose_from_file()
    • parameterized_pose_from_pdbblock()
  • pyrosetta_help.ligands.nick module
    • LigandNicker
      • LigandNicker.__init__()
      • LigandNicker.constrain_migrated()
      • LigandNicker.from_pdbcode()
      • LigandNicker.get_mapping_between_poses()
      • LigandNicker.get_surrounding_residue()
      • LigandNicker.get_wanted_selector()
      • LigandNicker.make_atomID_map()
      • LigandNicker.make_constraint_foreign_hbond()
      • LigandNicker.migrate()
      • LigandNicker.relax_migrated()
    • chain_letter_to_number()
  • Module contents
• pyrosetta_help.per_atom package
  • Module contents
    • AtomicInteractions
      • AtomicInteractions.__init__()
      • AtomicInteractions.best_interactions
      • AtomicInteractions.describe_atom()
      • AtomicInteractions.describe_best()
      • AtomicInteractions.describe_interaction()
      • AtomicInteractions.expected_total
      • AtomicInteractions.get_cc_selector()
      • AtomicInteractions.get_target_selector()
      • AtomicInteractions.score_types
      • AtomicInteractions.term_relevance_cutoff
      • AtomicInteractions.total
    • NeighbourInteractions
      • NeighbourInteractions.__init__()
• pyrosetta_help.residue_decription package
  • Submodules
  • pyrosetta_help.residue_decription.betaturn module
    • get_betaturns()
  • pyrosetta_help.residue_decription.cis module
    • get_cis_residues()
  • pyrosetta_help.residue_decription.hbonds module
    • BondDataType
      • BondDataType.acc_atm_name
      • BondDataType.acc_resi
      • BondDataType.acc_resn
      • BondDataType.distance
      • BondDataType.don_atm_name
      • BondDataType.don_resi
      • BondDataType.don_resn
      • BondDataType.energy
    • get_hbond_dicts()
    • hbond2dict()
  • pyrosetta_help.residue_decription.ss module
    • get_ss()
  • pyrosetta_help.residue_decription.xlinks module
    • get_xlink_details()
    • get_xlink_idx()
    • is_xlinked()
  • Module contents
• pyrosetta_help.score_mutants package
  • Submodules
  • pyrosetta_help.score_mutants.mutation module
    • Mutation
      • Mutation.__init__()
      • Mutation.assert_valid()
      • Mutation.is_valid()
      • Mutation.parse_mutation()
  • pyrosetta_help.score_mutants.scores module
    • extend_scores()
    • get_highest_contributor()
    • get_largest_contributor()
    • get_lowest_contributor()
  • pyrosetta_help.score_mutants.variant module
    • MutantScorer
      • MutantScorer.CA_RMSD()
      • MutantScorer.FA_RMSD()
      • MutantScorer.__init__()
      • MutantScorer.convert_name3_to_name1_mutation()
      • MutantScorer.delta_scoredict()
      • MutantScorer.does_contain()
      • MutantScorer.from_file()
      • MutantScorer.get_neighbor_vector()
      • MutantScorer.get_present_chains()
      • MutantScorer.get_scoredict()
      • MutantScorer.get_unweighted_scorefxn()
      • MutantScorer.get_wscoredict()
      • MutantScorer.has_interface()
      • MutantScorer.has_residue()
      • MutantScorer.make_mutant()
      • MutantScorer.make_output_folder()
      • MutantScorer.movement()
      • MutantScorer.parse_mutation()
      • MutantScorer.prefix_dict()
      • MutantScorer.relax_around_mover()
      • MutantScorer.score_interface()
      • MutantScorer.score_mutation()
      • MutantScorer.score_mutations()
      • MutantScorer.score_only()
      • MutantScorer.vector2list()
  • Module contents
• pyrosetta_help.threading package
  • Module contents
    • get_alignment()
    • get_nonprotein_pose()
    • make_fragment_sets()
    • oligomer_thread()
    • rangify()
    • steal_ligands()
    • thread()
    • write_grishin()
• pyrosetta_help.weights package
  • Submodules
  • pyrosetta_help.weights.terms module
  • Module contents
    • WeightWatcher
      • WeightWatcher.compare()
      • WeightWatcher.find_metion()
      • WeightWatcher.folder
      • WeightWatcher.get_ref_values_badly()
      • WeightWatcher.get_scorefxn()
      • WeightWatcher.get_scorefxn_block()
      • WeightWatcher.get_scorefxn_comments()
      • WeightWatcher.get_weight()
      • WeightWatcher.get_weights()
      • WeightWatcher.possible_scorefxn_names
      • WeightWatcher.pyrosetta_folder
      • WeightWatcher.term_meanings

Submodules

pyrosetta_help.colab_ops module

pyrosetta_help.colab_ops.assert_notebook()

Raises an error if the current environment is not a notebook.

pyrosetta_help.colab_ops.get_shell_mode() → str

The get_ipython().__class__.__name__ is a very nasty name, this replaces it with a nicer name for humans:

• Shell: ‘colab’

• ZMQInteractiveShell: ‘jupyter’

• TerminalInteractiveShell: ‘terminal’

• None: ‘impossible’

pyrosetta_help.colab_ops.install_and_import(package_name: str, pypi_name: None | str = None, alias_name: None | str = None)

This is an import / installer in case the !pip commands do not work. Which they do unless there are issues with the kernel.

If the module has a different name in pypi (pypi_name) than its import name (package_name), specify it.

pip install pypi_name import package_name as alias_name

pyrosetta_help.colab_ops.mount_google_drive(use_drive: bool) → str

Mount drive if needed and return the working directory. Change the working path and

Module contents