Index

_

__init__() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) (pyrosetta_help.blueprint_maker.Blueprinter.ResInfo method) (pyrosetta_help.chain_ops.chain_ops.ChainOps method) (pyrosetta_help.chain_ops.transmogrifier.Murinizer method) (pyrosetta_help.chain_ops.transmogrifier.Transmogrifier method) (pyrosetta_help.common_ops.faux_selectors.AlteredSelector method) (pyrosetta_help.common_ops.faux_selectors.RingSelector method) (pyrosetta_help.common_ops.faux_selectors.UnalteredSelector method) (pyrosetta_help.ligands.hunter.LigandHunter method) (pyrosetta_help.ligands.nick.LigandNicker method) (pyrosetta_help.per_atom.AtomicInteractions method) (pyrosetta_help.per_atom.NeighbourInteractions method) (pyrosetta_help.score_mutants.mutation.Mutation method) (pyrosetta_help.score_mutants.variant.MutantScorer method)

A

acc_atm_name (pyrosetta_help.residue_decription.hbonds.BondDataType attribute) acc_resi (pyrosetta_help.residue_decription.hbonds.BondDataType attribute) acc_resn (pyrosetta_help.residue_decription.hbonds.BondDataType attribute) add_bfactor_from_score() (in module pyrosetta_help.common_ops.utils) add_interchain_pae_constraints() (in module pyrosetta_help.alphafold.constraints) add_pae_constraints() (in module pyrosetta_help.alphafold.constraints) add_stretch_constraint() (in module pyrosetta_help.alphafold.constraints) AF2NotebookAnalyser (class in pyrosetta_help.alphafold.multimodel)

align_seqs() (pyrosetta_help.chain_ops.transmogrifier.Transmogrifier method) AlteredSelector (class in pyrosetta_help.common_ops.faux_selectors) apply() (pyrosetta_help.common_ops.faux_selectors.AlteredSelector method) (pyrosetta_help.common_ops.faux_selectors.RingSelector method) (pyrosetta_help.common_ops.faux_selectors.UnalteredSelector method) assert_notebook() (in module pyrosetta_help.colab_ops) assert_valid() (pyrosetta_help.score_mutants.mutation.Mutation method) assign_chain_letter() (in module pyrosetta_help.common_ops.utils) AtomicInteractions (class in pyrosetta_help.per_atom)

B

best_interactions (pyrosetta_help.per_atom.AtomicInteractions property) Blueprinter (class in pyrosetta_help.blueprint_maker)

Blueprinter.ResInfo (class in pyrosetta_help.blueprint_maker) BondDataType (class in pyrosetta_help.residue_decription.hbonds)

C

CA_RMSD() (pyrosetta_help.score_mutants.variant.MutantScorer method) calculate_interface() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) candidate_ligands (pyrosetta_help.ligands.hunter.LigandHunter property) chain_letter_to_number() (in module pyrosetta_help.ligands.nick) ChainOps (class in pyrosetta_help.chain_ops.chain_ops) check_pyrosetta() (in module pyrosetta_help.installer) clarify_selector() (in module pyrosetta_help.common_ops.utils) cofactor_codes (pyrosetta_help.ligands.hunter.LigandHunter property) cofactor_reference (pyrosetta_help.ligands.hunter.LigandHunter property)

compare() (pyrosetta_help.weights.WeightWatcher method) configure_logger() (in module pyrosetta_help.init_ops.log) constrain() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) constrain_and_relax() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) constrain_migrated() (pyrosetta_help.ligands.nick.LigandNicker method) constraints2pandas() (in module pyrosetta_help.common_ops.constraints) convert_name3_to_name1_mutation() (pyrosetta_help.score_mutants.variant.MutantScorer static method) correct_numbering() (in module pyrosetta_help.common_ops.utils) count_ligands() (in module pyrosetta_help.common_ops.utils) covert_A2B() (pyrosetta_help.chain_ops.transmogrifier.Transmogrifier method)

D

delta_scoredict() (pyrosetta_help.score_mutants.variant.MutantScorer method) describe_atom() (pyrosetta_help.per_atom.AtomicInteractions method) describe_best() (pyrosetta_help.per_atom.AtomicInteractions method) describe_interaction() (pyrosetta_help.per_atom.AtomicInteractions method) distance (pyrosetta_help.residue_decription.hbonds.BondDataType attribute) do_chainwise_relax() (in module pyrosetta_help.common_ops.minimize) do_local_relax() (in module pyrosetta_help.common_ops.minimize) does_contain() (pyrosetta_help.score_mutants.variant.MutantScorer method) don_atm_name (pyrosetta_help.residue_decription.hbonds.BondDataType attribute)

don_resi (pyrosetta_help.residue_decription.hbonds.BondDataType attribute) don_resn (pyrosetta_help.residue_decription.hbonds.BondDataType attribute) download_cif() (in module pyrosetta_help.common_ops.downloads) download_map() (in module pyrosetta_help.common_ops.downloads) download_opm() (in module pyrosetta_help.common_ops.downloads) download_pdb() (in module pyrosetta_help.common_ops.downloads) download_pyrosetta() (in module pyrosetta_help.installer) dump() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) (pyrosetta_help.chain_ops.chain_ops.ChainOps method) dump_pdbs() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method)

E

energy (pyrosetta_help.residue_decription.hbonds.BondDataType attribute)

expected_total (pyrosetta_help.per_atom.AtomicInteractions property) extend_scores() (in module pyrosetta_help.score_mutants.scores)

F

FA_RMSD() (pyrosetta_help.score_mutants.variant.MutantScorer method) find_interface_residues() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) find_metion() (pyrosetta_help.weights.WeightWatcher method) fix_offset() (in module pyrosetta_help.common_ops.utils)

folder (pyrosetta_help.weights.WeightWatcher attribute) from_chain_ops() (pyrosetta_help.chain_ops.transmogrifier.Transmogrifier class method) from_file() (pyrosetta_help.score_mutants.variant.MutantScorer class method) from_pdbcode() (pyrosetta_help.ligands.nick.LigandNicker class method)

G

get() (pyrosetta_help.blueprint_maker.Blueprinter.ResInfo class method) get_alignment() (in module pyrosetta_help.threading) get_all_log_entries() (in module pyrosetta_help.init_ops.log) get_alphafold2_error() (in module pyrosetta_help.alphafold.retrieval) get_AtomID() (in module pyrosetta_help.common_ops.constraints) get_AtomID_by_NGL_sele() (in module pyrosetta_help.common_ops.constraints) get_AtomID_from_pymol_line() (in module pyrosetta_help.common_ops.constraints) get_betaturns() (in module pyrosetta_help.residue_decription.betaturn) get_bfactor_vector() (in module pyrosetta_help.common_ops.faux_selectors) get_cc_selector() (pyrosetta_help.per_atom.AtomicInteractions method) get_cis_residues() (in module pyrosetta_help.residue_decription.cis) get_entry() (pyrosetta_help.chain_ops.chain_ops.ChainOps method) get_entry_of_key() (pyrosetta_help.chain_ops.chain_ops.ChainOps method) get_errors() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) get_hbond_dicts() (in module pyrosetta_help.residue_decription.hbonds) get_highest_contributor() (in module pyrosetta_help.score_mutants.scores) get_interactions() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) get_largest_contributor() (in module pyrosetta_help.score_mutants.scores) get_last_res_in_chain() (in module pyrosetta_help.common_ops.utils) get_latest_release_url() (in module pyrosetta_help.installer) get_local_relax() (in module pyrosetta_help.common_ops.minimize) get_local_scorefxn() (in module pyrosetta_help.common_ops.minimize) get_log_entries() (in module pyrosetta_help.init_ops.log) get_lowest_contributor() (in module pyrosetta_help.score_mutants.scores) get_mapping_between_poses() (pyrosetta_help.ligands.nick.LigandNicker method) get_median_interface_bfactors() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method)

get_most_common_ligands() (pyrosetta_help.ligands.hunter.LigandHunter method) get_neighbor_vector() (pyrosetta_help.score_mutants.variant.MutantScorer method) get_NGL_selection_from_AtomID() (in module pyrosetta_help.common_ops.constraints) get_nonprotein_pose() (in module pyrosetta_help.threading) get_os_name() (in module pyrosetta_help.installer) get_pdb_entry_by_ligand() (pyrosetta_help.ligands.hunter.LigandHunter method) get_pdbstr() (in module pyrosetta_help.common_ops.utils) get_pose_of_chain() (pyrosetta_help.chain_ops.chain_ops.ChainOps method) get_poses() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) get_present_chains() (pyrosetta_help.score_mutants.variant.MutantScorer method) get_ref_values_badly() (pyrosetta_help.weights.WeightWatcher method) get_scoredict() (pyrosetta_help.score_mutants.variant.MutantScorer method) get_scorefxn() (pyrosetta_help.weights.WeightWatcher method) get_scorefxn_block() (pyrosetta_help.weights.WeightWatcher method) get_scorefxn_comments() (pyrosetta_help.weights.WeightWatcher method) get_shell_mode() (in module pyrosetta_help.colab_ops) get_smiles() (in module pyrosetta_help.ligands.load) get_ss() (in module pyrosetta_help.residue_decription.ss) get_surrounding_residue() (pyrosetta_help.ligands.nick.LigandNicker method) get_target_selector() (pyrosetta_help.per_atom.AtomicInteractions method) get_unweighted_scorefxn() (pyrosetta_help.score_mutants.variant.MutantScorer method) get_wanted_selector() (pyrosetta_help.ligands.nick.LigandNicker method) get_weight() (pyrosetta_help.weights.WeightWatcher method) get_weights() (pyrosetta_help.weights.WeightWatcher method) get_wscoredict() (pyrosetta_help.score_mutants.variant.MutantScorer method) get_xlink_details() (in module pyrosetta_help.residue_decription.xlinks) get_xlink_idx() (in module pyrosetta_help.residue_decription.xlinks)

H

has_interface() (pyrosetta_help.score_mutants.variant.MutantScorer method)

has_residue() (pyrosetta_help.score_mutants.variant.MutantScorer method) hbond2dict() (in module pyrosetta_help.residue_decription.hbonds)

I

install_and_import() (in module pyrosetta_help.colab_ops) install_pyrosetta() (in module pyrosetta_help.installer)

is_valid() (pyrosetta_help.score_mutants.mutation.Mutation method) is_xlinked() (in module pyrosetta_help.residue_decription.xlinks)

L

ligand_data (pyrosetta_help.ligands.hunter.LigandHunter property) LigandHunter (class in pyrosetta_help.ligands.hunter)

LigandNicker (class in pyrosetta_help.ligands.nick) load() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser class method) (pyrosetta_help.chain_ops.chain_ops.ChainOps method)

M

make_310_helical() (in module pyrosetta_help.common_ops.ss_changes) make_AF2_dataframe() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) make_alpha_helical() (in module pyrosetta_help.common_ops.ss_changes) make_atomID_map() (pyrosetta_help.ligands.nick.LigandNicker method) make_blank_pose() (in module pyrosetta_help.common_ops.utils) make_constraint_foreign_hbond() (pyrosetta_help.ligands.nick.LigandNicker method) make_constraint_from_pymol_line() (in module pyrosetta_help.common_ops.constraints) make_fragment_sets() (in module pyrosetta_help.threading) make_mutant() (pyrosetta_help.score_mutants.variant.MutantScorer method) make_option_string() (in module pyrosetta_help.init_ops.make_options) make_output_folder() (pyrosetta_help.score_mutants.variant.MutantScorer method) make_pae_constraint() (in module pyrosetta_help.alphafold.constraints) make_pae_plot() (in module pyrosetta_help.alphafold.plot) make_phosphorylated() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) make_pi_helical() (in module pyrosetta_help.common_ops.ss_changes) make_sheet() (in module pyrosetta_help.common_ops.ss_changes) make_ss() (in module pyrosetta_help.common_ops.ss_changes) measure_distance_matrix() (in module pyrosetta_help.common_ops.distances) measure_inter_residue_distance() (in module pyrosetta_help.common_ops.distances) measure_ligand_distances() (in module pyrosetta_help.common_ops.distances) migrate() (pyrosetta_help.ligands.nick.LigandNicker method) missing_codes (pyrosetta_help.ligands.hunter.LigandHunter attribute) module pyrosetta_help pyrosetta_help.alphafold pyrosetta_help.alphafold.constraints pyrosetta_help.alphafold.multimodel pyrosetta_help.alphafold.plot pyrosetta_help.alphafold.retrieval pyrosetta_help.alphafold.superimpose pyrosetta_help.blueprint_maker pyrosetta_help.chain_ops pyrosetta_help.chain_ops.chain_ops pyrosetta_help.chain_ops.transmogrifier pyrosetta_help.colab_ops pyrosetta_help.common_ops pyrosetta_help.common_ops.constraints pyrosetta_help.common_ops.distances pyrosetta_help.common_ops.downloads pyrosetta_help.common_ops.faux_selectors pyrosetta_help.common_ops.minimize pyrosetta_help.common_ops.ss_changes pyrosetta_help.common_ops.utils pyrosetta_help.init_ops pyrosetta_help.init_ops.log pyrosetta_help.init_ops.make_options pyrosetta_help.installer pyrosetta_help.ligands pyrosetta_help.ligands.hunter pyrosetta_help.ligands.load pyrosetta_help.ligands.nick pyrosetta_help.per_atom pyrosetta_help.residue_decription pyrosetta_help.residue_decription.betaturn pyrosetta_help.residue_decription.cis pyrosetta_help.residue_decription.hbonds pyrosetta_help.residue_decription.ss pyrosetta_help.residue_decription.xlinks pyrosetta_help.score_mutants pyrosetta_help.score_mutants.mutation pyrosetta_help.score_mutants.scores pyrosetta_help.score_mutants.variant pyrosetta_help.threading pyrosetta_help.weights pyrosetta_help.weights.terms

mount_google_drive() (in module pyrosetta_help.colab_ops) movement() (pyrosetta_help.score_mutants.variant.MutantScorer method) Murinizer (class in pyrosetta_help.chain_ops.transmogrifier) MutantScorer (class in pyrosetta_help.score_mutants.variant) Mutation (class in pyrosetta_help.score_mutants.mutation)

N

NeighbourInteractions (class in pyrosetta_help.per_atom)

O

oligomer_thread() (in module pyrosetta_help.threading)

OrListSelector() (in module pyrosetta_help.common_ops.faux_selectors)

P

parameterized_pose_from_file() (in module pyrosetta_help.ligands.load) parameterized_pose_from_pdbblock() (in module pyrosetta_help.ligands.load) parse() (in module pyrosetta_help.installer) parse_mutation() (pyrosetta_help.score_mutants.mutation.Mutation method) (pyrosetta_help.score_mutants.variant.MutantScorer method) parse_phosphosite() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser class method) pdb_info (pyrosetta_help.blueprint_maker.Blueprinter.ResInfo attribute) pose2pandas() (in module pyrosetta_help.common_ops.utils) pose_from_alphafold2() (in module pyrosetta_help.alphafold.retrieval) pose_from_file() (in module pyrosetta_help.common_ops.utils) pose_range() (in module pyrosetta_help.common_ops.utils) poses (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser property) possible_scorefxn_names (pyrosetta_help.weights.WeightWatcher property) prefix_dict() (pyrosetta_help.score_mutants.variant.MutantScorer method) prep_ED() (in module pyrosetta_help.common_ops.minimize) print_bad_constraint_scores() (in module pyrosetta_help.common_ops.constraints) print_constraint_score() (in module pyrosetta_help.common_ops.constraints) print_constraint_scores() (in module pyrosetta_help.common_ops.constraints) pyrosetta_folder (pyrosetta_help.weights.WeightWatcher attribute) pyrosetta_help module pyrosetta_help.alphafold module pyrosetta_help.alphafold.constraints module pyrosetta_help.alphafold.multimodel module pyrosetta_help.alphafold.plot module pyrosetta_help.alphafold.retrieval module pyrosetta_help.alphafold.superimpose module pyrosetta_help.blueprint_maker module pyrosetta_help.chain_ops module pyrosetta_help.chain_ops.chain_ops module pyrosetta_help.chain_ops.transmogrifier module pyrosetta_help.colab_ops module pyrosetta_help.common_ops module pyrosetta_help.common_ops.constraints module pyrosetta_help.common_ops.distances module pyrosetta_help.common_ops.downloads module

pyrosetta_help.common_ops.faux_selectors module pyrosetta_help.common_ops.minimize module pyrosetta_help.common_ops.ss_changes module pyrosetta_help.common_ops.utils module pyrosetta_help.init_ops module pyrosetta_help.init_ops.log module pyrosetta_help.init_ops.make_options module pyrosetta_help.installer module pyrosetta_help.ligands module pyrosetta_help.ligands.hunter module pyrosetta_help.ligands.load module pyrosetta_help.ligands.nick module pyrosetta_help.per_atom module pyrosetta_help.residue_decription module pyrosetta_help.residue_decription.betaturn module pyrosetta_help.residue_decription.cis module pyrosetta_help.residue_decription.hbonds module pyrosetta_help.residue_decription.ss module pyrosetta_help.residue_decription.xlinks module pyrosetta_help.score_mutants module pyrosetta_help.score_mutants.mutation module pyrosetta_help.score_mutants.scores module pyrosetta_help.score_mutants.variant module pyrosetta_help.threading module pyrosetta_help.weights module pyrosetta_help.weights.terms module

R

rangify() (in module pyrosetta_help.threading) relax() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) relax_around_mover() (pyrosetta_help.score_mutants.variant.MutantScorer method)

relax_migrated() (pyrosetta_help.ligands.nick.LigandNicker method) reshape_errors() (in module pyrosetta_help.alphafold.retrieval) RingSelector (class in pyrosetta_help.common_ops.faux_selectors)

S

score_interface() (pyrosetta_help.score_mutants.variant.MutantScorer method) score_mutation() (pyrosetta_help.score_mutants.variant.MutantScorer method) score_mutations() (pyrosetta_help.score_mutants.variant.MutantScorer method) score_only() (pyrosetta_help.score_mutants.variant.MutantScorer method)

score_types (pyrosetta_help.per_atom.AtomicInteractions attribute) set() (pyrosetta_help.blueprint_maker.Blueprinter.ResInfo method) sidechain_relax() (pyrosetta_help.alphafold.multimodel.AF2NotebookAnalyser method) steal_ligands() (in module pyrosetta_help.threading) superimpose_by_pLDDT() (in module pyrosetta_help.alphafold.superimpose)

T

term_meanings (pyrosetta_help.weights.WeightWatcher attribute) term_relevance_cutoff (pyrosetta_help.per_atom.AtomicInteractions attribute) thread() (in module pyrosetta_help.threading)

to_dataframe() (pyrosetta_help.ligands.hunter.LigandHunter method) total (pyrosetta_help.per_atom.AtomicInteractions property) Transmogrifier (class in pyrosetta_help.chain_ops.transmogrifier) transmogrify() (pyrosetta_help.chain_ops.transmogrifier.Transmogrifier method)

U

UnalteredSelector (class in pyrosetta_help.common_ops.faux_selectors)

V

vector2list() (pyrosetta_help.score_mutants.variant.MutantScorer method)

W

WeightWatcher (class in pyrosetta_help.weights)

what_is_chain() (in module pyrosetta_help.common_ops.utils) write_grishin() (in module pyrosetta_help.threading)