Index

_

__class__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __delattr__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __dir__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __eq__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __eq__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __format__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __ge__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __getattribute__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __getitem__() (pyrosetta.rosetta.core.pose.Pose method) __getstate__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __gt__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __hash__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __hash__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __iadd__() (pyrosetta.rosetta.core.pose.Pose method) __imul__() (pyrosetta.rosetta.core.pose.Pose method) __init__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __init_subclass__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __int__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __iter__() (pyrosetta.rosetta.core.pose.Pose method) __le__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute)

__len__() (pyrosetta.rosetta.core.pose.Pose method) __lt__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __members__ (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) __module__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __ne__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __ne__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __new__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __reduce__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __reduce_ex__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __repr__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __repr__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __setattr__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBInfo attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.Pose attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __setstate__() (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) __sizeof__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) __str__ (pyrosetta.rosetta.core.pose.MiniPose attribute) (pyrosetta.rosetta.core.pose.PDBPoseMap attribute) (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescription attribute) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile attribute) (pyrosetta.rosetta.core.pose.xyzStripeHashPose attribute) __str__() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) __subclasshook__() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.PoseCoordPickMode method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

A

aa() (pyrosetta.rosetta.core.pose.Pose method) add_all_rosetta_options() (in module pyrosetta.rosetta) add_comment() (in module pyrosetta.rosetta.core.pose) add_constraint() (pyrosetta.rosetta.core.pose.Pose method) add_constraints() (pyrosetta.rosetta.core.pose.Pose method) add_lower_terminus_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_pose() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) add_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) add_rosetta_options_0() (in module pyrosetta.rosetta) add_rosetta_options_1() (in module pyrosetta.rosetta) add_rosetta_options_10() (in module pyrosetta.rosetta) add_rosetta_options_11() (in module pyrosetta.rosetta) add_rosetta_options_12() (in module pyrosetta.rosetta) add_rosetta_options_13() (in module pyrosetta.rosetta) add_rosetta_options_14() (in module pyrosetta.rosetta) add_rosetta_options_15() (in module pyrosetta.rosetta) add_rosetta_options_2() (in module pyrosetta.rosetta) add_rosetta_options_3() (in module pyrosetta.rosetta) add_rosetta_options_4() (in module pyrosetta.rosetta) add_rosetta_options_5() (in module pyrosetta.rosetta) add_rosetta_options_6() (in module pyrosetta.rosetta) add_rosetta_options_7() (in module pyrosetta.rosetta) add_rosetta_options_8() (in module pyrosetta.rosetta) add_rosetta_options_9() (in module pyrosetta.rosetta) add_score_line_string() (in module pyrosetta.rosetta.core.pose) add_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) add_upper_terminus_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_variant_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_variant_type_to_residue() (in module pyrosetta.rosetta.core.pose) addVirtualResAsRoot() (in module pyrosetta.rosetta.core.pose) all_atom_center() (in module pyrosetta.rosetta.core.pose)

alpha() (pyrosetta.rosetta.core.pose.Pose method) alt_loc() (pyrosetta.rosetta.core.pose.PDBInfo method) annotated_sequence() (pyrosetta.rosetta.core.pose.Pose method) annotated_to_oneletter_sequence() (in module pyrosetta.rosetta.core.pose) append_polymer_residue_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) append_pose_by_jump() (pyrosetta.rosetta.core.pose.Pose method) append_pose_to_pose() (in module pyrosetta.rosetta.core.pose) append_pose_with_glycan_residues() (in module pyrosetta.rosetta.core.pose) append_res() (pyrosetta.rosetta.core.pose.PDBInfo method) append_residue_by_atoms() (pyrosetta.rosetta.core.pose.Pose method) append_residue_by_bond() (pyrosetta.rosetta.core.pose.Pose method) append_residue_by_jump() (pyrosetta.rosetta.core.pose.Pose method) append_subpose_to_pose() (in module pyrosetta.rosetta.core.pose) apply_transform_Rx_plus_v() (pyrosetta.rosetta.core.pose.Pose method) assign() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.W128_T method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) atom_id_to_named_atom_id() (in module pyrosetta.rosetta.core.pose) atom_name() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) atom_names_list() (pyrosetta.rosetta.core.pose.MiniPose method) atom_tree() (pyrosetta.rosetta.core.pose.Pose method) attach_to() (pyrosetta.rosetta.core.pose.PDBInfo method) attributes_for_get_resnum() (in module pyrosetta.rosetta.core.pose) attributes_for_get_resnum_list() (in module pyrosetta.rosetta.core.pose) attributes_for_parse_resnum() (in module pyrosetta.rosetta.core.pose)

B

ball() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) batch_get_xyz() (pyrosetta.rosetta.core.pose.Pose method) batch_set_xyz() (pyrosetta.rosetta.core.pose.Pose method)

begin() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) beta() (pyrosetta.rosetta.core.pose.Pose method) bfactor() (pyrosetta.rosetta.core.pose.PDBInfo method)

C

canonical_atom_count() (in module pyrosetta.rosetta.core.pose) canonical_residue_count() (in module pyrosetta.rosetta.core.pose) center() (pyrosetta.rosetta.core.pose.Pose method) center_of_mass() (in module pyrosetta.rosetta.core.pose) chain() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) chain_end_res() (in module pyrosetta.rosetta.core.pose) chain_sequence() (pyrosetta.rosetta.core.pose.Pose method) chi() (pyrosetta.rosetta.core.pose.Pose method) clash() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) clash_amount() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) clash_check_ball() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) clash_check_residue_pairs() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) clash_not_resid() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) clash_raw() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) cleanATOM() (in module pyrosetta.toolbox) cleanCRYS() (in module pyrosetta.toolbox) clear() (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) clear_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) clear_sequence_constraints() (pyrosetta.rosetta.core.pose.Pose method)

clearPoseExtraScore() (in module pyrosetta.rosetta.core.pose) clearPoseExtraScores() (in module pyrosetta.rosetta.core.pose) clone() (pyrosetta.rosetta.core.pose.Pose method) compare_atom_coordinates() (in module pyrosetta.rosetta.core.pose) compare_binary_protein_silent_struct() (in module pyrosetta.rosetta.core.pose) compute_unique_chains() (in module pyrosetta.rosetta.core.pose) conditional_erase() (pyrosetta.rosetta.core.pose.PDBPoseMap method) conf2pdb_chain() (in module pyrosetta.rosetta.core.pose) conformation() (pyrosetta.rosetta.core.pose.Pose method) conformation_ptr() (pyrosetta.rosetta.core.pose.Pose method) const_data_cache() (pyrosetta.rosetta.core.pose.Pose method) constraint_set() (pyrosetta.rosetta.core.pose.Pose method) convert_from_std_map() (in module pyrosetta.rosetta.core.pose) coords() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) copy() (pyrosetta.rosetta.core.pose.PDBInfo method) copy_segment() (pyrosetta.rosetta.core.pose.Pose method) correctly_add_cutpoint_variants() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_lower_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_upper_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) corresponding_residue_in_current() (pyrosetta.rosetta.core.pose.Pose method) create_subpose() (in module pyrosetta.rosetta.core.pose) crystinfo() (pyrosetta.rosetta.core.pose.PDBInfo method)

D

data() (pyrosetta.rosetta.core.pose.Pose method) debug_pdb() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) declare_cutpoint_chemical_bond() (in module pyrosetta.rosetta.core.pose) decrement_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) definite_terminal_root() (in module pyrosetta.rosetta.core.pose) delete_comment() (in module pyrosetta.rosetta.core.pose) delete_polymer_residue() (pyrosetta.rosetta.core.pose.Pose method) delete_res() (pyrosetta.rosetta.core.pose.PDBInfo method) delete_residue_range_slow() (pyrosetta.rosetta.core.pose.Pose method)

delete_residue_slow() (pyrosetta.rosetta.core.pose.Pose method) delta() (pyrosetta.rosetta.core.pose.Pose method) detach_from() (pyrosetta.rosetta.core.pose.PDBInfo method) detached_copy() (pyrosetta.rosetta.core.pose.Pose method) dof() (pyrosetta.rosetta.core.pose.Pose method) dump_cif() (pyrosetta.rosetta.core.pose.Pose method) dump_comment_pdb() (in module pyrosetta.rosetta.core.pose) dump_file() (pyrosetta.rosetta.core.pose.Pose method) dump_pdb() (pyrosetta.rosetta.core.pose.Pose method) dump_scored_pdb() (pyrosetta.rosetta.core.pose.Pose method)

E

effective_lower_terminus_based_on_working_res() (in module pyrosetta.rosetta.core.pose) effective_upper_terminus_based_on_working_res() (in module pyrosetta.rosetta.core.pose) empty() (pyrosetta.rosetta.core.pose.Pose method) empty_record() (pyrosetta.rosetta.core.pose.PDBInfo method) end() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

energies() (pyrosetta.rosetta.core.pose.Pose method) energy_from_pose() (in module pyrosetta.rosetta.core.pose) epsilon() (pyrosetta.rosetta.core.pose.Pose method) erase() (pyrosetta.rosetta.core.pose.PDBPoseMap method) extract_pose_balls() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) extract_tag_from_pose() (in module pyrosetta.rosetta.core.pose)

F

fill() (pyrosetta.rosetta.core.pose.PDBPoseMap method) fill_pairs() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) find() (pyrosetta.rosetta.core.pose.PDBPoseMap method) fix_pdbinfo_damaged_by_insertion() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants() (in module pyrosetta.rosetta.core.pose)

fix_up_residue_type_variants_at_strand_beginning() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_end() (in module pyrosetta.rosetta.core.pose) fname() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) fold_tree() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method)

G

gamma() (pyrosetta.rosetta.core.pose.Pose method) generate_resfile_from_pdb() (in module pyrosetta.toolbox) generate_resfile_from_pose() (in module pyrosetta.toolbox) get_all_comments() (in module pyrosetta.rosetta.core.pose) get_all_score_line_strings() (in module pyrosetta.rosetta.core.pose) get_bb_torsion() (in module pyrosetta.rosetta.core.pose) get_center_of_mass() (in module pyrosetta.rosetta.core.pose) get_chain_from_chain_id() (in module pyrosetta.rosetta.core.pose) get_chain_from_jump_id() (in module pyrosetta.rosetta.core.pose) get_chain_id_from_chain() (in module pyrosetta.rosetta.core.pose) get_chain_id_from_jump_id() (in module pyrosetta.rosetta.core.pose) get_chain_ids_from_chain() (in module pyrosetta.rosetta.core.pose) get_chain_ids_from_chains() (in module pyrosetta.rosetta.core.pose) get_chain_residues() (in module pyrosetta.rosetta.core.pose) get_chains() (in module pyrosetta.rosetta.core.pose) get_comment() (in module pyrosetta.rosetta.core.pose) get_constraints_from_link_records() (in module pyrosetta.rosetta.core.pose) get_definite_terminal_root() (in module pyrosetta.rosetta.core.pose) get_hash_excluding_chain() (in module pyrosetta.rosetta.core.pose) get_hash_from_chain() (in module pyrosetta.rosetta.core.pose) get_hbonds() (in module pyrosetta.toolbox) get_jump_id_from_chain() (in module pyrosetta.rosetta.core.pose) get_jump_id_from_chain_id() (in module pyrosetta.rosetta.core.pose) get_jump_ids_from_chain() (in module pyrosetta.rosetta.core.pose) get_jump_ids_from_chain_ids() (in module pyrosetta.rosetta.core.pose) get_num_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) get_num_unrecognized_res() (pyrosetta.rosetta.core.pose.PDBInfo method) get_pdb2pose_numbering_as_stdmap() (in module pyrosetta.rosetta.core.pose)

get_residues_from_chains() (in module pyrosetta.rosetta.core.pose) get_reslabels() (pyrosetta.rosetta.core.pose.PDBInfo method) get_resnum() (in module pyrosetta.rosetta.core.pose) get_resnum_list() (in module pyrosetta.rosetta.core.pose) get_resnum_list_ordered() (in module pyrosetta.rosetta.core.pose) get_resnumber_from_reference_pose() (in module pyrosetta.rosetta.core.pose) get_resnums_for_chain() (in module pyrosetta.rosetta.core.pose) get_resnums_for_chain_id() (in module pyrosetta.rosetta.core.pose) get_restype_for_pose() (in module pyrosetta.rosetta.core.pose) get_rsd_type_from_aa() (in module pyrosetta.rosetta.core.pose) get_score_line_string() (in module pyrosetta.rosetta.core.pose) get_secstruct() (in module pyrosetta.toolbox) get_self_ptr() (pyrosetta.rosetta.core.pose.Pose method) get_self_weak_ptr() (pyrosetta.rosetta.core.pose.Pose method) get_sequence_len() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_excluding_chain() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_excluding_chains() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_from_chain() (in module pyrosetta.rosetta.core.pose) get_sha1_hash_from_chains() (in module pyrosetta.rosetta.core.pose) get_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrecognized_res_name() (pyrosetta.rosetta.core.pose.PDBInfo method) get_unrecognized_res_size() (pyrosetta.rosetta.core.pose.PDBInfo method) getPoseExtraScore() (in module pyrosetta.rosetta.core.pose) glycan_tree_set() (pyrosetta.rosetta.core.pose.Pose method) grid_atoms() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) grid_size() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) grid_size2() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) grid_stripe() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

H

has_chain() (in module pyrosetta.rosetta.core.pose) has_dof() (pyrosetta.rosetta.core.pose.Pose method)

has_reference_pose() (pyrosetta.rosetta.core.pose.Pose method) hasPoseExtraScore() (in module pyrosetta.rosetta.core.pose) header_information() (pyrosetta.rosetta.core.pose.PDBInfo method)

I

icode() (pyrosetta.rosetta.core.pose.PDBInfo method) increment_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) init() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) init_posehash() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) initialize_atomid_map() (in module pyrosetta.rosetta.core.pose) initialize_atomid_map_AtomID() (in module pyrosetta.rosetta.core.pose) initialize_disulfide_bonds() (in module pyrosetta.rosetta.core.pose) insert() (pyrosetta.rosetta.core.pose.PDBPoseMap method) insert_residue_by_bond() (pyrosetta.rosetta.core.pose.Pose method) insert_residue_by_jump() (pyrosetta.rosetta.core.pose.Pose method) insertion_code() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method)

is_atom_axial_or_equatorial_to_ring() (in module pyrosetta.rosetta.core.pose) is_centroid() (pyrosetta.rosetta.core.pose.Pose method) is_fullatom() (pyrosetta.rosetta.core.pose.Pose method) is_het() (pyrosetta.rosetta.core.pose.PDBInfo method) is_ideal_pose() (in module pyrosetta.rosetta.core.pose) is_ideal_position() (in module pyrosetta.rosetta.core.pose) is_lower_terminus() (in module pyrosetta.rosetta.core.pose) is_observing() (pyrosetta.rosetta.core.pose.PDBInfo method) is_position_conserved_residue() (in module pyrosetta.rosetta.core.pose) is_referencepose_number() (in module pyrosetta.rosetta.core.pose) is_upper_terminus() (in module pyrosetta.rosetta.core.pose)

J

jump() (pyrosetta.rosetta.core.pose.Pose method)

jumps_from_pose() (in module pyrosetta.rosetta.core.pose) just_modeling_RNA() (in module pyrosetta.rosetta.core.pose)

L

linenum() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method)

M

make_atom_map() (in module pyrosetta.rosetta.core.pose) make_pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) make_pose_from_sequence() (in module pyrosetta.rosetta.core.pose) mass() (in module pyrosetta.rosetta.core.pose) metric() (pyrosetta.rosetta.core.pose.Pose method)

MiniPose (class in pyrosetta.rosetta.core.pose) minirosetta_svn_url() (in module pyrosetta.rosetta.core) minirosetta_svn_version() (in module pyrosetta.rosetta.core) modeltag() (pyrosetta.rosetta.core.pose.PDBInfo method) mutate_residue() (in module pyrosetta.toolbox)

N

name() (pyrosetta.rosetta.core.pose.PDBInfo method) named_atom_id_to_atom_id() (in module pyrosetta.rosetta.core.pose) named_stub_id_to_stub_id() (in module pyrosetta.rosetta.core.pose) natom() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) natoms() (pyrosetta.rosetta.core.pose.PDBInfo method) nbcount() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) nbcount_raw() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) noncanonical_atom_count() (in module pyrosetta.rosetta.core.pose) noncanonical_chi_count() (in module pyrosetta.rosetta.core.pose) noncanonical_residue_count() (in module pyrosetta.rosetta.core.pose)

nres() (pyrosetta.rosetta.core.pose.PDBInfo method) nres_protein() (in module pyrosetta.rosetta.core.pose) num_atoms() (in module pyrosetta.rosetta.core.pose) num_chains() (pyrosetta.rosetta.core.pose.Pose method) num_chi_angles() (in module pyrosetta.rosetta.core.pose) num_hbond_acceptors() (in module pyrosetta.rosetta.core.pose) num_hbond_donors() (in module pyrosetta.rosetta.core.pose) num_heavy_atoms() (in module pyrosetta.rosetta.core.pose) num_jump() (pyrosetta.rosetta.core.pose.Pose method) number() (pyrosetta.rosetta.core.pose.PDBInfo method)

O

observer_cache() (pyrosetta.rosetta.core.pose.Pose method) obsolete() (pyrosetta.rosetta.core.pose.PDBInfo method) occupancy() (pyrosetta.rosetta.core.pose.PDBInfo method)

omega() (pyrosetta.rosetta.core.pose.Pose method) on_connection_change() (pyrosetta.rosetta.core.pose.PDBInfo method) on_identity_change() (pyrosetta.rosetta.core.pose.PDBInfo method) on_length_change() (pyrosetta.rosetta.core.pose.PDBInfo method)

P

parse_PDBnum_icode() (in module pyrosetta.rosetta.core.pose) parse_resnum() (in module pyrosetta.rosetta.core.pose) parse_sequence() (in module pyrosetta.rosetta.core.pose) partition_pose_by_jump() (in module pyrosetta.rosetta.core.pose) pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) pdb_info() (pyrosetta.rosetta.core.pose.Pose method) pdb_to_pose() (in module pyrosetta.rosetta.core.pose) PDBInfo (class in pyrosetta.rosetta.core.pose) PDBPoseMap (class in pyrosetta.rosetta.core.pose) pdbslice() (in module pyrosetta.rosetta.core.pose) phi() (pyrosetta.rosetta.core.pose.Pose method) Pose (class in pyrosetta.rosetta.core.pose) pose2pdb() (pyrosetta.rosetta.core.pose.PDBInfo method) pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) pose_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) pose_max_nbr_radius() (in module pyrosetta.rosetta.core.pose) pose_numbered() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) pose_residue_is_terminal() (in module pyrosetta.rosetta.core.pose) pose_to_pdb() (in module pyrosetta.rosetta.core.pose) PoseCoordPickMode (class in pyrosetta.rosetta.core.pose)

PoseCoordPickMode_ALL (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_BB (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_BNP (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CA (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CB (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CB_else_CA (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CBorCA (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_HVY (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_HVY_IF_NP (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_N_C_O (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_N_CA_C (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_N_CA_C_CB (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_NBR (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_NUL (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) prepend_polymer_residue_before_seqpos() (pyrosetta.rosetta.core.pose.Pose method) prepend_res() (pyrosetta.rosetta.core.pose.PDBInfo method) print_metric() (pyrosetta.rosetta.core.pose.Pose method) psi() (pyrosetta.rosetta.core.pose.Pose method) pyrosetta.method_bindings (module) pyrosetta.rosetta (module) pyrosetta.rosetta.core (module) pyrosetta.rosetta.core.pose (module) pyrosetta.toolbox (module)

R

read_comment_pdb() (in module pyrosetta.rosetta.core.pose) read_psipred_ss2_file() (in module pyrosetta.rosetta.core.pose) real_to_virtual() (pyrosetta.rosetta.core.pose.Pose method) rebuild_pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) reference_pose_from_current() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_set() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_set_cop() (pyrosetta.rosetta.core.pose.Pose method) remarks() (pyrosetta.rosetta.core.pose.PDBInfo method) remove_constraint() (pyrosetta.rosetta.core.pose.Pose method) remove_constraints() (pyrosetta.rosetta.core.pose.Pose method) remove_ligand_canonical_residues() (in module pyrosetta.rosetta.core.pose) remove_lower_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_nonprotein_residues() (in module pyrosetta.rosetta.core.pose) remove_upper_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type_from_residue() (in module pyrosetta.rosetta.core.pose) remove_virtual_residues() (in module pyrosetta.rosetta.core.pose) renumber_pdbinfo_based_on_conf_chains() (in module pyrosetta.rosetta.core.pose) reorder_root_partition_res() (in module pyrosetta.rosetta.core.pose) replace_pose_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.pose) replace_res() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_res_remap_bfactors() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_residue() (pyrosetta.rosetta.core.pose.Pose method)

reroot() (in module pyrosetta.rosetta.core.pose) res_haslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) res_in_chain() (in module pyrosetta.rosetta.core.pose) res_name() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) res_num() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) resi() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) residue() (pyrosetta.rosetta.core.pose.Pose method) residue_center_of_mass() (in module pyrosetta.rosetta.core.pose) residue_data() (pyrosetta.rosetta.core.pose.Pose method) residue_type() (pyrosetta.rosetta.core.pose.Pose method) residue_type_ptr() (pyrosetta.rosetta.core.pose.Pose method) residue_type_set_for_pose() (pyrosetta.rosetta.core.pose.Pose method) residue_types_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) residue_types_from_sequence() (in module pyrosetta.rosetta.core.pose) ResidueIndexDescription (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionFromFile (class in pyrosetta.rosetta.core.pose) resindex() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) resize_atom_records() (pyrosetta.rosetta.core.pose.PDBInfo method) resize_residue_records() (pyrosetta.rosetta.core.pose.PDBInfo method) resolve_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) restrict_non_nbrs_from_repacking() (in module pyrosetta.toolbox) return_nearest_residue() (in module pyrosetta.rosetta.core.pose)

S

sanity_check() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) scoring_begin() (pyrosetta.rosetta.core.pose.Pose method) scoring_end() (pyrosetta.rosetta.core.pose.Pose method) secstruct() (pyrosetta.rosetta.core.pose.Pose method) segmentID() (pyrosetta.rosetta.core.pose.PDBInfo method) sequence() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) sequence_map_from_pdbinfo() (in module pyrosetta.rosetta.core.pose) set_alpha() (pyrosetta.rosetta.core.pose.Pose method) set_bb_torsion() (in module pyrosetta.rosetta.core.pose) set_beta() (pyrosetta.rosetta.core.pose.Pose method) set_bfactors_from_atom_id_map() (in module pyrosetta.rosetta.core.pose) set_chains() (pyrosetta.rosetta.core.pose.PDBInfo method) set_chi() (pyrosetta.rosetta.core.pose.Pose method) set_const_data() (pyrosetta.rosetta.core.pose.Pose method) set_crystinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_delta() (pyrosetta.rosetta.core.pose.Pose method) set_dof() (pyrosetta.rosetta.core.pose.Pose method) set_epsilon() (pyrosetta.rosetta.core.pose.Pose method) set_gamma() (pyrosetta.rosetta.core.pose.Pose method) set_jump() (pyrosetta.rosetta.core.pose.Pose method) set_new_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_new_energies_object() (pyrosetta.rosetta.core.pose.Pose method) set_omega() (pyrosetta.rosetta.core.pose.Pose method) set_phi() (pyrosetta.rosetta.core.pose.Pose method) set_psi() (pyrosetta.rosetta.core.pose.Pose method)

set_reasonable_fold_tree() (in module pyrosetta.rosetta.core.pose) set_resinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_ring_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_secstruct() (pyrosetta.rosetta.core.pose.Pose method) set_ss_from_phipsi() (in module pyrosetta.rosetta.core.pose) set_svn_version_and_url() (in module pyrosetta.rosetta.core) set_theta() (pyrosetta.rosetta.core.pose.Pose method) set_torsion() (pyrosetta.rosetta.core.pose.Pose method) set_xyz() (pyrosetta.rosetta.core.pose.Pose method) set_zeta() (pyrosetta.rosetta.core.pose.Pose method) setPoseExtraScore() (in module pyrosetta.rosetta.core.pose) setup_dof_mask_from_move_map() (in module pyrosetta.rosetta.core.pose) setup_dof_to_torsion_map() (in module pyrosetta.rosetta.core.pose) short_desc() (pyrosetta.rosetta.core.pose.PDBInfo method) show() (pyrosetta.rosetta.core.pose.PDBInfo method) size() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) sort_pose_by_score() (in module pyrosetta.rosetta.core.pose) split_by_chain() (pyrosetta.rosetta.core.pose.Pose method) stepwise_addable_pose_residue() (in module pyrosetta.rosetta.core.pose) stepwise_addable_residue() (in module pyrosetta.rosetta.core.pose) stub_from_id() (pyrosetta.rosetta.core.pose.Pose method) stub_id_to_named_stub_id() (in module pyrosetta.rosetta.core.pose) swap_transform() (in module pyrosetta.rosetta.core.pose)

T

tag_from_pose() (in module pyrosetta.rosetta.core.pose) tag_into_pose() (in module pyrosetta.rosetta.core.pose) temp() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) temperature() (pyrosetta.rosetta.core.pose.PDBInfo method) theta() (pyrosetta.rosetta.core.pose.Pose method) tighten_memory() (pyrosetta.rosetta.core.pose.PDBInfo method) torsion() (pyrosetta.rosetta.core.pose.Pose method)

total_atoms() (pyrosetta.rosetta.core.pose.Pose method) total_energy_from_pose() (in module pyrosetta.rosetta.core.pose) total_residue() (pyrosetta.rosetta.core.pose.Pose method) transfer_constraint_set() (pyrosetta.rosetta.core.pose.Pose method) transfer_jumps() (in module pyrosetta.rosetta.core.pose) transfer_phi_psi() (in module pyrosetta.rosetta.core.pose) translation() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) translation_real() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

U

unassigned() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) UnrecognizedAtomRecord (class in pyrosetta.rosetta.core.pose) update_actcoord() (pyrosetta.rosetta.core.pose.Pose method)

update_actcoords() (pyrosetta.rosetta.core.pose.Pose method) update_cutpoint_virtual_atoms_if_connected() (in module pyrosetta.rosetta.core.pose) update_orbital_coords() (pyrosetta.rosetta.core.pose.Pose method) update_pose_chains_from_pdb_chains() (pyrosetta.rosetta.core.pose.Pose method) update_residue_neighbors() (pyrosetta.rosetta.core.pose.Pose method)

V

variant_types() (pyrosetta.rosetta.core.pose.MiniPose method) variant_types_list() (pyrosetta.rosetta.core.pose.MiniPose method)

virtual_to_real() (pyrosetta.rosetta.core.pose.Pose method) virtual_type_for_pose() (in module pyrosetta.rosetta.core.pose)

W

W128_T (class in pyrosetta.rosetta)

X

xdim() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) xyz() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

xyzStripeHashPose (class in pyrosetta.rosetta.core.pose)

Y

ydim() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

Z

zdim() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method)

zero_reference_pose_mapping_at_seqpos() (pyrosetta.rosetta.core.pose.Pose method) zeta() (pyrosetta.rosetta.core.pose.Pose method)