Index

A

aa() (rosetta.core.pose.Pose method) add_comment() (in module rosetta.core.pose) add_constraint() (rosetta.core.pose.Pose method) add_constraints() (rosetta.core.pose.Pose method) add_lower_terminus_type_to_pose_residue() (in module rosetta.core.pose) add_reslabel() (rosetta.core.pose.PDBInfo method) add_score_line_string() (in module rosetta.core.pose) add_unrecognized_atoms() (rosetta.core.pose.PDBInfo method) add_upper_terminus_type_to_pose_residue() (in module rosetta.core.pose) add_variant_type_to_pose_residue() (in module rosetta.core.pose) add_variant_type_to_residue() (in module rosetta.core.pose) addVirtualResAsRoot() (in module rosetta.core.pose) alpha() (rosetta.core.pose.Pose method) alt_loc() (rosetta.core.pose.PDBInfo method) annotated_sequence() (rosetta.core.pose.Pose method) annotated_to_oneletter_sequence() (in module rosetta.core.pose)

append_polymer_residue_after_seqpos() (rosetta.core.pose.Pose method) append_pose_by_jump() (rosetta.core.pose.Pose method) append_pose_to_pose() (in module rosetta.core.pose) append_pose_with_glycan_residues() (in module rosetta.core.pose) append_res() (rosetta.core.pose.PDBInfo method) append_residue_by_atoms() (rosetta.core.pose.Pose method) append_residue_by_bond() (rosetta.core.pose.Pose method) append_residue_by_jump() (rosetta.core.pose.Pose method) append_subpose_to_pose() (in module rosetta.core.pose) apply_transform_Rx_plus_v() (rosetta.core.pose.Pose method) assign() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.PDBInfo method) (rosetta.core.pose.PDBPoseMap method) (rosetta.core.pose.Pose method) (rosetta.core.pose.ResidueIndexDescription method) (rosetta.core.pose.ResidueIndexDescriptionFromFile method) (rosetta.core.pose.UnrecognizedAtomRecord method) atom_id_to_named_atom_id() (in module rosetta.core.pose) atom_name() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.UnrecognizedAtomRecord method) atom_names_list() (rosetta.core.pose.MiniPose method) atom_tree() (rosetta.core.pose.Pose method) attach_to() (rosetta.core.pose.PDBInfo method)

B

batch_get_xyz() (rosetta.core.pose.Pose method) batch_set_xyz() (rosetta.core.pose.Pose method)

beta() (rosetta.core.pose.Pose method) bfactor() (rosetta.core.pose.PDBInfo method)

C

canonical_atom_count() (in module rosetta.core.pose) canonical_residue_count() (in module rosetta.core.pose) center() (rosetta.core.pose.Pose method) center_of_mass() (in module rosetta.core.pose) chain() (rosetta.core.pose.PDBInfo method) (rosetta.core.pose.Pose method) (rosetta.core.pose.ResidueIndexDescription method) chain_end_res() (in module rosetta.core.pose) chain_sequence() (rosetta.core.pose.Pose method) chi() (rosetta.core.pose.Pose method) clear() (rosetta.core.pose.PDBPoseMap method) (rosetta.core.pose.Pose method) clear_reslabel() (rosetta.core.pose.PDBInfo method) clear_sequence_constraints() (rosetta.core.pose.Pose method) clearPoseExtraScore() (in module rosetta.core.pose) clearPoseExtraScores() (in module rosetta.core.pose) clone() (rosetta.core.pose.Pose method) compare_atom_coordinates() (in module rosetta.core.pose) compare_binary_protein_silent_struct() (in module rosetta.core.pose)

compute_unique_chains() (in module rosetta.core.pose) conditional_erase() (rosetta.core.pose.PDBPoseMap method) conf2pdb_chain() (in module rosetta.core.pose) conformation() (rosetta.core.pose.Pose method) conformation_ptr() (rosetta.core.pose.Pose method) const_data_cache() (rosetta.core.pose.Pose method) constraint_set() (rosetta.core.pose.Pose method) convert_from_std_map() (in module rosetta.core.pose) coords() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.UnrecognizedAtomRecord method) copy() (rosetta.core.pose.PDBInfo method) copy_segment() (rosetta.core.pose.Pose method) correctly_add_cutpoint_variants() (in module rosetta.core.pose) corresponding_residue_in_current() (rosetta.core.pose.Pose method) create_subpose() (in module rosetta.core.pose) crystinfo() (rosetta.core.pose.PDBInfo method)

D

data() (rosetta.core.pose.Pose method) decrement_reference_pose_mapping_after_seqpos() (rosetta.core.pose.Pose method) delete_comment() (in module rosetta.core.pose) delete_polymer_residue() (rosetta.core.pose.Pose method) delete_res() (rosetta.core.pose.PDBInfo method) delete_residue_range_slow() (rosetta.core.pose.Pose method) delete_residue_slow() (rosetta.core.pose.Pose method) delta() (rosetta.core.pose.Pose method)

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

E

empty() (rosetta.core.pose.Pose method) empty_record() (rosetta.core.pose.PDBInfo method) energies() (rosetta.core.pose.Pose method) energy_from_pose() (in module rosetta.core.pose)

epsilon() (rosetta.core.pose.Pose method) erase() (rosetta.core.pose.PDBPoseMap method) extract_tag_from_pose() (in module rosetta.core.pose)

F

fill() (rosetta.core.pose.PDBPoseMap method) find() (rosetta.core.pose.PDBPoseMap method)

fname() (rosetta.core.pose.ResidueIndexDescriptionFromFile method) fold_tree() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.Pose method)

G

gamma() (rosetta.core.pose.Pose method) get_all_comments() (in module rosetta.core.pose) get_all_score_line_strings() (in module rosetta.core.pose) get_bb_torsion() (in module rosetta.core.pose) get_center_of_mass() (in module rosetta.core.pose) get_chain_from_chain_id() (in module rosetta.core.pose) get_chain_from_jump_id() (in module rosetta.core.pose) get_chain_id_from_chain() (in module rosetta.core.pose) get_chain_id_from_jump_id() (in module rosetta.core.pose) get_chain_ids_from_chain() (in module rosetta.core.pose) get_chain_ids_from_chains() (in module rosetta.core.pose) get_chain_residues() (in module rosetta.core.pose) get_chains() (in module rosetta.core.pose) get_comment() (in module rosetta.core.pose) get_constraints_from_link_records() (in module rosetta.core.pose) get_hash_excluding_chain() (in module rosetta.core.pose) get_hash_from_chain() (in module rosetta.core.pose) get_jump_id_from_chain() (in module rosetta.core.pose) get_jump_id_from_chain_id() (in module rosetta.core.pose)

get_jump_ids_from_chain() (in module rosetta.core.pose) get_jump_ids_from_chain_ids() (in module rosetta.core.pose) get_num_unrecognized_atoms() (rosetta.core.pose.PDBInfo method) get_num_unrecognized_res() (rosetta.core.pose.PDBInfo method) get_reslabels() (rosetta.core.pose.PDBInfo method) get_resnum() (in module rosetta.core.pose) get_resnum_list() (in module rosetta.core.pose) get_resnum_list_ordered() (in module rosetta.core.pose) get_resnumber_from_reference_pose() (in module rosetta.core.pose) get_rsd_type_from_aa() (in module rosetta.core.pose) get_score_line_string() (in module rosetta.core.pose) get_self_ptr() (rosetta.core.pose.Pose method) get_self_weak_ptr() (rosetta.core.pose.Pose method) get_sequence_len() (in module rosetta.core.pose) get_sha1_hash_excluding_chain() (in module rosetta.core.pose) get_unrecognized_atoms() (rosetta.core.pose.PDBInfo method) get_unrecognized_res_name() (rosetta.core.pose.PDBInfo method) get_unrecognized_res_size() (rosetta.core.pose.PDBInfo method) getPoseExtraScore() (in module rosetta.core.pose)

H

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

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

I

icode() (rosetta.core.pose.PDBInfo method) increment_reference_pose_mapping_after_seqpos() (rosetta.core.pose.Pose method) initialize_atomid_map_AtomID() (in module rosetta.core.pose) initialize_atomid_map_core_id_AtomID_t() (in module rosetta.core.pose) initialize_disulfide_bonds() (in module rosetta.core.pose) insert() (rosetta.core.pose.PDBPoseMap method) insert_residue_by_bond() (rosetta.core.pose.Pose method) insert_residue_by_jump() (rosetta.core.pose.Pose method) insertion_code() (rosetta.core.pose.ResidueIndexDescription method) is_atom_axial_or_equatorial_to_ring() (in module rosetta.core.pose)

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

J

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

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

L

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

M

make_atom_map() (in module rosetta.core.pose) make_pose_from_saccharide_sequence() (in module rosetta.core.pose) make_pose_from_sequence() (in module rosetta.core.pose) mass() (in module rosetta.core.pose)

metric() (rosetta.core.pose.Pose method) MiniPose (class in rosetta.core.pose) modeltag() (rosetta.core.pose.PDBInfo method)

N

n_residue() (rosetta.core.pose.Pose method) name() (rosetta.core.pose.PDBInfo method) named_atom_id_to_atom_id() (in module rosetta.core.pose) named_stub_id_to_stub_id() (in module rosetta.core.pose) natoms() (rosetta.core.pose.PDBInfo method) noncanonical_atom_count() (in module rosetta.core.pose) noncanonical_chi_count() (in module rosetta.core.pose) noncanonical_residue_count() (in module rosetta.core.pose) nres() (rosetta.core.pose.PDBInfo method)

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

O

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

on_connection_change() (rosetta.core.pose.PDBInfo method) on_identity_change() (rosetta.core.pose.PDBInfo method) on_length_change() (rosetta.core.pose.PDBInfo method)

P

parse_PDBnum_icode() (in module rosetta.core.pose) parse_resnum() (in module rosetta.core.pose) parse_sequence() (in module rosetta.core.pose) partition_pose_by_jump() (in module rosetta.core.pose) pdb2pose() (rosetta.core.pose.PDBInfo method) pdb_info() (rosetta.core.pose.Pose method) pdb_to_pose() (in module rosetta.core.pose) PDBInfo (class in rosetta.core.pose) PDBPoseMap (class in rosetta.core.pose) pdbslice() (in module rosetta.core.pose) phi() (rosetta.core.pose.Pose method) Pose (class in rosetta.core.pose)

pose2pdb() (rosetta.core.pose.PDBInfo method) pose_from_saccharide_sequence() (in module rosetta.core.pose) pose_index() (rosetta.core.pose.ResidueIndexDescription method) pose_max_nbr_radius() (in module rosetta.core.pose) pose_numbered() (rosetta.core.pose.ResidueIndexDescription method) pose_residue_is_terminal() (in module rosetta.core.pose) pose_to_pdb() (in module rosetta.core.pose) prepend_polymer_residue_before_seqpos() (rosetta.core.pose.Pose method) prepend_res() (rosetta.core.pose.PDBInfo method) print_metric() (rosetta.core.pose.Pose method) psi() (rosetta.core.pose.Pose method)

R

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

replace_res_remap_bfactors() (rosetta.core.pose.PDBInfo method) replace_residue() (rosetta.core.pose.Pose method) res_haslabel() (rosetta.core.pose.PDBInfo method) res_in_chain() (in module rosetta.core.pose) res_name() (rosetta.core.pose.UnrecognizedAtomRecord method) res_num() (rosetta.core.pose.UnrecognizedAtomRecord method) residue() (rosetta.core.pose.Pose method) residue_center_of_mass() (in module rosetta.core.pose) residue_type() (rosetta.core.pose.Pose method) residue_types_from_saccharide_sequence() (in module rosetta.core.pose) residue_types_from_sequence() (in module rosetta.core.pose) ResidueIndexDescription (class in rosetta.core.pose) ResidueIndexDescriptionFromFile (class in rosetta.core.pose) resindex() (rosetta.core.pose.ResidueIndexDescription method) resize_atom_records() (rosetta.core.pose.PDBInfo method) resize_residue_records() (rosetta.core.pose.PDBInfo method) resolve_index() (rosetta.core.pose.ResidueIndexDescription method) (rosetta.core.pose.ResidueIndexDescriptionFromFile method) return_nearest_residue() (in module rosetta.core.pose) rosetta.core.pose (module)

S

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

set_phi() (rosetta.core.pose.Pose method) set_psi() (rosetta.core.pose.Pose method) set_reasonable_fold_tree() (in module rosetta.core.pose) set_resinfo() (rosetta.core.pose.PDBInfo method) set_ring_conformation() (rosetta.core.pose.Pose method) set_secstruct() (rosetta.core.pose.Pose method) set_ss_from_phipsi() (in module rosetta.core.pose) set_theta() (rosetta.core.pose.Pose method) set_torsion() (rosetta.core.pose.Pose method) set_xyz() (rosetta.core.pose.Pose method) set_zeta() (rosetta.core.pose.Pose method) setPoseExtraScore() (in module rosetta.core.pose) setup_dof_mask_from_move_map() (in module rosetta.core.pose) setup_dof_to_torsion_map() (in module rosetta.core.pose) size() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.PDBPoseMap method) sort_pose_by_score() (in module rosetta.core.pose) split_by_chain() (rosetta.core.pose.Pose method) stub_from_id() (rosetta.core.pose.Pose method) stub_id_to_named_stub_id() (in module rosetta.core.pose) swap_transform() (in module rosetta.core.pose)

T

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

total_atoms() (rosetta.core.pose.Pose method) total_energy_from_pose() (in module rosetta.core.pose) total_residue() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.Pose method) transfer_constraint_set() (rosetta.core.pose.Pose method) transfer_jumps() (in module rosetta.core.pose) transfer_phi_psi() (in module rosetta.core.pose)

U

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

update_orbital_coords() (rosetta.core.pose.Pose method) update_pose_chains_from_pdb_chains() (rosetta.core.pose.Pose method) update_residue_neighbors() (rosetta.core.pose.Pose method)

V

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

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

X

xyz() (rosetta.core.pose.MiniPose method) (rosetta.core.pose.Pose method)

Z

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

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