Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

aa() (in Pose)	add_rosetta_options_6() (in rosetta)	append_residue_by_bond() (in Pose)
add_all_rosetta_options() (in rosetta)	add_rosetta_options_7() (in rosetta)	append_residue_by_jump() (in Pose)
add_comment() (in rosetta.core.pose)	add_rosetta_options_8() (in rosetta)	append_subpose_to_pose() (in rosetta.core.pose)
add_constraint() (in Pose)	add_rosetta_options_9() (in rosetta)	apply_transform_Rx_plus_v() (in Pose)
add_constraints() (in Pose)	add_score_line_string() (in rosetta.core.pose)	assign() (in W128_T)
add_lower_terminus_type_to_pose_residue() (in rosetta.core.pose)	add_unrecognized_atoms() (in PDBInfo)	assign() (in MiniPose)
add_pose() (in xyzStripeHashPose)	add_upper_terminus_type_to_pose_residue() (in rosetta.core.pose)	assign() (in PDBInfo)
add_reslabel() (in PDBInfo)	add_variant_type_to_pose_residue() (in rosetta.core.pose)	assign() (in PDBPoseMap)
add_rosetta_options_0() (in rosetta)	add_variant_type_to_residue() (in rosetta.core.pose)	assign() (in Pose)
add_rosetta_options_1() (in rosetta)	addVirtualResAsRoot() (in rosetta.core.pose)	assign() (in ResidueIndexDescription)
add_rosetta_options_10() (in rosetta)	alpha() (in Pose)	assign() (in ResidueIndexDescriptionFromFile)
add_rosetta_options_11() (in rosetta)	alt_loc() (in PDBInfo)	assign() (in UnrecognizedAtomRecord)
add_rosetta_options_12() (in rosetta)	annotated_sequence() (in Pose)	assign() (in xyzStripeHashPose)
add_rosetta_options_13() (in rosetta)	annotated_to_oneletter_sequence() (in rosetta.core.pose)	atom_id_to_named_atom_id() (in rosetta.core.pose)
add_rosetta_options_14() (in rosetta)	append_polymer_residue_after_seqpos() (in Pose)	atom_name() (in MiniPose)
add_rosetta_options_15() (in rosetta)	append_pose_by_jump() (in Pose)	atom_name() (in UnrecognizedAtomRecord)
add_rosetta_options_2() (in rosetta)	append_pose_to_pose() (in rosetta.core.pose)	atom_names_list() (in MiniPose)
add_rosetta_options_3() (in rosetta)	append_pose_with_glycan_residues() (in rosetta.core.pose)	atom_tree() (in Pose)
add_rosetta_options_4() (in rosetta)	append_res() (in PDBInfo)	attach_to() (in PDBInfo)
add_rosetta_options_5() (in rosetta)	append_residue_by_atoms() (in Pose)

B

BASE (in rosetta)	batch_get_xyz() (in Pose)	beta() (in Pose)
BASE (in RNAAtomType)	batch_set_xyz() (in Pose)	bfactor() (in PDBInfo)

C

canonical_atom_count() (in rosetta.core.pose)	clear_reslabel() (in PDBInfo)	const_data_cache() (in Pose)
canonical_residue_count() (in rosetta.core.pose)	clear_sequence_constraints() (in Pose)	constraint_set() (in Pose)
center() (in Pose)	clearPoseExtraScore() (in rosetta.core.pose)	convert_from_std_map() (in rosetta.core.pose)
center_of_mass() (in rosetta.core.pose)	clearPoseExtraScores() (in rosetta.core.pose)	coords() (in MiniPose)
chain() (in PDBInfo)	clone() (in Pose)	coords() (in UnrecognizedAtomRecord)
chain() (in Pose)	compare_atom_coordinates() (in rosetta.core.pose)	copy() (in PDBInfo)
chain() (in ResidueIndexDescription)	compare_binary_protein_silent_struct() (in rosetta.core.pose)	copy_segment() (in Pose)
chain_end_res() (in rosetta.core.pose)	compute_unique_chains() (in rosetta.core.pose)	core (in rosetta)
chain_sequence() (in Pose)	conditional_erase() (in PDBPoseMap)	correctly_add_cutpoint_variants() (in rosetta.core.pose)
chi() (in Pose)	conf2pdb_chain() (in rosetta.core.pose)	corresponding_residue_in_current() (in Pose)
clear() (in PDBPoseMap)	conformation() (in Pose)	create_subpose() (in rosetta.core.pose)
clear() (in Pose)	conformation_ptr() (in Pose)	crystinfo() (in PDBInfo)

D

data() (in Pose)	delete_residue_slow() (in Pose)	dump_comment_pdb() (in rosetta.core.pose)
decrement_reference_pose_mapping_after_seqpos() (in Pose)	delta() (in Pose)	dump_file() (in Pose)
delete_comment() (in rosetta.core.pose)	detach_from() (in PDBInfo)	dump_pdb() (in Pose)
delete_polymer_residue() (in Pose)	detached_copy() (in Pose)	dump_scored_pdb() (in Pose)
delete_res() (in PDBInfo)	dof() (in Pose)
delete_residue_range_slow() (in Pose)	dump_cif() (in Pose)

E

empty() (in Pose)	energy_from_pose() (in rosetta.core.pose)	extra (in _xmlNode)
empty_record() (in PDBInfo)	epsilon() (in Pose)	extract_pose_balls() (in xyzStripeHashPose)
energies() (in Pose)	erase() (in PDBPoseMap)	extract_tag_from_pose() (in rosetta.core.pose)

F

fill() (in PDBPoseMap)	fname() (in ResidueIndexDescriptionFromFile)	fold_tree() (in Pose)
find() (in PDBPoseMap)	fold_tree() (in MiniPose)

G

gamma() (in Pose)	get_comment() (in rosetta.core.pose)	get_resnum_list_ordered() (in rosetta.core.pose)
get_all_comments() (in rosetta.core.pose)	get_constraints_from_link_records() (in rosetta.core.pose)	get_resnumber_from_reference_pose() (in rosetta.core.pose)
get_all_score_line_strings() (in rosetta.core.pose)	get_hash_excluding_chain() (in rosetta.core.pose)	get_rsd_type_from_aa() (in rosetta.core.pose)
get_bb_torsion() (in rosetta.core.pose)	get_hash_from_chain() (in rosetta.core.pose)	get_score_line_string() (in rosetta.core.pose)
get_center_of_mass() (in rosetta.core.pose)	get_jump_id_from_chain() (in rosetta.core.pose)	get_self_ptr() (in Pose)
get_chain_from_chain_id() (in rosetta.core.pose)	get_jump_id_from_chain_id() (in rosetta.core.pose)	get_self_weak_ptr() (in Pose)
get_chain_from_jump_id() (in rosetta.core.pose)	get_jump_ids_from_chain() (in rosetta.core.pose)	get_sequence_len() (in rosetta.core.pose)
get_chain_id_from_chain() (in rosetta.core.pose)	get_jump_ids_from_chain_ids() (in rosetta.core.pose)	get_sha1_hash_excluding_chain() (in rosetta.core.pose)
get_chain_id_from_jump_id() (in rosetta.core.pose)	get_num_unrecognized_atoms() (in PDBInfo)	get_unrecognized_atoms() (in PDBInfo)
get_chain_ids_from_chain() (in rosetta.core.pose)	get_num_unrecognized_res() (in PDBInfo)	get_unrecognized_res_name() (in PDBInfo)
get_chain_ids_from_chains() (in rosetta.core.pose)	get_reslabels() (in PDBInfo)	get_unrecognized_res_size() (in PDBInfo)
get_chain_residues() (in rosetta.core.pose)	get_resnum() (in rosetta.core.pose)	getPoseExtraScore() (in rosetta.core.pose)
get_chains() (in rosetta.core.pose)	get_resnum_list() (in rosetta.core.pose)

H

has_chain() (in rosetta.core.pose)	has_reference_pose() (in Pose)	header_information() (in PDBInfo)
has_dof() (in Pose)	hasPoseExtraScore() (in rosetta.core.pose)

I

icode() (in PDBInfo)	insert_residue_by_bond() (in Pose)	is_ideal_pose() (in rosetta.core.pose)
increment_reference_pose_mapping_after_seqpos() (in Pose)	insert_residue_by_jump() (in Pose)	is_ideal_position() (in rosetta.core.pose)
init_posehash() (in xyzStripeHashPose)	insertion_code() (in ResidueIndexDescription)	is_lower_terminus() (in rosetta.core.pose)
initialize_atomid_map_AtomID() (in rosetta.core.pose)	is_atom_axial_or_equatorial_to_ring() (in rosetta.core.pose)	is_observing() (in PDBInfo)
initialize_atomid_map_core_id_AtomID_t() (in rosetta.core.pose)	is_centroid() (in Pose)	is_position_conserved_residue() (in rosetta.core.pose)
initialize_disulfide_bonds() (in rosetta.core.pose)	is_fullatom() (in Pose)	is_referencepose_number() (in rosetta.core.pose)
insert() (in PDBPoseMap)	is_het() (in PDBInfo)	is_upper_terminus() (in rosetta.core.pose)

J

jump() (in Pose)	jumps_from_pose() (in rosetta.core.pose)

L

line (in _xmlNode)	linenum() (in ResidueIndexDescriptionFromFile)

M

make_atom_map() (in rosetta.core.pose)	mass() (in rosetta.core.pose)	minirosetta_svn_url() (in rosetta.core)
make_pose_from_saccharide_sequence() (in rosetta.core.pose)	metric() (in Pose)	minirosetta_svn_version() (in rosetta.core)
make_pose_from_sequence() (in rosetta.core.pose)	MiniPose (in rosetta.core.pose)	modeltag() (in PDBInfo)

N

O

observer_cache() (in Pose)	omega() (in Pose)	on_length_change() (in PDBInfo)
obsolete() (in PDBInfo)	on_connection_change() (in PDBInfo)
occupancy() (in PDBInfo)	on_identity_change() (in PDBInfo)

P

parse_PDBnum_icode() (in rosetta.core.pose)	pose_numbered() (in ResidueIndexDescription)	PoseCoordPickMode_HVY (in rosetta.core.pose)
parse_resnum() (in rosetta.core.pose)	pose_residue_is_terminal() (in rosetta.core.pose)	PoseCoordPickMode_HVY_IF_NP (in PoseCoordPickMode)
parse_sequence() (in rosetta.core.pose)	pose_to_pdb() (in rosetta.core.pose)	PoseCoordPickMode_HVY_IF_NP (in rosetta.core.pose)
partition_pose_by_jump() (in rosetta.core.pose)	PoseCoordPickMode (in rosetta.core.pose)	PoseCoordPickMode_N_C_O (in PoseCoordPickMode)
pdb2pose() (in PDBInfo)	PoseCoordPickMode_ALL (in PoseCoordPickMode)	PoseCoordPickMode_N_C_O (in rosetta.core.pose)
pdb_info() (in Pose)	PoseCoordPickMode_ALL (in rosetta.core.pose)	PoseCoordPickMode_N_CA_C (in PoseCoordPickMode)
pdb_to_pose() (in rosetta.core.pose)	PoseCoordPickMode_BB (in PoseCoordPickMode)	PoseCoordPickMode_N_CA_C (in rosetta.core.pose)
PDBInfo (in rosetta.core.pose)	PoseCoordPickMode_BB (in rosetta.core.pose)	PoseCoordPickMode_N_CA_C_CB (in PoseCoordPickMode)
PDBPoseMap (in rosetta.core.pose)	PoseCoordPickMode_BNP (in PoseCoordPickMode)	PoseCoordPickMode_N_CA_C_CB (in rosetta.core.pose)
pdbslice() (in rosetta.core.pose)	PoseCoordPickMode_BNP (in rosetta.core.pose)	PoseCoordPickMode_NBR (in PoseCoordPickMode)
phi() (in Pose)	PoseCoordPickMode_CA (in PoseCoordPickMode)	PoseCoordPickMode_NBR (in rosetta.core.pose)
PHOSPHATE (in rosetta)	PoseCoordPickMode_CA (in rosetta.core.pose)	PoseCoordPickMode_NUL (in PoseCoordPickMode)
PHOSPHATE (in RNAAtomType)	PoseCoordPickMode_CB (in PoseCoordPickMode)	PoseCoordPickMode_NUL (in rosetta.core.pose)
pose (in rosetta.core)	PoseCoordPickMode_CB (in rosetta.core.pose)	prepend_polymer_residue_before_seqpos() (in Pose)
Pose (in rosetta.core.pose)	PoseCoordPickMode_CB_else_CA (in PoseCoordPickMode)	prepend_res() (in PDBInfo)
pose2pdb() (in PDBInfo)	PoseCoordPickMode_CB_else_CA (in rosetta.core.pose)	print_metric() (in Pose)
pose_from_saccharide_sequence() (in rosetta.core.pose)	PoseCoordPickMode_CBorCA (in PoseCoordPickMode)	psi() (in Pose)
pose_index() (in ResidueIndexDescription)	PoseCoordPickMode_CBorCA (in rosetta.core.pose)
pose_max_nbr_radius() (in rosetta.core.pose)	PoseCoordPickMode_HVY (in PoseCoordPickMode)

R

read_comment_pdb() (in rosetta.core.pose)	remove_variant_type_from_residue() (in rosetta.core.pose)	residue_type() (in Pose)
read_psipred_ss2_file() (in rosetta.core.pose)	remove_virtual_residues() (in rosetta.core.pose)	residue_types_from_saccharide_sequence() (in rosetta.core.pose)
rebuild_pdb2pose() (in PDBInfo)	renumber_pdbinfo_based_on_conf_chains() (in rosetta.core.pose)	residue_types_from_sequence() (in rosetta.core.pose)
reference_pose_from_current() (in Pose)	reorder_saccharide_residue_types() (in rosetta.core.pose)	ResidueIndexDescription (in rosetta.core.pose)
reference_pose_set() (in Pose)	replace_pose_residue_copying_existing_coordinates() (in rosetta.core.pose)	ResidueIndexDescriptionFromFile (in rosetta.core.pose)
reference_pose_set_cop() (in Pose)	replace_res() (in PDBInfo)	resindex() (in ResidueIndexDescription)
remarks() (in PDBInfo)	replace_res_remap_bfactors() (in PDBInfo)	resize_atom_records() (in PDBInfo)
remove_constraint() (in Pose)	replace_residue() (in Pose)	resize_residue_records() (in PDBInfo)
remove_constraints() (in Pose)	res_haslabel() (in PDBInfo)	resolve_index() (in ResidueIndexDescription)
remove_ligand_canonical_residues() (in rosetta.core.pose)	res_in_chain() (in rosetta.core.pose)	resolve_index() (in ResidueIndexDescriptionFromFile)
remove_lower_terminus_type_from_pose_residue() (in rosetta.core.pose)	res_name() (in UnrecognizedAtomRecord)	return_nearest_residue() (in rosetta.core.pose)
remove_nonprotein_residues() (in rosetta.core.pose)	res_num() (in UnrecognizedAtomRecord)	RNAAtomType (in rosetta)
remove_upper_terminus_type_from_pose_residue() (in rosetta.core.pose)	residue() (in Pose)	rosetta
remove_variant_type_from_pose_residue() (in rosetta.core.pose)	residue_center_of_mass() (in rosetta.core.pose)

S

scoring_begin() (in Pose)	set_epsilon() (in Pose)	set_xyz() (in Pose)
scoring_end() (in Pose)	set_gamma() (in Pose)	set_zeta() (in Pose)
secstruct() (in Pose)	set_jump() (in Pose)	setPoseExtraScore() (in rosetta.core.pose)
segmentID() (in PDBInfo)	set_new_conformation() (in Pose)	setup_dof_mask_from_move_map() (in rosetta.core.pose)
sequence() (in MiniPose)	set_new_energies_object() (in Pose)	setup_dof_to_torsion_map() (in rosetta.core.pose)
sequence() (in Pose)	set_omega() (in Pose)	size() (in MiniPose)
sequence_map_from_pdbinfo() (in rosetta.core.pose)	set_phi() (in Pose)	size() (in PDBPoseMap)
set_alpha() (in Pose)	set_psi() (in Pose)	sort_pose_by_score() (in rosetta.core.pose)
set_bb_torsion() (in rosetta.core.pose)	set_reasonable_fold_tree() (in rosetta.core.pose)	split_by_chain() (in Pose)
set_beta() (in Pose)	set_resinfo() (in PDBInfo)	stub_from_id() (in Pose)
set_bfactors_from_atom_id_map() (in rosetta.core.pose)	set_ring_conformation() (in Pose)	stub_id_to_named_stub_id() (in rosetta.core.pose)
set_chains() (in PDBInfo)	set_secstruct() (in Pose)	SUGAR (in RNAAtomType)
set_chi() (in Pose)	set_ss_from_phipsi() (in rosetta.core.pose)	SUGAR (in rosetta)
set_crystinfo() (in PDBInfo)	set_svn_version_and_url() (in rosetta.core)	swap_transform() (in rosetta.core.pose)
set_delta() (in Pose)	set_theta() (in Pose)
set_dof() (in Pose)	set_torsion() (in Pose)

T

tag_from_pose() (in rosetta.core.pose)	tm_isdst (in tm)	total_atoms() (in Pose)
tag_into_pose() (in rosetta.core.pose)	tm_mday (in tm)	total_energy_from_pose() (in rosetta.core.pose)
temp() (in UnrecognizedAtomRecord)	tm_min (in tm)	total_residue() (in MiniPose)
temperature() (in PDBInfo)	tm_mon (in tm)	total_residue() (in Pose)
theta() (in Pose)	tm_sec (in tm)	transfer_constraint_set() (in Pose)
tighten_memory() (in PDBInfo)	tm_wday (in tm)	transfer_jumps() (in rosetta.core.pose)
tm (in rosetta)	tm_yday (in tm)	transfer_phi_psi() (in rosetta.core.pose)
tm_gmtoff (in tm)	tm_year (in tm)	type (in _xmlNode)
tm_hour (in tm)	torsion() (in Pose)

U

unassigned() (in ResidueIndexDescription)	update_actcoords() (in Pose)	update_residue_neighbors() (in Pose)
UnrecognizedAtomRecord (in rosetta.core.pose)	update_orbital_coords() (in Pose)
update_actcoord() (in Pose)	update_pose_chains_from_pdb_chains() (in Pose)

V

variant_types() (in MiniPose)	variant_types_list() (in MiniPose)

W

W128_T (in rosetta)

X

xyz() (in MiniPose)	xyz() (in Pose)	xyzStripeHashPose (in rosetta.core.pose)

Z

zero_reference_pose_mapping_at_seqpos() (in Pose)	zeta() (in Pose)

_

__eq__() (in RNAAtomType)	__init__() (in xyzStripeHashPose)	__new__() (in ResidueIndexDescriptionFromFile)
__eq__() (in PoseCoordPickMode)	__init__() (in tm)	__new__() (in UnrecognizedAtomRecord)
__hash__() (in RNAAtomType)	__int__() (in RNAAtomType)	__new__() (in xyzStripeHashPose)
__hash__() (in PoseCoordPickMode)	__int__() (in PoseCoordPickMode)	__new__() (in tm)
__init__() (in RNAAtomType)	__ne__() (in RNAAtomType)	__package__ (in rosetta)
__init__() (in W128_T)	__ne__() (in PoseCoordPickMode)	__package__ (in rosetta.core)
__init__() (in _xmlNode)	__new__() (in RNAAtomType)	__package__ (in rosetta.core.pose)
__init__() (in MiniPose)	__new__() (in W128_T)	__repr__() (in RNAAtomType)
__init__() (in PDBInfo)	__new__() (in _xmlNode)	__repr__() (in PoseCoordPickMode)
__init__() (in PDBPoseMap)	__new__() (in MiniPose)	__str__() (in PDBInfo)
__init__() (in Pose)	__new__() (in PDBInfo)	__str__() (in Pose)
__init__() (in PoseCoordPickMode)	__new__() (in PDBPoseMap)	__str__() (in UnrecognizedAtomRecord)
__init__() (in ResidueIndexDescription)	__new__() (in Pose)	_xmlNode (in rosetta)
__init__() (in ResidueIndexDescriptionFromFile)	__new__() (in PoseCoordPickMode)
__init__() (in UnrecognizedAtomRecord)	__new__() (in ResidueIndexDescription)