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Rosetta
3.8
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This is the complete list of members for core::pose::Pose, including all inherited members.
aa(Size const seqpos) const | core::pose::Pose | |
add_constraint(scoring::constraints::ConstraintCOP cst) | core::pose::Pose | |
add_constraints(scoring::constraints::ConstraintCOPs csts) | core::pose::Pose | |
alpha(Size const pos) const | core::pose::Pose | |
annotated_sequence(bool show_all_variants=false) const | core::pose::Pose | |
append_polymer_residue_after_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) | core::pose::Pose | |
append_pose_by_jump(Pose const &src, Size const jump_anchor_residue, std::string const &jump_anchor_atom="", std::string const &jump_root_atom="") | core::pose::Pose | |
append_residue_by_atoms(conformation::Residue const &new_rsd, bool const build_ideal_geometry, std::string const &connect_atom, Size const anchor_rsd_seqpos, std::string const &anchor_connect_atom, bool const start_new_chain=false, bool const lookup_bond_length=false) | core::pose::Pose | |
append_residue_by_bond(conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int const connection=0, Size const anchor_residue=0, int const anchor_connection=0, bool const start_new_chain=false, bool const lookup_bond_length=false) | core::pose::Pose | |
append_residue_by_jump(conformation::Residue const &new_rsd, Size const jump_anchor_residue, std::string const &jump_anchor_atom="", std::string const &jump_root_atom="", bool const start_new_chain=false) | core::pose::Pose | |
apply_transform_Rx_plus_v(numeric::xyzMatrix< Real > const &R, Vector const &v) | core::pose::Pose | |
atom_tree() const | core::pose::Pose | |
AtomID typedef | core::pose::Pose | |
attach_conformation_obs(MemFn fn, Ptr ptr) | core::pose::Pose | inline |
attach_destruction_obs(MemFn fn, Ptr ptr) | core::pose::Pose | inline |
attach_energy_obs(MemFn fn, Ptr ptr) | core::pose::Pose | inline |
attach_general_obs(MemFn fn, Ptr ptr) | core::pose::Pose | inline |
BasicDataCache typedef | core::pose::Pose | |
BasicDataCacheOP typedef | core::pose::Pose | |
batch_get_xyz(utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > &points) const | core::pose::Pose | |
batch_set_xyz(utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &points) | core::pose::Pose | |
begin() noexcept | core::pose::Pose | |
begin() const noexcept | core::pose::Pose | |
beta(Size const seqpos) const | core::pose::Pose | |
buffer_observers() const | core::pose::Pose | private |
center() | core::pose::Pose | |
chain(Size const seqpos) const | core::pose::Pose | |
chain_sequence(core::Size const chain_in) const | core::pose::Pose | |
chi(int const chino, Size const seqpos) const | core::pose::Pose | |
chi(Size const seqpos) const | core::pose::Pose | |
clear() | core::pose::Pose | |
clear_sequence_constraints() | core::pose::Pose | |
clone() const | core::pose::Pose | |
conformation() const | core::pose::Pose | inline |
conformation() | core::pose::Pose | inline |
Conformation typedef | core::pose::Pose | |
conformation_ | core::pose::Pose | private |
conformation_obs_hub_ | core::pose::Pose | mutableprivate |
conformation_ptr() const | core::pose::Pose | |
conformation_ptr() | core::pose::Pose | |
ConformationCOP typedef | core::pose::Pose | |
ConformationEvent typedef | core::pose::Pose | |
ConformationOP typedef | core::pose::Pose | |
const_data_cache() const | core::pose::Pose | |
const_iterator typedef | core::pose::Pose | |
constant_cache_ | core::pose::Pose | private |
ConstDataMap typedef | core::pose::Pose | |
ConstDataMapOP typedef | core::pose::Pose | |
constraint_set() const | core::pose::Pose | |
constraint_set(ConstraintSetOP) | core::pose::Pose | |
constraint_set_ | core::pose::Pose | private |
ConstraintSetCOP typedef | core::pose::Pose | |
ConstraintSetOP typedef | core::pose::Pose | |
copy_segment(Size const size, Pose const &src, Size const begin, Size const src_begin) | core::pose::Pose | |
corresponding_residue_in_current(core::Size const ref_residue_index, std::string const &ref_pose_name) const | core::pose::Pose | |
data() const | core::pose::Pose | inline |
data() | core::pose::Pose | inline |
data_cache_ | core::pose::Pose | private |
decrement_reference_pose_mapping_after_seqpos(core::Size const seqpos) | core::pose::Pose | |
delete_polymer_residue(Size const seqpos) | core::pose::Pose | |
delete_residue_range_slow(Size const start, Size const end) | core::pose::Pose | |
delete_residue_slow(Size const seqpos) | core::pose::Pose | |
delta(Size const pos) const | core::pose::Pose | |
destruction_obs_hub_ | core::pose::Pose | mutableprivate |
DestructionEvent typedef | core::pose::Pose | |
detach_conformation_obs(MemFn fn, Ptr ptr) const | core::pose::Pose | inline |
detach_destruction_obs(MemFn fn, Ptr ptr) const | core::pose::Pose | inline |
detach_energy_obs(MemFn fn, Ptr ptr) const | core::pose::Pose | inline |
detach_general_obs(MemFn fn, Ptr ptr) const | core::pose::Pose | inline |
detached_copy(Pose const &src) | core::pose::Pose | |
dof(DOF_ID const &id) const | core::pose::Pose | |
DOF_ID typedef | core::pose::Pose | |
dump_cif(std::string const &file_name) const | core::pose::Pose | |
dump_file(std::string const &file_name) const | core::pose::Pose | |
dump_pdb(std::string const &file_name) const | core::pose::Pose | |
dump_pdb(std::ostream &out) const | core::pose::Pose | |
dump_pdb(std::ostream &out, utility::vector1< core::Size > const &residue_indices) const | core::pose::Pose | |
dump_scored_pdb(std::string const &file_name, scoring::ScoreFunction const &scorefxn) | core::pose::Pose | |
empty() const | core::pose::Pose | |
end() noexcept | core::pose::Pose | |
end() const noexcept | core::pose::Pose | |
energies() const | core::pose::Pose | inline |
energies() | core::pose::Pose | inline |
energies_ | core::pose::Pose | private |
energy_obs_hub_ | core::pose::Pose | mutableprivate |
EnergyEvent typedef | core::pose::Pose | |
epsilon(Size const seqpos) const | core::pose::Pose | |
fold_tree() const | core::pose::Pose | |
fold_tree(kinematics::FoldTree const &fold_tree_in) | core::pose::Pose | |
gamma(Size const seqpos) const | core::pose::Pose | |
general_obs_hub_ | core::pose::Pose | mutableprivate |
GeneralEvent typedef | core::pose::Pose | |
get_self_ptr() const | core::pose::Pose | inline |
get_self_ptr() | core::pose::Pose | inline |
get_self_weak_ptr() const | core::pose::Pose | inline |
get_self_weak_ptr() | core::pose::Pose | inline |
glycan_tree_set() const | core::pose::Pose | |
has_dof(DOF_ID const &id) const | core::pose::Pose | |
has_reference_pose() const | core::pose::Pose | |
increment_reference_pose_mapping_after_seqpos(core::Size const seqpos) | core::pose::Pose | |
init(void) | core::pose::Pose | private |
insert_residue_by_bond(Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false) | core::pose::Pose | |
insert_residue_by_jump(Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, std::string const &anchor_atomno="", std::string const &root_atomno="") | core::pose::Pose | |
is_centroid() const | core::pose::Pose | |
is_fullatom() const | core::pose::Pose | |
iterator typedef | core::pose::Pose | |
jump(int const jump_number) const | core::pose::Pose | |
jump(AtomID const &id) const | core::pose::Pose | |
metric(std::string const &calculator_name, std::string const &key, basic::MetricValueBase &val) const | core::pose::Pose | |
metrics_ | core::pose::Pose | mutableprivate |
NamedAtomID typedef | core::pose::Pose | |
notify_conformation_obs(ConformationEvent const &e, bool const fire_general=true) | core::pose::Pose | private |
notify_destruction_obs(DestructionEvent const &e) | core::pose::Pose | private |
notify_energy_obs(EnergyEvent const &e, bool const fire_general=true) | core::pose::Pose | private |
notify_general_obs(GeneralEvent const &e) | core::pose::Pose | private |
num_jump() const | core::pose::Pose | |
observer_cache() const | core::pose::Pose | inline |
observer_cache() | core::pose::Pose | inline |
observer_cache_ | core::pose::Pose | private |
ObserverCache typedef | core::pose::Pose | |
ObserverCacheOP typedef | core::pose::Pose | |
omega(Size const seqpos) const | core::pose::Pose | |
on_conf_xyz_change(core::conformation::signals::XYZEvent const &event) | core::pose::Pose | private |
operator=(Pose const &src) | core::pose::Pose | |
pdb_info() const | core::pose::Pose | |
pdb_info() | core::pose::Pose | |
pdb_info(PDBInfoOP new_info) | core::pose::Pose | |
pdb_info_ | core::pose::Pose | private |
phi(Size const seqpos) const | core::pose::Pose | |
Pose() | core::pose::Pose | |
Pose(Pose const &src) | core::pose::Pose | |
Pose(Pose const &src, Size residue_begin, Size residue_end) | core::pose::Pose | |
prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) | core::pose::Pose | |
print_metric(std::string const &calculator_name, std::string const &key) const | core::pose::Pose | |
psi(Size const seqpos) const | core::pose::Pose | |
real_to_virtual(core::Size seqpos) | core::pose::Pose | |
reference_pose_from_current(std::string const &ref_pose_name, bool override_current=false) | core::pose::Pose | |
reference_pose_set() | core::pose::Pose | |
reference_pose_set_ | core::pose::Pose | private |
reference_pose_set_cop() const | core::pose::Pose | |
remove_constraint(scoring::constraints::ConstraintCOP cst, bool object_comparison=false) | core::pose::Pose | |
remove_constraints(scoring::constraints::ConstraintCOPs csts, bool object_comparison=false) | core::pose::Pose | |
remove_constraints() | core::pose::Pose | |
replace_residue(Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone) | core::pose::Pose | |
replace_residue(int const seqpos, Residue const &new_rsd_in, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | core::pose::Pose | |
Residue typedef | core::pose::Pose | |
residue(Size const seqpos) const | core::pose::Pose | |
residue_type(Size const seqpos) const | core::pose::Pose | |
residue_type_set_for_pose(core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const | core::pose::Pose | |
scoring_begin(scoring::ScoreFunction const &info) | core::pose::Pose | |
scoring_end(scoring::ScoreFunction const &scorefxn) | core::pose::Pose | |
secstruct(Size const seqpos) const | core::pose::Pose | |
secstruct() const | core::pose::Pose | |
sequence() const | core::pose::Pose | |
sequence(core::Size resnum_start, core::Size resnum_end) const | core::pose::Pose | |
set_alpha(Size const seqpos, Real const setting) | core::pose::Pose | |
set_beta(Size const seqpos, Real const setting) | core::pose::Pose | |
set_chi(int const chino, Size const seqpos, Real const setting) | core::pose::Pose | |
set_chi(Size const seqpos, Real const setting) | core::pose::Pose | |
set_const_data(std::string const &category, std::string const &name, T const &original) | core::pose::Pose | inline |
set_const_data(std::string const &category, std::string const &name, Pose const &original) | core::pose::Pose | inline |
set_delta(Size const seqpos, Real const setting) | core::pose::Pose | |
set_dof(DOF_ID const &id, Real const setting) | core::pose::Pose | |
set_epsilon(Size const seqpos, Real const setting) | core::pose::Pose | |
set_gamma(Size const seqpos, Real const setting) | core::pose::Pose | |
set_jump(int const jump_number, const kinematics::Jump &new_jump) | core::pose::Pose | |
set_jump(AtomID const &id, const kinematics::Jump &new_jump) | core::pose::Pose | |
set_new_conformation(conformation::ConformationCOP new_conformation) | core::pose::Pose | |
set_new_energies_object(scoring::EnergiesOP energies) | core::pose::Pose | |
set_omega(Size const seqpos, Real const setting) | core::pose::Pose | |
set_phi(Size const seqpos, Real const setting) | core::pose::Pose | |
set_psi(Size const seqpos, Real const setting) | core::pose::Pose | |
set_ring_conformation(uint const seqpos, uint const ring_num, core::chemical::rings::RingConformer const &conformer) | core::pose::Pose | |
set_secstruct(Size const seqpos, char const setting) | core::pose::Pose | |
set_theta(Size const seqpos, Real const setting) | core::pose::Pose | |
set_torsion(TorsionID const &id, Real const setting) | core::pose::Pose | |
set_xyz(AtomID const &id, PointPosition const &point) | core::pose::Pose | |
set_xyz(NamedAtomID const &id, PointPosition const &point) | core::pose::Pose | |
set_zeta(Size const seqpos, Real const setting) | core::pose::Pose | |
size() const | core::pose::Pose | |
split_by_chain() const | core::pose::Pose | |
split_by_chain(Size chain_id) const | core::pose::Pose | |
store_const_data(std::string const &category, std::string const &name, utility::pointer::ReferenceCountCOP) | core::pose::Pose | private |
stub_from_id(id::NamedStubID const &id) | core::pose::Pose | |
theta(Size const seqpos) const | core::pose::Pose | |
torsion(TorsionID const &id) const | core::pose::Pose | |
TorsionID typedef | core::pose::Pose | |
total_atoms() const | core::pose::Pose | |
total_residue() const | core::pose::Pose | inline |
transfer_constraint_set(const pose::Pose &pose) | core::pose::Pose | |
unbuffer_observers() const | core::pose::Pose | private |
update_actcoord(Size resid) | core::pose::Pose | |
update_actcoords() | core::pose::Pose | |
update_orbital_coords(Size resid) | core::pose::Pose | |
update_pose_chains_from_pdb_chains() | core::pose::Pose | |
update_residue_neighbors() | core::pose::Pose | |
virtual_to_real(core::Size seqpos) | core::pose::Pose | |
xyz(AtomID const &id) const | core::pose::Pose | |
xyz(NamedAtomID const &id) const | core::pose::Pose | |
zero_reference_pose_mapping_at_seqpos(core::Size const seqpos) | core::pose::Pose | |
zeta(Size const seqpos) const | core::pose::Pose | |
~Pose() override | core::pose::Pose |