core::pose::Pose Member List

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 const &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_begin(Size const chain_num) const	core::pose::Pose
chain_end(Size const chain_num) 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_mmtf(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_branch_sequence(core::uint const start_residue) const	core::pose::Pose
glycan_tree_sequence(core::uint const residue_in_tree) const	core::pose::Pose
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_atoms(Residue const &new_rsd, Size const seqpos, 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
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
membrane_info() const	core::pose::Pose
membrane_info()	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
mu(Size const seqpos) const	core::pose::Pose
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_chains() const	core::pose::Pose
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_data(Size const seqpos)	core::pose::Pose
residue_data(Size const seqpos) const	core::pose::Pose
residue_type(Size const seqpos) const	core::pose::Pose
residue_type_ptr(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_mu(Size const seqpos, Real const setting)	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::VirtualBaseCOP)	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