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core::conformation::symmetry::MirrorSymmetricConformation Member List

This is the complete list of members for core::conformation::symmetry::MirrorSymmetricConformation, including all inherited members.

aa(Size seqpos) const core::conformation::Conformationinline
add_parameters_set(ParametersSetOP newset)core::conformation::Conformation
align_virtual_atoms_in_carbohydrate_residue(uint const sequence_position)core::conformation::Conformation
annotated_sequence(bool show_all_variants) const core::conformation::Conformation
append_polymer_residue_after_seqpos(conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) overridecore::conformation::symmetry::SymmetricConformationvirtual
append_residue_by_bond(conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false)core::conformation::Conformation
append_residue_by_jump(conformation::Residue const &new_rsd, Size const anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool const start_new_chain=false) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
apply_transform_Rx_plus_v(numeric::xyzMatrix< Real > const &R, Vector const &v) overridecore::conformation::symmetry::SymmetricConformationvirtual
apply_transformation(PointPosition Xin, core::Size residfrom, core::Size residto, bool rotationonly=false)core::conformation::symmetry::SymmetricConformationvirtual
apply_transformation_norecompute(PointPosition Xin, core::Size residfrom, core::Size residto, bool rotationonly=false) const core::conformation::symmetry::SymmetricConformationvirtual
atom_is_backbone_norefold(Size pos, Size atomno) const core::conformation::Conformation
atom_tree() const core::conformation::Conformationinline
AtomID typedefcore::conformation::Conformation
AtomID_Mask typedefcore::conformation::Conformation
atoms_are_bonded(AtomID const &id1, AtomID const &id2) const core::conformation::Conformation
AtomTree typedefcore::conformation::Conformation
AtomTreeOP typedefcore::conformation::Conformation
attach_connection_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
attach_general_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
attach_identity_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
attach_length_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
attach_xyz_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
backbone_torsion_angle_atoms(TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const core::conformation::Conformation
batch_get_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const core::conformation::Conformationvirtual
batch_set_xyz(utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &positions) overridecore::conformation::symmetry::SymmetricConformationvirtual
begin() noexceptcore::conformation::Conformationinline
begin() const noexceptcore::conformation::Conformationinline
block_signals()core::conformation::Conformation
blocking_signals() const core::conformation::Conformation
bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const core::conformation::Conformation
bond_length(AtomID const &atom1, AtomID const &atom2) const core::conformation::Conformation
bond_orientation(AtomID const &atom1, AtomID const &atom2) const core::conformation::Conformation
bond_orientation(core::id::TorsionID const torsion) const core::conformation::Conformation
bonded_neighbor_all_res(core::id::AtomID const &atomid, bool virt=false, bool skip_canonical_and_solvent=false, bool intra_res=true, bool inter_res=true) const core::conformation::Conformation
buffer_signals()core::conformation::Conformation
buffering_signals() const core::conformation::Conformation
chain_begin(Size chain) const core::conformation::Conformationinline
chain_end(Size chain) const core::conformation::Conformationinline
chain_endings() const core::conformation::Conformation
chain_endings(utility::vector1< Size > const &endings)core::conformation::Conformationvirtual
chains_from_termini()core::conformation::Conformationvirtual
check_valid_membrane() const core::conformation::Conformation
clear()core::conformation::Conformation
clear_glycan_trees()core::conformation::Conformation
clear_observers()core::conformation::Conformation
clear_parameters_set_list()core::conformation::Conformation
clear_Tsymm()core::conformation::symmetry::SymmetricConformationprotected
clone() const overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
Conformation()core::conformation::Conformation
Conformation(Conformation const &src)core::conformation::Conformation
ConnectionEvent typedefcore::conformation::Conformation
const_iterator typedefcore::conformation::Conformation
const_residue_(Size seqpos) const core::conformation::Conformationinlineprotected
const_residues() const core::conformation::Conformation
contains_carbohydrate_residues() const core::conformation::Conformationinline
contains_carbohydrate_residues(bool setting)core::conformation::Conformationinline
copy_segment(Size size, Conformation const &src, Size begin, Size src_begin)core::conformation::Conformation
create_new_parameters_set()core::conformation::Conformation
debug_pause(bool flag) const core::conformation::Conformation
debug_pause() const core::conformation::Conformation
debug_residue_torsions(bool verbose=false) const core::conformation::Conformation
declare_chemical_bond(Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2) overridecore::conformation::symmetry::SymmetricConformationvirtual
delete_chain_ending(Size const seqpos)core::conformation::Conformationvirtual
delete_polymer_residue(Size const seqpos)core::conformation::Conformationvirtual
delete_residue_range_slow(Size const range_begin, Size const range_end)core::conformation::Conformationvirtual
delete_residue_slow(Size const seqpos)core::conformation::Conformationvirtual
detach_connection_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
detach_general_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
detach_identity_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
detach_length_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
detach_xyz_obs(MemFn fn, Ptr ptr) const core::conformation::Conformationinline
detached_copy(Conformation const &src) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
detect_bonds()core::conformation::Conformation
detect_disulfides(utility::vector1< Size > const &disulf_one=utility::vector1< core::Size >(), utility::vector1< Size > const &disulf_two=utility::vector1< core::Size >()) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
detect_pseudobonds()core::conformation::Conformation
difference_type typedefcore::conformation::Conformation
dof(DOF_ID const &id) const core::conformation::Conformation
DOF_ID typedefcore::conformation::Conformation
dof_id_from_atom_ids(id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3, id::AtomID const &id4) const core::conformation::Conformation
dof_id_from_atom_ids(id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3) const core::conformation::Conformation
dof_id_from_atom_ids(id::AtomID const &id1, id::AtomID const &id2) const core::conformation::Conformation
dof_id_from_atom_ids(utility::vector1< id::AtomID > const &ids) const core::conformation::Conformation
dof_id_from_torsion_id(TorsionID const &id) const core::conformation::Conformation
DomainMap typedefcore::conformation::Conformation
downstream_jump_stub(int jump_number) const core::conformation::Conformation
empty() const core::conformation::Conformationinline
end() noexceptcore::conformation::Conformationinline
end() const noexceptcore::conformation::Conformationinline
fill_missing_atoms(id::AtomID_Mask missing)core::conformation::Conformationvirtual
fix_disulfides(utility::vector1< std::pair< Size, Size > > const &disulf_bonds)core::conformation::Conformationvirtual
flip_chirality(ResidueOP &new_rsd)core::conformation::symmetry::MirrorSymmetricConformationprivate
fold_tree(FoldTree const &fold_tree_in) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
core::conformation::symmetry::SymmetricConformation::fold_tree() const overridecore::conformation::symmetry::SymmetricConformationinlinevirtual
FoldTree typedefcore::conformation::Conformation
FoldTreeOP typedefcore::conformation::Conformation
force_update_residue_coordinates() const core::conformation::Conformationprotected
force_update_residue_torsions() const core::conformation::Conformationprotected
FragRT typedefcore::conformation::Conformation
FragXYZ typedefcore::conformation::Conformation
GeneralEvent typedefcore::conformation::Conformation
get_jump_atom_ids(core::Size jump_number, AtomID &upstream_id, AtomID &downstream_id) const core::conformation::Conformation
get_residue_mask() const overridecore::conformation::symmetry::SymmetricConformationvirtual
get_residue_weight(core::Size resid1, core::Size resid2) const overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
get_self_ptr() const core::conformation::Conformationinline
get_self_ptr()core::conformation::Conformationinline
get_self_weak_ptr() const core::conformation::Conformationinline
get_self_weak_ptr()core::conformation::Conformationinline
get_stub_transform(id::StubID const &stub_id1, id::StubID const &stub_id2) const core::conformation::Conformation
get_torsion_angle_atom_ids(TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const core::conformation::Conformation
get_transformation(core::Size resid, bool input_is_subunit_id=false)core::conformation::symmetry::SymmetricConformation
get_upstream_vrt(core::Size seqpos) const core::conformation::symmetry::SymmetricConformationprotected
glycan_tree_set() const core::conformation::Conformation
has_passport() const core::conformation::Conformationinlinevirtual
IdentityEvent typedefcore::conformation::Conformation
insert_chain_ending(Size const seqpos)core::conformation::Conformationvirtual
insert_conformation_by_jump(Conformation const &conf, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size const anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
insert_fragment(id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)core::conformation::Conformationvirtual
insert_ideal_geometry_at_polymer_bond(Size const seqpos)core::conformation::Conformationvirtual
insert_ideal_geometry_at_residue_connection(Size const pos1, Size const connid1)core::conformation::Conformationvirtual
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::conformation::Conformation
insert_residue_by_jump(Residue const &new_rsd_in, Size seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false)core::conformation::Conformation
inter_residue_connection_partner(Size seqpos, int connection_index) const core::conformation::Conformation
invert_Tsymm(char sub, core::Size subunit)core::conformation::symmetry::SymmetricConformationprotected
is_bonded(core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, bool virt=false, bool skip_canonical_and_solvent=false) const core::conformation::Conformation
is_centroid() const core::conformation::Conformation
is_fullatom() const core::conformation::Conformation
is_membrane() const core::conformation::Conformationinline
is_mixed_mode() const core::conformation::Conformation
is_protected() const core::conformation::Conformationinlinevirtual
iterator typedefcore::conformation::Conformation
jump(int jump_number) const core::conformation::Conformation
jump(AtomID const &id) const core::conformation::Conformation
Jump typedefcore::conformation::Conformation
jump_atom_id(int jump_number) const core::conformation::Conformation
jump_is_mirrored_core::conformation::symmetry::MirrorSymmetricConformationprivate
LengthEvent typedefcore::conformation::Conformation
membrane_info()core::conformation::Conformation
membrane_info() const core::conformation::Conformation
MirrorSymmetricConformation()core::conformation::symmetry::MirrorSymmetricConformation
MirrorSymmetricConformation(Conformation const &conf, SymmetryInfo const &symm_info)core::conformation::symmetry::MirrorSymmetricConformation
modifiable_residue_type_set_for_conf(core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const core::conformation::Conformation
n_parameters_sets() const core::conformation::Conformation
num_chains() const core::conformation::Conformationinline
operator=(Conformation const &src) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
Parameters typedefcore::conformation::Conformation
parameters_set(core::Size const index)core::conformation::Conformation
parameters_set(core::Size const index) const core::conformation::Conformation
ParametersCOP typedefcore::conformation::Conformation
ParametersOP typedefcore::conformation::Conformation
ParametersSet typedefcore::conformation::Conformation
ParametersSetCOP typedefcore::conformation::Conformation
ParametersSetOP typedefcore::conformation::Conformation
PartialAtomID typedefcore::conformation::Conformation
pop_passport()core::conformation::Conformationinlinevirtual
prepend_polymer_residue_before_seqpos(conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) overridecore::conformation::symmetry::SymmetricConformationvirtual
push_passport(core::environment::DofPassportCOP)core::conformation::Conformationinlinevirtual
rebuild_polymer_bond_dependent_atoms(Size const seqpos)core::conformation::Conformationvirtual
rebuild_polymer_bond_dependent_atoms_this_residue_only(Size const seqpos)core::conformation::Conformation
rebuild_residue_connection_dependent_atoms(Size seqpos, Size connid)core::conformation::Conformation
recalculate_transforms() overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
receive_observers_from(Conformation const &src)core::conformation::Conformation
replace_residue(Size const seqpos, Residue const &new_rsd, bool const orient_backbone) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
replace_residue(Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
res_is_mirrored(core::Size const seqpos) const core::conformation::symmetry::MirrorSymmetricConformation
res_is_mirrored_core::conformation::symmetry::MirrorSymmetricConformationprivate
reset_chain_endings()core::conformation::Conformationvirtual
reset_move_data()core::conformation::Conformationvirtual
reset_residue_type_set_for_conf(core::chemical::PoseResidueTypeSetCOP new_set, core::chemical::TypeSetMode mode=core::chemical::INVALID_t)core::conformation::Conformation
reset_structure_moved() const core::conformation::Conformationinline
residue(Size seqpos) const core::conformation::Conformationinline
residue_cop(Size seqpos) const core::conformation::Conformationinline
residue_data(Size seqpos) const core::conformation::Conformationinline
residue_data(Size seqpos)core::conformation::Conformationinline
residue_type(Size seqpos) const core::conformation::Conformationinline
residue_type_ptr(Size seqpos) const core::conformation::Conformationinline
residue_type_set_for_conf(core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const core::conformation::Conformation
residue_typeset_mode(bool majority=true) const core::conformation::Conformation
resolve_partial_atom_id(PartialAtomID const &partial_id) const core::conformation::Conformation
safely_append_polymer_residue_after_seqpos(conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) overridecore::conformation::symmetry::SymmetricConformationvirtual
safely_prepend_polymer_residue_before_seqpos(conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) overridecore::conformation::symmetry::SymmetricConformationvirtual
same_type_as_me(Conformation const &other, bool const recurse=true) const overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
secstruct(Size seqpos) const core::conformation::Conformationinline
sequence_matches(Conformation const &other) const core::conformation::Conformation
set_bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting) overridecore::conformation::symmetry::SymmetricConformationvirtual
set_bond_length(AtomID const &atom1, AtomID const &atom2, Real const setting) overridecore::conformation::symmetry::SymmetricConformationvirtual
set_dof(DOF_ID const &id, Real const setting) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
set_jump(int const jump_number, Jump const &new_jump) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
set_jump(AtomID const &id, Jump const &new_jump) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
set_jump_atom_stub_id(id::StubID const &id)core::conformation::Conformation
set_membrane_info(membrane::MembraneInfoOP mem_info)core::conformation::Conformation
set_noncanonical_connection(Size res_id_lower, Size lr_conn_id, Size res_id_upper, Size ur_conn_id)core::conformation::Conformation
set_polymeric_connection(Size res_id_lower, Size res_id_upper)core::conformation::Conformationvirtual
set_secstruct(Size const seqpos, char const setting) overridecore::conformation::symmetry::SymmetricConformationvirtual
set_stub_transform(id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt)core::conformation::Conformationvirtual
set_torsion(TorsionID const &id, Real const setting) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
set_torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false) overridecore::conformation::symmetry::MirrorSymmetricConformationvirtual
set_xyz(AtomID const &id, PointPosition const &position) overridecore::conformation::symmetry::SymmetricConformationvirtual
setup_glycan_trees()core::conformation::Conformation
sever_chemical_bond(Size seqpos1, Size res1_resconn_index, Size seqpos2, Size res2_resconn_index)core::conformation::Conformationvirtual
show_residue_connections() const core::conformation::Conformation
show_residue_connections(std::ostream &os) const core::conformation::Conformation
size() const core::conformation::Conformationinline
size_type typedefcore::conformation::Conformation
structure_moved() const core::conformation::Conformationinline
stub_from_id(id::StubID const &id) const core::conformation::Conformation
SymmetricConformation()core::conformation::symmetry::SymmetricConformation
SymmetricConformation(Conformation const &conf, SymmetryInfo const &symm_info)core::conformation::symmetry::SymmetricConformation
Symmetry_Info() const core::conformation::symmetry::SymmetricConformationvirtual
Symmetry_Info()core::conformation::symmetry::SymmetricConformationvirtual
synch_mirror_jumps_with_atomtree()core::conformation::symmetry::MirrorSymmetricConformationprivate
torsion(TorsionID const &id) const core::conformation::Conformation
torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const core::conformation::Conformation
TorsionID typedefcore::conformation::Conformation
unblock_signals()core::conformation::Conformation
update_actcoord(Size resid)core::conformation::Conformation
update_actcoords()core::conformation::Conformation
update_domain_map(DomainMap &domain_map) const core::conformation::Conformation
update_membrane_position(Vector center, Vector normal)core::conformation::Conformation
update_njumps_nres()core::conformation::symmetry::MirrorSymmetricConformationprivate
update_noncanonical_connection(Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id) overridecore::conformation::symmetry::SymmetricConformationvirtual
update_orbital_coords(Residue &rsd) const core::conformation::Conformation
update_orbital_coords(Size resid)core::conformation::Conformation
update_polymeric_connection(Size lower_seqpos, bool update_connection_dep_atoms=false)core::conformation::Conformation
update_residue_identities()core::conformation::symmetry::MirrorSymmetricConformation
upstream_jump_stub(int jump_number) const core::conformation::Conformation
xyz(AtomID const &id) const core::conformation::Conformation
XYZEvent typedefcore::conformation::Conformation
~Conformation() overridecore::conformation::Conformation
~MirrorSymmetricConformation() overridecore::conformation::symmetry::MirrorSymmetricConformation
~SymmetricConformation() overridecore::conformation::symmetry::SymmetricConformation
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