aa(Size seqpos) const | core::conformation::Conformation | inline |
add_parameters_set(ParametersSetOP newset) | core::conformation::Conformation | inlinevirtual |
append_polymer_residue_after_seqpos(Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) | core::conformation::Conformation | |
append_residue_by_bond(conformation::Residue const &new_rsd, bool build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool start_new_chain=false, bool lookup_bond_length=false) | core::conformation::Conformation | |
append_residue_by_jump(conformation::Residue const &new_rsd, Size anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool start_new_chain=false) | core::conformation::symmetry::SymmetricConformation | virtual |
apply_transformation(PointPosition Xin, core::Size residfrom, core::Size residto, bool rotationonly=false) | core::conformation::symmetry::SymmetricConformation | |
apply_transformation_norecompute(PointPosition Xin, core::Size residfrom, core::Size residto, bool rotationonly=false) const | core::conformation::symmetry::SymmetricConformation | |
atom_is_backbone_norefold(Size pos, Size atomno) const | core::conformation::Conformation | |
atom_tree() const | core::conformation::Conformation | inline |
AtomID typedef | core::conformation::Conformation | |
AtomID_Mask typedef | core::conformation::Conformation | |
AtomTree typedef | core::conformation::Conformation | |
AtomTreeOP typedef | core::conformation::Conformation | |
attach_connection_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
attach_general_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
attach_identity_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
attach_length_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
attach_xyz_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
batch_get_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const | core::conformation::Conformation | virtual |
batch_set_xyz(utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &positions) | core::conformation::symmetry::SymmetricConformation | virtual |
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 | |
bonded_neighbor_all_res(core::id::AtomID atomid, bool virt=false) const | core::conformation::Conformation | |
buffer_signals() | core::conformation::Conformation | |
buffering_signals() const | core::conformation::Conformation | |
chain_begin(Size chain) const | core::conformation::Conformation | inline |
chain_end(Size chain) const | core::conformation::Conformation | inline |
chain_endings() const | core::conformation::Conformation | |
chain_endings(utility::vector1< Size > const &endings) | core::conformation::Conformation | |
chains_from_termini() | core::conformation::Conformation | |
check_valid_membrane() const | core::conformation::Conformation | |
clear() | core::conformation::Conformation | |
clear_observers() | core::conformation::Conformation | |
clear_parameters_set_list() | core::conformation::Conformation | inlinevirtual |
clone() const | core::conformation::symmetry::SymmetricConformation | virtual |
Conformation() | core::conformation::Conformation | |
Conformation(Conformation const &src) | core::conformation::Conformation | |
ConnectionEvent typedef | core::conformation::Conformation | |
const_residues() const | core::conformation::Conformation | |
contains_carbohydrate_residues() const | core::conformation::Conformation | inline |
contains_carbohydrate_residues(bool setting) | core::conformation::Conformation | inline |
copy_segment(Size size, Conformation const &src, Size begin, Size src_begin) | core::conformation::Conformation | |
create_new_parameters_set() | core::conformation::Conformation | inlinevirtual |
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 seqpos1, std::string const &atom_name1, Size seqpos2, std::string const &atom_name2) | core::conformation::Conformation | |
delete_chain_ending(Size seqpos) | core::conformation::Conformation | |
delete_polymer_residue(Size seqpos) | core::conformation::Conformation | |
delete_residue_range_slow(Size range_begin, Size range_end) | core::conformation::Conformation | |
delete_residue_slow(Size seqpos) | core::conformation::Conformation | |
detach_connection_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
detach_general_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
detach_identity_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
detach_length_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
detach_xyz_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
detect_bonds() | core::conformation::Conformation | |
detect_disulfides() | core::conformation::symmetry::SymmetricConformation | virtual |
detect_pseudobonds() | core::conformation::Conformation | |
dof(DOF_ID const &id) const | core::conformation::Conformation | |
DOF_ID typedef | core::conformation::Conformation | |
dof_id_from_torsion_id(TorsionID const &id) const | core::conformation::Conformation | |
DomainMap typedef | core::conformation::Conformation | |
downstream_jump_stub(int jump_number) const | core::conformation::Conformation | |
empty() const | core::conformation::Conformation | inline |
fill_missing_atoms(id::AtomID_Mask missing) | core::conformation::Conformation | |
fix_disulfides(utility::vector1< std::pair< Size, Size > > disulf_bonds) | core::conformation::Conformation | |
fold_tree(FoldTree const &fold_tree_in) | core::conformation::symmetry::SymmetricConformation | virtual |
fold_tree() const | core::conformation::symmetry::SymmetricConformation | inlinevirtual |
FoldTree typedef | core::conformation::Conformation | |
FoldTreeOP typedef | core::conformation::Conformation | |
FragRT typedef | core::conformation::Conformation | |
FragXYZ typedef | core::conformation::Conformation | |
GeneralEvent typedef | core::conformation::Conformation | |
get_jump_atom_ids(core::Size jump_number, AtomID &upstream_id, AtomID &downstream_id) const | core::conformation::Conformation | |
get_residue_mask() const | core::conformation::symmetry::SymmetricConformation | virtual |
get_residue_weight(core::Size resid1, core::Size resid2) const | core::conformation::symmetry::SymmetricConformation | virtual |
get_self_ptr() const | core::conformation::Conformation | inline |
get_self_ptr() | core::conformation::Conformation | inline |
get_self_weak_ptr() const | core::conformation::Conformation | inline |
get_self_weak_ptr() | core::conformation::Conformation | inline |
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) | core::conformation::symmetry::SymmetricConformation | |
get_upstream_vrt(core::Size seqpos) const | core::conformation::symmetry::SymmetricConformation | private |
has_passport() const | core::conformation::Conformation | inlinevirtual |
IdentityEvent typedef | core::conformation::Conformation | |
insert_chain_ending(Size seqpos) | core::conformation::Conformation | |
insert_conformation_by_jump(Conformation const &conf, Size insert_seqpos, Size insert_jumppos, Size anchor_pos, Size anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") | core::conformation::symmetry::SymmetricConformation | virtual |
insert_fragment(id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz) | core::conformation::Conformation | |
insert_ideal_geometry_at_polymer_bond(Size seqpos) | core::conformation::Conformation | |
insert_ideal_geometry_at_residue_connection(Size pos1, Size connid1) | core::conformation::Conformation | |
insert_residue_by_bond(Residue const &new_rsd_in, Size seqpos, Size anchor_pos, bool build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool 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 | |
is_centroid() const | core::conformation::Conformation | |
is_fullatom() const | core::conformation::Conformation | |
is_membrane() const | core::conformation::Conformation | inline |
is_protected() const | core::conformation::Conformation | inlinevirtual |
is_residue_typeset(std::string tag) const | core::conformation::Conformation | |
jump(int jump_number) const | core::conformation::Conformation | |
jump(AtomID const &id) const | core::conformation::Conformation | |
Jump typedef | core::conformation::Conformation | |
jump_atom_id(int jump_number) const | core::conformation::Conformation | |
LengthEvent typedef | core::conformation::Conformation | |
membrane_info() | core::conformation::Conformation | |
membrane_info() const | core::conformation::Conformation | |
n_parameters_sets() const | core::conformation::Conformation | inlinevirtual |
num_chains() const | core::conformation::Conformation | inline |
operator=(SymmetricConformation const &src) | core::conformation::symmetry::SymmetricConformation | |
operator=(Conformation const &src) | core::conformation::symmetry::SymmetricConformation | virtual |
Parameters typedef | core::conformation::Conformation | |
parameters_set(core::Size const index) | core::conformation::Conformation | inlinevirtual |
parameters_set(core::Size const index) const | core::conformation::Conformation | inlinevirtual |
ParametersCOP typedef | core::conformation::Conformation | |
ParametersOP typedef | core::conformation::Conformation | |
ParametersSet typedef | core::conformation::Conformation | |
ParametersSetCOP typedef | core::conformation::Conformation | |
ParametersSetOP typedef | core::conformation::Conformation | |
pop_passport() | core::conformation::Conformation | inlinevirtual |
prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) | core::conformation::Conformation | |
push_passport(core::environment::DofPassportCOP) | core::conformation::Conformation | inlinevirtual |
rebuild_polymer_bond_dependent_atoms(Size seqpos) | core::conformation::Conformation | |
rebuild_polymer_bond_dependent_atoms_this_residue_only(Size seqpos) | core::conformation::Conformation | |
rebuild_residue_connection_dependent_atoms(Size seqpos, Size connid) | core::conformation::Conformation | |
recalculate_transforms() | core::conformation::symmetry::SymmetricConformation | |
receive_observers_from(Conformation const &src) | core::conformation::Conformation | |
replace_residue(Size seqpos, Residue const &new_rsd, bool orient_backbone) | core::conformation::symmetry::SymmetricConformation | virtual |
replace_residue(Size seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | core::conformation::symmetry::SymmetricConformation | virtual |
core::conformation::Conformation::replace_residue(Size seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | core::conformation::Conformation | virtual |
reset_chain_endings() | core::conformation::Conformation | |
reset_move_data() | core::conformation::Conformation | |
reset_structure_moved() const | core::conformation::Conformation | inline |
residue(Size seqpos) const | core::conformation::Conformation | inline |
residue_cop(Size seqpos) const | core::conformation::Conformation | inline |
residue_op(Size seqpos) | core::conformation::Conformation | inline |
residue_type(Size seqpos) const | core::conformation::Conformation | inline |
residues_ | core::conformation::Conformation | protected |
safely_append_polymer_residue_after_seqpos(Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) | core::conformation::Conformation | |
safely_prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) | core::conformation::Conformation | |
same_type_as_me(Conformation const &other, bool recurse) const | core::conformation::symmetry::SymmetricConformation | virtual |
secstruct(Size seqpos) const | core::conformation::Conformation | inline |
sequence_matches(Conformation const &other) const | core::conformation::Conformation | |
set_bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real setting) | core::conformation::symmetry::SymmetricConformation | virtual |
set_bond_length(AtomID const &atom1, AtomID const &atom2, Real setting) | core::conformation::symmetry::SymmetricConformation | virtual |
set_dof(DOF_ID const &id, Real setting) | core::conformation::symmetry::SymmetricConformation | virtual |
set_jump(int jump_number, Jump const &new_jump) | core::conformation::symmetry::SymmetricConformation | virtual |
set_jump(AtomID const &id, Jump const &new_jump) | core::conformation::symmetry::SymmetricConformation | virtual |
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::Conformation | |
set_secstruct(Size seqpos, char setting) | core::conformation::symmetry::SymmetricConformation | virtual |
set_stub_transform(id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt) | core::conformation::Conformation | |
set_torsion(TorsionID const &id, Real setting) | core::conformation::symmetry::SymmetricConformation | virtual |
set_torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real setting, bool quiet=false) | core::conformation::symmetry::SymmetricConformation | virtual |
set_xyz(AtomID const &id, PointPosition const &position) | core::conformation::symmetry::SymmetricConformation | virtual |
show_residue_connections() const | core::conformation::Conformation | |
show_residue_connections(std::ostream &os) const | core::conformation::Conformation | |
size() const | core::conformation::Conformation | inline |
structure_moved() const | core::conformation::Conformation | inline |
stub_from_id(id::StubID const &id) const | core::conformation::Conformation | |
symm_info_ | core::conformation::symmetry::SymmetricConformation | private |
SymmetricConformation() | core::conformation::symmetry::SymmetricConformation | |
SymmetricConformation(Conformation const &conf, SymmetryInfo const &symm_info) | core::conformation::symmetry::SymmetricConformation | |
Symmetry_Info() const | core::conformation::symmetry::SymmetricConformation | |
Symmetry_Info() | core::conformation::symmetry::SymmetricConformation | |
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 typedef | core::conformation::Conformation | |
Tsymm_ | core::conformation::symmetry::SymmetricConformation | private |
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_noncanonical_connection(Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id) | core::conformation::Conformation | |
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 | |
upstream_jump_stub(int jump_number) const | core::conformation::Conformation | |
xyz(AtomID const &id) const | core::conformation::Conformation | |
XYZEvent typedef | core::conformation::Conformation | |
~Conformation() | core::conformation::Conformation | virtual |
~SymmetricConformation() | core::conformation::symmetry::SymmetricConformation | virtual |