Rosetta Core  2014.35
core::conformation::Conformation Member List

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

aa(Size const seqpos) const core::conformation::Conformationinline
add_pseudobond(Size lr, Size lr_connid, Size ur, Size ur_connid, Size nbonds)core::conformation::Conformationprivate
append_polymer_residue_after_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)core::conformation::Conformation
append_residue(Residue const &new_rsd_in, bool const attach_by_jump, std::string const &root_atom, id::NamedAtomID anchor_id, bool const start_new_chain)core::conformation::Conformationprivate
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)core::conformation::Conformationvirtual
atom_is_backbone_norefold(Size const pos, Size const atomno) const core::conformation::Conformation
atom_tree() const core::conformation::Conformationinline
atom_tree_core::conformation::Conformationprivate
atom_tree_torsion(TorsionID const &tor_id) const core::conformation::Conformationprivate
AtomID typedefcore::conformation::Conformation
AtomID_Mask typedefcore::conformation::Conformation
atoms_are_bonded(AtomID const &id1, AtomID const &id2) const core::conformation::Conformationprivate
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::Conformationprivate
batch_get_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const core::conformation::Conformationvirtual
batch_set_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position)core::conformation::Conformationvirtual
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 const chain) const core::conformation::Conformationinline
chain_end(Size const chain) const core::conformation::Conformationinline
chain_endings() const core::conformation::Conformation
chain_endings(utility::vector1< Size > const &endings)core::conformation::Conformation
chain_endings_core::conformation::Conformationprivate
chains_from_termini()core::conformation::Conformation
check_valid_membrane() const core::conformation::Conformation
clear()core::conformation::Conformation
clear_observers()core::conformation::Conformation
clone() const core::conformation::Conformationvirtual
Conformation()core::conformation::Conformation
Conformation(Conformation const &src)core::conformation::Conformation
connection_obs_hub_core::conformation::Conformationmutableprivate
ConnectionEvent typedefcore::conformation::Conformation
const_residues() const core::conformation::Conformation
contains_carbohydrate_residues() const core::conformation::Conformationinline
contains_carbohydrate_residues(bool const setting)core::conformation::Conformationinline
contains_carbohydrate_residues_core::conformation::Conformationprivate
copy_segment(Size const size, Conformation const &src, Size const begin, Size const src_begin)core::conformation::Conformation
debug_pause(bool const 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)core::conformation::Conformation
delete_chain_ending(Size const seqpos)core::conformation::Conformation
delete_polymer_residue(Size const seqpos)core::conformation::Conformation
delete_residue_range_slow(Size const range_begin, Size const range_end)core::conformation::Conformation
delete_residue_slow(Size const seqpos)core::conformation::Conformation
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
detect_bonds()core::conformation::Conformation
detect_disulfides()core::conformation::Conformationvirtual
detect_pseudobonds()core::conformation::Conformation
dof(DOF_ID const &id) const core::conformation::Conformation
DOF_ID typedefcore::conformation::Conformation
dof_id_from_torsion_id(TorsionID const &id) const core::conformation::Conformation
dof_moved_core::conformation::Conformationprivate
DomainMap typedefcore::conformation::Conformation
downstream_jump_stub(int const jump_number) const core::conformation::Conformation
empty() const core::conformation::Conformationinline
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() const core::conformation::Conformationinlinevirtual
fold_tree(FoldTree const &fold_tree_in)core::conformation::Conformationvirtual
fold_tree_core::conformation::Conformationprivate
FoldTree typedefcore::conformation::Conformation
FoldTreeOP typedefcore::conformation::Conformation
FragRT typedefcore::conformation::Conformation
FragXYZ typedefcore::conformation::Conformation
general_obs_hub_core::conformation::Conformationmutableprivate
GeneralEvent typedefcore::conformation::Conformation
get_jump_atom_ids(core::Size const jump_number, AtomID &upstream_id, AtomID &downstream_id) const core::conformation::Conformation
get_residue_mask() const core::conformation::Conformationvirtual
get_residue_weight(core::Size, core::Size) const core::conformation::Conformationvirtual
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
has_passport() const core::conformation::Conformationinlinevirtual
identity_obs_hub_core::conformation::Conformationmutableprivate
IdentityEvent typedefcore::conformation::Conformation
in_place_copy(Conformation const &src)core::conformation::Conformationprivate
insert_chain_ending(Size const seqpos)core::conformation::Conformation
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="")core::conformation::Conformationvirtual
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 const seqpos)core::conformation::Conformation
insert_ideal_geometry_at_residue_connection(Size const pos1, Size const connid1)core::conformation::Conformation
insert_polymer_residue(Residue const &new_rsd_in, Size const seqpos, bool const join_lower, bool const join_upper)core::conformation::Conformationprivate
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 const 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 const seqpos, int const connection_index) const core::conformation::Conformation
is_centroid() const core::conformation::Conformation
is_fullatom() const core::conformation::Conformation
is_membrane() const core::conformation::Conformationinline
is_protected() const core::conformation::Conformationinlinevirtual
is_residue_typeset(std::string tag) const core::conformation::Conformation
Jump typedefcore::conformation::Conformation
jump(int const jump_number) const core::conformation::Conformation
jump(AtomID const &id) const core::conformation::Conformation
jump_atom_id(int const jump_number) const core::conformation::Conformation
length_obs_hub_core::conformation::Conformationmutableprivate
LengthEvent typedefcore::conformation::Conformation
membrane_info()core::conformation::Conformation
membrane_info() const core::conformation::Conformation
membrane_info_core::conformation::Conformationprivate
notify_connection_obs(ConnectionEvent const &e) const core::conformation::Conformationprivate
notify_general_obs(GeneralEvent const &e) const core::conformation::Conformationprivate
notify_identity_obs(IdentityEvent const &e, bool const fire_general=true) const core::conformation::Conformationprivate
notify_length_obs(LengthEvent const &e, bool const fire_general=true) const core::conformation::Conformationprivate
notify_xyz_obs(XYZEvent const &e, bool const fire_general=true) const core::conformation::Conformationprivate
num_chains() const core::conformation::Conformationinline
operator=(Conformation const &src)core::conformation::Conformationvirtual
pop_passport()core::conformation::Conformationinlinevirtual
pre_nresidue_change()core::conformation::Conformationprivate
prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)core::conformation::Conformation
push_passport(core::environment::DofPassportCOP)core::conformation::Conformationinlinevirtual
rebuild_polymer_bond_dependent_atoms(Size const seqpos)core::conformation::Conformation
rebuild_polymer_bond_dependent_atoms(Size const seqpos, int const upper_lower)core::conformation::Conformationprivate
rebuild_polymer_bond_dependent_atoms_this_residue_only(Size const seqpos)core::conformation::Conformation
rebuild_residue_connection_dependent_atoms(Size const seqpos, Size const connid)core::conformation::Conformation
receive_observers_from(Conformation const &src)core::conformation::Conformation
rederive_chain_endings()core::conformation::Conformationprivate
rederive_chain_ids()core::conformation::Conformationprivate
replace_residue(Size const seqpos, Residue const &new_rsd, bool const orient_backbone)core::conformation::Conformationvirtual
replace_residue(Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)core::conformation::Conformationvirtual
reset_chain_endings()core::conformation::Conformation
reset_move_data()core::conformation::Conformation
reset_structure_moved() const core::conformation::Conformationinline
residue(Size const seqpos) const core::conformation::Conformationinline
residue_(Size const seqpos) const core::conformation::Conformationinlineprivate
residue_coordinates_need_updating_core::conformation::Conformationmutableprivate
residue_torsions_need_updating_core::conformation::Conformationmutableprivate
residue_type(Size const seqpos) const core::conformation::Conformationinline
residues_core::conformation::Conformationprotected
residues_append(Residue const &new_rsd, bool const start_new_chain, bool const by_jump=false, std::string const &root_atom="", id::NamedAtomID anchor_id=id::BOGUS_NAMED_ATOM_ID)core::conformation::Conformationprivate
residues_delete(Size const seqpos)core::conformation::Conformationprivate
residues_insert(Size const seqpos, Residue const &new_rsd, bool const use_lower_chain=false, bool const new_chain=false)core::conformation::Conformationprivate
residues_replace(Size const seqpos, Residue const &new_rsd)core::conformation::Conformationprivate
safely_append_polymer_residue_after_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)core::conformation::Conformation
safely_prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)core::conformation::Conformation
same_type_as_me(Conformation const &other, bool recurse) const core::conformation::Conformationvirtual
secstruct(Size const seqpos) const core::conformation::Conformationinline
secstruct_core::conformation::Conformationprivate
sequence_matches(Conformation const &other) const core::conformation::Conformation
set_bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting)core::conformation::Conformationvirtual
set_bond_length(AtomID const &atom1, AtomID const &atom2, Real const setting)core::conformation::Conformationvirtual
set_dof(DOF_ID const &id, Real const setting)core::conformation::Conformationvirtual
set_dof_moved(AtomID const &id)core::conformation::Conformationinlineprivate
set_dof_moved(DOF_ID const &id)core::conformation::Conformationinlineprivate
set_jump(int const jump_number, Jump const &new_jump)core::conformation::Conformationvirtual
set_jump(AtomID const &id, Jump const &new_jump)core::conformation::Conformationvirtual
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 const seqpos, char const setting)core::conformation::Conformationinlinevirtual
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 const setting)core::conformation::Conformationvirtual
set_torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false)core::conformation::Conformationvirtual
set_xyz(AtomID const &id, PointPosition const &position)core::conformation::Conformationvirtual
set_xyz_moved(AtomID const &id)core::conformation::Conformationinlineprivate
set_xyz_moved(utility::vector1< AtomID > const &ids)core::conformation::Conformationinlineprivate
setup_atom_tree()core::conformation::Conformationprivate
show_residue_connections() const core::conformation::Conformation
show_residue_connections(std::ostream &os) const core::conformation::Conformation
size() const core::conformation::Conformationinline
structure_moved() const core::conformation::Conformationinline
structure_moved_core::conformation::Conformationmutableprivate
stub_from_id(id::StubID const &id) const core::conformation::Conformation
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_noncanonical_connection(Size const lower_seqpos, Size const lr_conn_id, Size const upper_seqpos, Size const 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 const lower_seqpos, bool const update_connection_dep_atoms=false)core::conformation::Conformation
update_residue_coordinates() const core::conformation::Conformationprivate
update_residue_coordinates(Size const seqpos, bool const fire_signal=true) const core::conformation::Conformationprivate
update_residue_torsions() const core::conformation::Conformationprivate
update_residue_torsions(Size const seqpos, bool const fire_signal=true) const core::conformation::Conformationprivate
update_sequence_numbering(Size const new_size, utility::vector1< Size > const &old2new)core::conformation::Conformationprivate
upstream_jump_stub(int const jump_number) const core::conformation::Conformation
xyz(AtomID const &id) const core::conformation::Conformation
xyz_moved_core::conformation::Conformationprivate
xyz_obs_hub_core::conformation::Conformationmutableprivate
XYZEvent typedefcore::conformation::Conformation
~Conformation()core::conformation::Conformationvirtual