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core::kinematics::AtomTree Member List

This is the complete list of members for core::kinematics::AtomTree, including all inherited members.

Atom typedefcore::kinematics::AtomTree
atom(AtomID const &id) const core::kinematics::AtomTree
atom_dont_do_update(AtomID const &id) const core::kinematics::AtomTree
atom_pointer(AtomID const &id)core::kinematics::AtomTreeinlineprivate
atom_pointer(AtomID const &id) const core::kinematics::AtomTreeinlineprivate
atom_pointer_core::kinematics::AtomTreeprivate
AtomCOP typedefcore::kinematics::AtomTree
AtomID typedefcore::kinematics::AtomTree
AtomID_Mask typedefcore::kinematics::AtomTree
AtomIDs typedefcore::kinematics::AtomTree
AtomOP typedefcore::kinematics::AtomTree
AtomTree(AtomPointer2D const &new_atom_pointer, bool const from_xyz=true)core::kinematics::AtomTree
AtomTree()core::kinematics::AtomTree
AtomTree(AtomTree const &src)core::kinematics::AtomTree
attach_topological_observer(AtomTreeCAP observer) const core::kinematics::AtomTreeprivate
batch_set_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &xyz)core::kinematics::AtomTree
bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const core::kinematics::AtomTree
bond_angle_dof_id(AtomID const &atom1_in_id, AtomID const &atom2_in_id, AtomID const &atom3_in_id, Real &offset) const core::kinematics::AtomTree
bond_length(AtomID const &atom1, AtomID const &atom2) const core::kinematics::AtomTree
bond_length_dof_id(AtomID const &atom1_in_id, AtomID const &atom2_in_id) const core::kinematics::AtomTree
clear()core::kinematics::AtomTree
copy_coords(AtomTree const &src)core::kinematics::AtomTree
delete_seqpos(Size const seqpos)core::kinematics::AtomTree
detach_topological_observer(AtomTreeCAP observer) const core::kinematics::AtomTreeprivate
detached_copy(AtomTree const &src)core::kinematics::AtomTree
dof(DOF_ID const &id) const core::kinematics::AtomTree
dof_changeset_core::kinematics::AtomTreemutableprivate
DOF_ID typedefcore::kinematics::AtomTree
DOF_ID_Mask typedefcore::kinematics::AtomTree
DOF_Type typedefcore::kinematics::AtomTree
empty() const core::kinematics::AtomTreeinline
external_coordinate_residues_changed_core::kinematics::AtomTreeprivate
find_root_from_atom_pointer()core::kinematics::AtomTreeprivate
FragRT typedefcore::kinematics::AtomTree
FragXYZ typedefcore::kinematics::AtomTree
get_frag_atoms(StubID const &id, FragXYZ const &frag_xyz, AtomCOP &frag_atom, AtomCOP &nonfrag_atom) const core::kinematics::AtomTreeprivate
get_frag_descendant_local_xyz(AtomCOP atom, FragXYZ const &frag_xyz, bool &fail) const core::kinematics::AtomTreeprivate
get_frag_local_stub(StubID const &stubid, FragXYZ const &frag_xyz, bool &fail) const core::kinematics::AtomTreeprivate
get_frag_local_xyz(AtomID const &id, FragXYZ const &frag_xyz, bool &fail) const core::kinematics::AtomTreeprivate
get_frag_parent_local_xyz(AtomCOP child, FragXYZ const &frag_xyz, bool &fail) const core::kinematics::AtomTreeprivate
get_frag_pseudo_stub_id(AtomID const &id, FragXYZ const &frag_xyz, bool &fail) const core::kinematics::AtomTreeprivate
get_jump_atom_id(StubID const &stub_id1, StubID const &stub_id2, int &direction) const core::kinematics::AtomTree
get_stub_transform(StubID const &stub_id1, StubID const &stub_id2) const core::kinematics::AtomTree
has(AtomID const &id) const core::kinematics::AtomTreeinline
insert_fragment(StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz, utility::vector1< AtomID > &moving_atoms)core::kinematics::AtomTree
insert_single_fragment(StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz, utility::vector1< AtomID > &moving_atoms)core::kinematics::AtomTreeprivate
internal_coords_need_updating_core::kinematics::AtomTreemutableprivate
jump(AtomID const &id) const core::kinematics::AtomTree
note_coordinate_change_registered() const core::kinematics::AtomTree
notify_topological_change(AtomTreeCAP observee) const core::kinematics::AtomTreeprivate
operator=(AtomTree const &src)core::kinematics::AtomTree
promote_sameresidue_nonjump_child(AtomID const &parent_atom_id)core::kinematics::AtomTree
replace_residue_subtree(id::BondID const &incoming, utility::vector1< id::BondID > const &outgoing, AtomPointer1D const &new_atoms)core::kinematics::AtomTree
replace_tree(AtomPointer2D const &new_atom_pointer, bool const from_xyz=true)core::kinematics::AtomTree
residue_xyz_change_list_begin() const core::kinematics::AtomTree
residue_xyz_change_list_end() const core::kinematics::AtomTree
root() const core::kinematics::AtomTreeinline
root_core::kinematics::AtomTreeprivate
set_bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting)core::kinematics::AtomTree
set_bond_length(AtomID const &atom1, AtomID const &atom2, Real const setting)core::kinematics::AtomTree
set_dof(DOF_ID const &id, Real const setting)core::kinematics::AtomTree
set_jump(AtomID const &id, Jump const &jump)core::kinematics::AtomTree
set_jump_atom_stub_id(StubID const &id)core::kinematics::AtomTree
set_jump_now(AtomID const &id, Jump const &jump)core::kinematics::AtomTree
set_new_topology()core::kinematics::AtomTreeprivate
set_stub_transform(StubID const &stub_id1, StubID const &stub_id2, RT const &target_rt)core::kinematics::AtomTree
set_torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false)core::kinematics::AtomTree
set_weak_pointer_to_self(AtomTreeCAP self_pointer)core::kinematics::AtomTree
set_xyz(AtomID const &id, PointPosition const &xyz)core::kinematics::AtomTree
size() const core::kinematics::AtomTreeinline
stub_from_id(StubID const &id) const core::kinematics::AtomTreeinline
StubID typedefcore::kinematics::AtomTree
this_weak_ptr_core::kinematics::AtomTreeprivate
topological_match_to() const core::kinematics::AtomTreeinline
topological_match_to_core::kinematics::AtomTreemutableprivate
topological_observers() const core::kinematics::AtomTreeinline
topological_observers_core::kinematics::AtomTreemutableprivate
torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const core::kinematics::AtomTree
torsion_angle_dof_id(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, bool const quiet=false) const core::kinematics::AtomTreeinline
torsion_angle_dof_id(AtomID const &atom1_in_id, AtomID const &atom2_in_id, AtomID const &atom3_in_id, AtomID const &atom4_in_id, Real &offset, bool const quiet=false) const core::kinematics::AtomTree
update_atom_ids_from_atom_pointer()core::kinematics::AtomTreeprivate
update_domain_map(DomainMap &domain_map, AtomID_Mask const &dof_moved, AtomID_Mask const &xyz_moved) const core::kinematics::AtomTree
update_internal_coords() const core::kinematics::AtomTreeprivate
update_sequence_numbering(Size const new_size, utility::vector1< int > const &old2new)core::kinematics::AtomTree
update_xyz_coords() const core::kinematics::AtomTreeprivate
xyz(AtomID const &id) const core::kinematics::AtomTree
xyz_coords_need_updating_core::kinematics::AtomTreemutableprivate
~AtomTree() overridecore::kinematics::AtomTree
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