| add_coordinate_constraints_from_map(core::pose::Pose &pose, core::pose::Pose const &reference_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::Real const &constraint_x0, core::Real const &constraint_tol) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| add_to_atom_id_map_after_checks(std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, std::string const &atom_name, core::Size const n1, core::Size const n2, core::pose::Pose const &pose1, core::pose::Pose const &pose2, bool const do_the_checks=true) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| annotated_sequence_used_for_atom_id_maps_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| apply(core::pose::Pose &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| calc_rms_atom_id_map_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| check_alignment_tolerance_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| check_matching_atom_names(core::pose::Pose const &pose1, core::pose::Pose const &pose2, bool const verbose=true) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| check_matching_atom_names(core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, bool const verbose=true) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| complete_moving_atom_id_map_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| create_coordinate_constraint_atom_id_map(core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| create_coordinate_constraints(core::pose::Pose &pose, core::Real const rmsd_screen) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| do_checks(std::string const &atom_name, core::Size const n, core::pose::Pose const &pose) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| do_superimposition(core::pose::Pose &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| filter_virtual_atoms(std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| get_calc_rms_atom_id_map(std::map< core::id::AtomID, core::id::AtomID > &calc_rms_atom_id_map, core::pose::Pose const &pose, utility::vector1< core::Size > const &calc_rms_res) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| get_res_list_in_reference(core::pose::Pose const &pose) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| get_rmsd_no_superimpose(core::pose::Pose const &pose, bool const check_align=true) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| get_rmsd_no_superimpose(core::pose::Pose const &pose, core::pose::Pose const &pose_reference, bool const check_align=true) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| get_rmsd_over_all_poses(core::pose::Pose &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| get_rmsd_res_and_superimpose_res_in_pose(core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| get_root_triad_atom_id_map(core::pose::Pose const &pose) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| initialize(core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| mod_reference_pose_local_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| natoms_rmsd() const | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| natoms_superimpose_rmsd() const | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| output_atom_id_map(std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| output_atom_id_map(std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::pose::Pose const &pose1, core::pose::Pose const &pose2) const | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| reference_pose_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| reference_pose_local_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| rmsd() const | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| rmsd_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| rmsd_over_alignment_atoms() const | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| rmsd_res_in_pose() | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| rmsd_res_in_pose_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| root_partition_res_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| set_root_partition_res(utility::vector1< core::Size > const &setting) | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| set_superimpose_over_all_instantiated(bool const &setting) | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| set_user_defined_calc_rms_res(utility::vector1< core::Size > const &setting) | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| StepWisePoseAligner(core::pose::Pose const &reference_pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | |
| superimpose_atom_id_map() | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| superimpose_atom_id_map_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| superimpose_over_all_instantiated() const | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| superimpose_over_all_instantiated_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| superimpose_recursively(core::pose::Pose &pose, core::Real &rmsd_over_all, core::Size &natoms_over_all) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| superimpose_res_in_pose() | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| superimpose_res_in_pose_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| superimpose_rmsd() const | protocols::stepwise::modeler::align::StepWisePoseAligner | inline |
| superimpose_rmsd_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| update_calc_rms_atom_id_map(core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| update_reference_pose_local(core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| update_superimpose_atom_id_map(core::pose::Pose const &pose) | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| user_defined_calc_rms_res_ | protocols::stepwise::modeler::align::StepWisePoseAligner | private |
| ~StepWisePoseAligner() override | protocols::stepwise::modeler::align::StepWisePoseAligner | |
1.8.7