| align_VDW_rep_screen_pose(core::pose::Pose &VDW_rep_screen_pose, core::pose::Pose const &working_pose, utility::vector1< core::Size > const &VDW_rep_screen_align_res, utility::vector1< core::Size > const &working_align_res, bool const verbose) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| atom_bin_size_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| bin_max_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| bin_min_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| bin_offset_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| check_atom_bin_in_range(Atom_Bin const &atom_pos_bin) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| check_VDW_screen_bin_is_setup() const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| create_VDW_rep_screen_pose(VDW_RepScreeninfo &VDW_rep_screen_info, core::pose::Pose const &working_pose, std::map< core::Size, core::Size > &full_to_sub, bool const verbose) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| create_VDW_screen_bin(core::pose::Pose const &pose, utility::vector1< core::Size > const &ignore_res_list, bool const is_prepend, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose=false) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| create_VDW_screen_bin(utility::vector1< VDW_RepScreeninfo > const &VDW_rep_screen_info_list, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| create_VDW_screen_bin(utility::vector1< core::pose::Pose > const &pose_list, utility::vector1< utility::vector1< core::Size > > const &list_of_ignore_res_list, utility::vector1< bool > const list_of_is_prepend, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| FARFAR_setup_using_user_input_VDW_pose(utility::vector1< std::string > const &VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| get_atom_bin(numeric::xyzVector< core::Real > const &atom_pos) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| get_atom_pos(Atom_Bin const &atom_bin) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| get_matching_res_in_VDW_rep_screen_pose(core::pose::Pose const &VDW_rep_screen_pose, core::pose::Pose const &working_pose, utility::vector1< core::Size > const &VDW_rep_screen_align_res, utility::vector1< core::Size > const &working_align_res, std::map< core::Size, core::Size > &full_to_sub) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| is_atom_bin_in_range(Atom_Bin const &atom_pos_bin) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| is_reference_xyz_setup_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| is_VDW_screen_bin_setup_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| max_distance_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| num_atom_pos_bin_out_of_range_message_outputted_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| num_clash_atom_cutoff_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| output_atom_bin(std::string const filename) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| output_pdb_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| physical_pose_clash_dist_cutoff_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| reference_xyz_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| reference_xyz_consistency_check(numeric::xyzVector< core::Real > const &inputted_reference_xyz) const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| RNA_VDW_BinChecker() | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| set_output_pdb(bool const setting) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | inline |
| set_physical_pose_clash_dist_cutoff(core::Real const &setting) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | inline |
| set_reference_xyz(numeric::xyzVector< core::Real > const &reference_xyz) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| set_VDW_rep_alignment_RMSD_CUTOFF(core::Real const &setting) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | inline |
| set_VDW_rep_delete_matching_res(utility::vector1< std::string > const &setting) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | inline |
| setup_using_user_input_VDW_pose(utility::vector1< std::string > const &VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, StepWiseRNA_JobParametersCOP const &job_parameters) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| setup_using_working_pose(core::pose::Pose const &const_working_pose, StepWiseRNA_JobParametersCOP const &job_parameters) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| tolerate_off_range_atom_bin_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| update_VDW_screen_bin(core::pose::Pose const &pose, utility::vector1< core::Size > const &ignore_res_list, bool const is_prepend, std::ofstream &outfile_act) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| use_VDW_rep_pose_for_screening_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| user_inputted_VDW_screen_pose() const | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| user_inputted_VDW_screen_pose_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| VDW_rep_alignment_RMSD_CUTOFF_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| VDW_rep_ignore_matching_res_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| VDW_rep_screen(core::pose::Pose const &screening_pose, core::Size const &moving_res, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| VDW_rep_screen(core::pose::Pose const &screening_pose, core::Size const &moving_res) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| VDW_rep_screen_info_list_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| VDW_rep_screen_with_act_pose(core::pose::Pose const &screening_pose, utility::vector1< core::Size > const &moving_res_list, bool const local_verbose=true) | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | |
| VDW_rep_screen_with_physical_pose_verbose_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| VDW_screen_bin_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| write_to_file_ | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | private |
| ~RNA_VDW_BinChecker() | protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker | virtual |
1.8.7