protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker Member List

This is the complete list of members for protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker, including all inherited members.

align_pose_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
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)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
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, bool const setup_working_align)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
align_working_pose(core::pose::Pose &working_pose) const	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
atom_bin_size_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
bin_max_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
bin_min_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
bin_offset_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
check_atom_bin_in_range(core::pose::rna::Atom_Bin const &atom_pos_bin)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
check_VDW_screen_bin_is_setup() const	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
create_VDW_rep_screen_pose(core::pose::rna::VDW_RepScreenInfo &VDW_rep_screen_info, core::pose::Pose const &working_pose, std::map< core::Size, core::Size > &full_to_sub, bool const verbose)	protocols::stepwise::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker
create_VDW_screen_bin(utility::vector1< core::pose::rna::VDW_RepScreenInfo > const &VDW_rep_screen_info_list, numeric::xyzVector< core::Real > const &reference_xyz, bool const verbose)	protocols::stepwise::modeler::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::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker
FARFAR_setup_using_user_input_VDW_pose(utility::vector1< std::string > const &All_VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, bool const include_side_chains)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
get_atom_pos(core::pose::rna::Atom_Bin const &atom_bin) const	protocols::stepwise::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker	private
get_reference_xyz(core::pose::Pose const &pose, core::Size const reference_res)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
get_reference_xyz_average(core::pose::Pose const &pose)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
get_VDW_align_res()	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
include_side_chains_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
is_reference_xyz_setup_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
is_VDW_screen_bin_setup_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
max_distance_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
num_atom_pos_bin_out_of_range_message_outputted_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
num_clash_atom_cutoff_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
occupied_xyz_bins_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
optimize_memory_usage_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
optimize_speed_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
output_atom_bin(std::string const filename) const	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
output_pdb_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
physical_pose_clash_dist_cutoff_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
read_in_VDW_rep_screen_pose(core::pose::rna::VDW_RepScreenInfo &VDW_rep_screen_info) const	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
reference_xyz_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
reference_xyz_consistency_check(numeric::xyzVector< core::Real > const &inputted_reference_xyz) const	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
RNA_VDW_BinChecker(core::pose::Pose const &pose)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
RNA_VDW_BinChecker()	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
set_num_clash_atom_cutoff(core::Size const setting)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	inline
set_output_pdb(bool const setting)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	inline
set_physical_pose_clash_dist_cutoff(core::Real const &setting)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	inline
set_reference_xyz(numeric::xyzVector< core::Real > const &reference_xyz)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
set_VDW_rep_alignment_RMSD_CUTOFF(core::Real const &setting)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	inline
set_VDW_rep_delete_matching_res(utility::vector1< std::string > const &setting)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	inline
setup_using_user_input_VDW_pose(utility::vector1< std::string > const &All_VDW_rep_screen_pose_info, core::pose::Pose const &const_working_pose, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
setup_using_working_pose(core::pose::Pose const &const_working_pose, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
setup_working_alignment(core::pose::Pose &working_pose)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
stored_align_working_atom_id_map_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
tolerate_off_range_atom_bin_	protocols::stepwise::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker
use_VDW_rep_pose_for_screening_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
user_inputted_VDW_screen_pose() const	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
user_inputted_VDW_screen_pose_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
vdw_align_res_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
vdw_align_res_set_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
VDW_rep_alignment_RMSD_CUTOFF_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
VDW_rep_ignore_matching_res_	protocols::stepwise::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker
VDW_rep_screen(core::pose::Pose const &screening_pose, core::Size const &moving_res)	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
VDW_rep_screen_info_list_	protocols::stepwise::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker
VDW_rep_screen_with_physical_pose_verbose_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
VDW_screen_bin_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
verbose_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
write_to_file_	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker	private
~RNA_VDW_BinChecker() override	protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker