protocols::stepwise::sampling::rna::rigid_body Namespace Reference

Classes
struct	BaseBin
struct	compare_base_bin
struct	compare_int_pair

Typedefs
typedef std::map< BaseBin, int, compare_base_bin >	BaseBinMap

Functions
core::kinematics::Stub	get_sugar_stub (conformation::Residue const &rsd, bool const is_prepend, bool const verbose)
BaseBin	get_euler_stub_bin (numeric::xyzVector< core::Real > const &centroid, rotamer_sampler::rigid_body::EulerAngles const &euler_angles)
int	DOF_bin_value (std::map< BaseBin, int, compare_base_bin >::const_iterator const &base_bin_it, std::string const &DOF)
Real	DOF_bin_size (std::string const &DOF)
void	analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const foldername)
void	analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const foldername)
void	translate_then_rotate_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &vector, numeric::xyzMatrix< core::Real > const matrix, bool const verbose)
core::Real	get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const atom_name)
void	initialize_xyz_parameters (Distance &max_distance, Distance &max_distance_squared, int &centroid_bin_min, int &centroid_bin_max, utility::vector1< core::conformation::ResidueOP > const &moving_rsd_at_origin_list, Size const gap_size_to_anchor)
utility::vector1 < core::conformation::ResidueOP >	setup_residue_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)
utility::vector1 < core::pose::PoseOP >	setup_pose_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)
utility::vector1 < core::pose::PoseOP >	setup_pose_with_moving_residue_alternative_list (pose::Pose const &pose, Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)

Typedef Documentation

typedef std::map< BaseBin, int, compare_base_bin > protocols::stepwise::sampling::rna::rigid_body::BaseBinMap

Function Documentation

void protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map	(	std::map< BaseBin, int, compare_base_bin > const &	base_bin_map,
		std::string const &	DOF_one,
		std::string const &	DOF_two,
		std::string const	foldername
	)

References DOF_bin_size(), DOF_bin_value(), filename(), and core::chemical::rna::TR.

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::apply(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::apply(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply().

void protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map	(	std::map< BaseBin, int, compare_base_bin > const &	base_bin_map,
		std::string const	foldername
	)

References STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, STANDARD_EULER_Z_BIN_SIZE, and core::chemical::rna::TR.

core::Real protocols::stepwise::sampling::rna::rigid_body::DOF_bin_size

(

std::string const &

DOF

)

References exit, STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, STANDARD_EULER_Z_BIN_SIZE, and utility_exit_with_message.

Referenced by analyze_base_bin_map().

int protocols::stepwise::sampling::rna::rigid_body::DOF_bin_value	(	std::map< BaseBin, int, compare_base_bin >::const_iterator const &	base_bin_it,
		std::string const &	DOF
	)

References exit, and utility_exit_with_message.

Referenced by analyze_base_bin_map().

BaseBin protocols::stepwise::sampling::rna::rigid_body::get_euler_stub_bin	(	numeric::xyzVector< core::Real > const &	centroid,
		rotamer_sampler::rigid_body::EulerAngles const &	euler_angles
	)

References protocols::rotamer_sampler::rigid_body::EulerAngles::alpha(), protocols::stepwise::sampling::rna::rigid_body::BaseBin::centroid_x, protocols::stepwise::sampling::rna::rigid_body::BaseBin::centroid_y, protocols::stepwise::sampling::rna::rigid_body::BaseBin::centroid_z, protocols::stepwise::sampling::rna::rigid_body::BaseBin::euler_alpha, protocols::stepwise::sampling::rna::rigid_body::BaseBin::euler_gamma, protocols::stepwise::sampling::rna::rigid_body::BaseBin::euler_z, protocols::rotamer_sampler::rigid_body::EulerAngles::gamma(), STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, STANDARD_EULER_Z_BIN_SIZE, and protocols::rotamer_sampler::rigid_body::EulerAngles::z().

core::Real protocols::stepwise::sampling::rna::rigid_body::get_max_centroid_to_atom_distance	(	utility::vector1< core::conformation::ResidueOP > const &	rsd_at_origin_list,
		std::string const	atom_name
	)

References centroid, distance(), core::chemical::rna::get_rna_base_centroid(), length, core::chemical::name_from_aa(), runtime_assert, core::chemical::rna::TR, and core::conformation::Residue::xyz().

Referenced by initialize_xyz_parameters().

core::kinematics::Stub protocols::stepwise::sampling::rna::rigid_body::get_sugar_stub	(	conformation::Residue const &	rsd,
		bool const	is_prepend,
		bool const	verbose
	)

References chemical, numeric::xyzMatrix< Real >::cols(), cross(), core::conformation::Residue::is_RNA(), numeric::xyzVector< class >::normalize(), protocols::stepwise::sampling::rna::output_boolean(), runtime_assert, core::chemical::rna::TR, and core::conformation::Residue::xyz().

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::get_reference_stub(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::get_reference_stub(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::get_reference_stub().

void protocols::stepwise::sampling::rna::rigid_body::initialize_xyz_parameters	(	Distance &	max_distance,
		Distance &	max_distance_squared,
		int &	centroid_bin_min,
		int &	centroid_bin_max,
		utility::vector1< core::conformation::ResidueOP > const &	moving_rsd_at_origin_list,
		Size const	gap_size_to_anchor
	)

References get_max_centroid_to_atom_distance(), O3I_C5I_PLUS_ONE_MAX_DIST, O3I_C5I_PLUS_TWO_MAX_DIST, and STANDARD_CENTROID_BIN_SIZE.

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_xyz_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_xyz_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_xyz_grid_parameters(), and protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_xyz_grid_parameters().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::rigid_body::setup_pose_at_origin_list	(	pose::Pose const &	pose,
		Size const &	moving_res,
		bool const	extra_chi,
		bool const	use_phenix_geo
	)

References protocols::rotamer_sampler::rigid_body::set_to_origin(), and setup_pose_with_moving_residue_alternative_list().

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), and setup_residue_at_origin_list().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::rigid_body::setup_pose_with_moving_residue_alternative_list	(	pose::Pose const &	pose,
		Size const &	moving_res,
		bool const	extra_chi,
		bool const	use_phenix_geo
	)

References core::chemical::rna::ANTI, core::chemical::rna::ANY_CHI, core::chemical::rna::ANY_PUCKER, core::pose::Pose::clone(), core::chemical::rna::is_purine(), and core::pose::Pose::residue().

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_moving_residue_pose_list(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_moving_residue_pose_list(), and setup_pose_at_origin_list().

utility::vector1< core::conformation::ResidueOP > protocols::stepwise::sampling::rna::rigid_body::setup_residue_at_origin_list	(	pose::Pose const &	pose,
		Size const &	moving_res,
		bool const	extra_chi,
		bool const	use_phenix_geo
	)

References setup_pose_at_origin_list().

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

void protocols::stepwise::sampling::rna::rigid_body::translate_then_rotate_pose	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > const &	vector,
		numeric::xyzMatrix< core::Real > const	matrix,
		bool const	verbose
	)

References at(), core::chemical::ResidueType::atom_name(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::chemical::rna::TR, core::conformation::Residue::type(), and core::pose::Pose::xyz().