StepWiseRNA_FloatingBaseSamplerUtil.hh File Reference

#include <protocols/stepwise/sampling/rna/rigid_body/FloatingBaseClasses.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <string>
#include <map>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <numeric/angle.functions.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Residue.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Util.hh>
#include <protocols/rotamer_sampler/rigid_body/EulerAngles.hh>
#include <protocols/stepwise/sampling/rna/checker/RNA_VDW_BinChecker.fwd.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_JobParameters.hh>
#include <core/pose/Pose.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::stepwise
	protocols::stepwise::sampling
	protocols::stepwise::sampling::rna
	protocols::stepwise::sampling::rna::rigid_body

Macros
#define	STANDARD_CENTROID_BIN_SIZE   1.0
#define	STANDARD_EULER_ANGLE_BIN_SIZE   20
#define	STANDARD_EULER_Z_BIN_SIZE   0.05

Typedefs
typedef numeric::xyzMatrix < core::Real >	Matrix

Functions
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)
core::kinematics::Stub	protocols::stepwise::sampling::rna::rigid_body::get_sugar_stub (conformation::Residue const &rsd, bool const is_prepend, bool const verbose)
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)
Real	protocols::stepwise::sampling::rna::rigid_body::DOF_bin_size (std::string const &DOF)
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)
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)
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)
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)
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)
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)
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)
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)

Detailed Description

Detailed:

Author

Parin Sripakdeevong

Macro Definition Documentation

#define STANDARD_CENTROID_BIN_SIZE   1.0

Referenced by protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map(), protocols::stepwise::sampling::rna::rigid_body::DOF_bin_size(), protocols::stepwise::sampling::rna::rigid_body::get_euler_stub_bin(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_euler_angle_grid_parameters(), and protocols::stepwise::sampling::rna::rigid_body::initialize_xyz_parameters().

#define STANDARD_EULER_ANGLE_BIN_SIZE   20

Referenced by protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map(), protocols::stepwise::sampling::rna::rigid_body::DOF_bin_size(), protocols::stepwise::sampling::rna::rigid_body::get_euler_stub_bin(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_euler_angle_grid_parameters(), and protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_euler_angle_grid_parameters().

#define STANDARD_EULER_Z_BIN_SIZE   0.05

Referenced by protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map(), protocols::stepwise::sampling::rna::rigid_body::DOF_bin_size(), protocols::stepwise::sampling::rna::rigid_body::get_euler_stub_bin(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_euler_angle_grid_parameters(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_euler_angle_grid_parameters(), and protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_euler_angle_grid_parameters().

Typedef Documentation

typedef numeric::xyzMatrix< core::Real > Matrix