util.cc File Reference

#include <protocols/toolbox/rigid_body/util.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/id/AtomID.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <utility/tools/make_vector1.hh>
#include <basic/Tracer.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/conversions.hh>

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

Functions
static thread_local basic::Tracer	TR ("protocols.toolbox.rigid_body.FloatingBaseUtil")
void	protocols::toolbox::rigid_body::get_atom_coordinates (utility::vector1< std::pair< id::AtomID, numeric::xyzVector< Real > > > &xyz_list, Size const &seq_num, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
void	protocols::toolbox::rigid_body::get_specific_atom_coordinate (Size const atom_index, Vector &atom_pos, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
void	protocols::toolbox::rigid_body::get_specific_atom_coordinate (Vector &atom_pos, kinematics::Stub const &moving_res_base_stub)
void	protocols::toolbox::rigid_body::get_specific_atom_coordinate (std::string const &atom_name, Vector &atom_pos, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
Size	protocols::toolbox::rigid_body::figure_out_reference_res_for_jump (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	protocols::toolbox::rigid_body::figure_out_moving_partition_res (pose::Pose const &pose, Size const moving_res, Size const reference_res)
void	protocols::toolbox::rigid_body::set_to_origin (pose::Pose &pose, Size const seq_num, utility::vector1< Size > const &move_res_list, bool verbose=false)
void	protocols::toolbox::rigid_body::set_to_origin (pose::Pose &pose, Size const seq_num, bool verbose)
kinematics::Stub	protocols::toolbox::rigid_body::initialize_stub (conformation::Residue const &rsd)
PoseCOP	protocols::toolbox::rigid_body::transform_moving_partition_to_origin (pose::Pose const &pose_start, Size const moving_res, utility::vector1< Size > const &moving_partition_res)
void	protocols::toolbox::rigid_body::create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)
void	protocols::toolbox::rigid_body::create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)
void	protocols::toolbox::rigid_body::get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)
void	protocols::toolbox::rigid_body::translate (pose::Pose &pose, Vector const shift, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
void	protocols::toolbox::rigid_body::rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res, Vector const &centroid)
void	protocols::toolbox::rigid_body::rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
void	protocols::toolbox::rigid_body::get_base_centroid_and_rotation_matrix (pose::Pose const &pose, Size const i, Vector &centroid, Matrix &M)
void	protocols::toolbox::rigid_body::translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i, utility::vector1< Size > const moving_res, bool const do_not_rotate)
void	protocols::toolbox::rigid_body::translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i)

Detailed Description

Author

Rhiju Das, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu

Function Documentation

static thread_local basic::Tracer TR ( "protocols.toolbox.rigid_body.FloatingBaseUtil"  )

static