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util.hh File Reference
#include <core/id/AtomID.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/kinematics/Stub.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <numeric/xyzMatrix.hh>
#include <string>

Namespaces

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

Typedefs

typedef numeric::xyzMatrix
< core::Real
protocols::toolbox::rigid_body::Matrix
 

Functions

void protocols::toolbox::rigid_body::get_atom_coordinates (utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > &xyz_list, core::Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::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 (core::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 (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, core::Size const moving_res)
 
utility::vector1< core::Sizeprotocols::toolbox::rigid_body::figure_out_moving_partition_res (pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
 
void protocols::toolbox::rigid_body::set_to_origin (pose::Pose &pose, core::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, core::Size const moving_res, utility::vector1< core::Size > const &moving_partition_res)
 
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::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::translate (pose::Pose &pose, Vector const &shift, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res)
 
void protocols::toolbox::rigid_body::rotate (pose::Pose &pose, Matrix const &M, pose::Pose const &ref_pose, utility::vector1< core::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< core::Size > const &moving_res)
 
void protocols::toolbox::rigid_body::get_base_centroid_and_rotation_matrix (pose::Pose const &pose, core::Size const i, Vector &centroid, Matrix &M)
 
void protocols::toolbox::rigid_body::translate_and_rotate_residue_to_origin (pose::Pose &pose, core::Size const i, utility::vector1< core::Size > const &moving_res, bool const do_not_rotate)
 
void protocols::toolbox::rigid_body::translate_and_rotate_residue_to_origin (pose::Pose &pose, core::Size const i)
 

Detailed Description

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