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Typedefs | Functions
protocols::toolbox::rigid_body Namespace Reference

Typedefs

typedef numeric::xyzMatrix
< core::Real
Matrix
 

Functions

void get_atom_coordinates (utility::vector1< std::pair< id::AtomID, numeric::xyzVector< Real > > > &xyz_list, core::Size const &seq_num, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
 
void 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 get_specific_atom_coordinate (Vector &atom_pos, kinematics::Stub const &moving_res_base_stub)
 
void 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 figure_out_reference_res_for_jump (pose::Pose const &pose, core::Size const moving_res)
 
utility::vector1< core::Sizefigure_out_moving_partition_res (pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
 
void set_to_origin (pose::Pose &pose, core::Size const seq_num, utility::vector1< core::Size > const &move_res_list, bool verbose=false)
 
void set_to_origin (pose::Pose &pose, core::Size const seq_num, bool verbose)
 
kinematics::Stub initialize_stub (conformation::Residue const &rsd)
 
PoseCOP transform_moving_partition_to_origin (pose::Pose const &pose_start, core::Size const moving_res, utility::vector1< core::Size > const &moving_partition_res)
 
void create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)
 
void create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)
 
void get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)
 
void translate (pose::Pose &pose, Vector const &shift, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res)
 
void rotate (pose::Pose &pose, Matrix const &M, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res, Vector const &centroid)
 
void rotate (pose::Pose &pose, Matrix const &M, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res)
 
void get_base_centroid_and_rotation_matrix (pose::Pose const &pose, core::Size const i, Vector &centroid, Matrix &M)
 
void 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 translate_and_rotate_residue_to_origin (pose::Pose &pose, core::Size const i)
 
void 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)
 

Typedef Documentation

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

Function Documentation

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 
)

Referenced by get_euler_angles().

utility::vector1< core::Size > protocols::toolbox::rigid_body::figure_out_moving_partition_res ( pose::Pose const &  pose,
core::Size const  moving_res,
core::Size const  reference_res 
)
core::Size protocols::toolbox::rigid_body::figure_out_reference_res_for_jump ( pose::Pose const &  pose,
core::Size const  moving_res 
)
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_atom_coordinates ( utility::vector1< std::pair< id::AtomID, numeric::xyzVector< Real > > > &  xyz_list,
core::Size const &  seq_num,
conformation::Residue const &  rsd_at_origin,
kinematics::Stub const &  moving_res_base_stub 
)
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::get_euler_angles ( Real alpha,
Real beta,
Real gamma,
Matrix  M1,
Matrix  M2,
bool const  verbose 
)
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 ( 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 
)
core::kinematics::Stub protocols::toolbox::rigid_body::initialize_stub ( conformation::Residue const &  rsd)
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::set_to_origin ( pose::Pose pose,
core::Size const  seq_num,
utility::vector1< core::Size > const &  move_res_list,
bool  verbose = false 
)
void protocols::toolbox::rigid_body::set_to_origin ( pose::Pose pose,
core::Size const  seq_num,
bool  verbose 
)
core::pose::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::translate ( pose::Pose pose,
Vector const &  shift,
pose::Pose const &  ref_pose,
utility::vector1< core::Size > const &  moving_res 
)
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 
)