Rosetta Protocols  2014.35
Classes | Typedefs | Functions
protocols::stepwise::sampler::rigid_body Namespace Reference

Classes

class  EulerAngles
 
class  RigidBodyStepWiseSampler
 
class  RigidBodyStepWiseSamplerValueRange
 
class  RigidBodyStepWiseSamplerWithResidueAlternatives
 
class  RigidBodyStepWiseSamplerWithResidueList
 

Typedefs

typedef
utility::pointer::owning_ptr
< EulerAngles
EulerAnglesOP
 
typedef
utility::pointer::owning_ptr
< EulerAngles const > 
EulerAnglesCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSampler
RigidBodyStepWiseSamplerOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSampler
const > 
RigidBodyStepWiseSamplerCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSamplerValueRange
RigidBodyStepWiseSamplerValueRangeOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSamplerValueRange
const > 
RigidBodyStepWiseSamplerValueRangeCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSamplerWithResidueAlternatives
RigidBodyStepWiseSamplerWithResidueAlternativesOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSamplerWithResidueAlternatives
const > 
RigidBodyStepWiseSamplerWithResidueAlternativesCOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSamplerWithResidueList
RigidBodyStepWiseSamplerWithResidueListOP
 
typedef
utility::pointer::owning_ptr
< RigidBodyStepWiseSamplerWithResidueList
const > 
RigidBodyStepWiseSamplerWithResidueListCOP
 

Functions

void 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 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 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, Size const moving_res)
 
utility::vector1< Sizefigure_out_moving_partition_res (pose::Pose const &pose, Size const moving_res, Size const reference_res)
 
void set_to_origin (pose::Pose &pose, Size const seq_num, utility::vector1< Size > const &move_res_list, bool verbose=false)
 
void set_to_origin (pose::Pose &pose, 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, Size const moving_res, utility::vector1< 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< Size > const &moving_res)
 
void rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res, Vector const &centroid)
 
void rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
 
void get_base_centroid_and_rotation_matrix (pose::Pose const &pose, Size const i, Vector &centroid, Matrix &M)
 
void translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i, utility::vector1< Size > const moving_res, bool const do_not_rotate)
 
void translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i)
 

Typedef Documentation

Function Documentation

void protocols::stepwise::sampler::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::stepwise::sampler::rigid_body::create_euler_rotation ( Matrix M,
Real const &  alpha,
Real const &  beta,
Real const &  gamma 
)

Referenced by get_euler_angles().

utility::vector1< Size > protocols::stepwise::sampler::rigid_body::figure_out_moving_partition_res ( pose::Pose const &  pose,
Size const  moving_res,
Size const  reference_res 
)
Size protocols::stepwise::sampler::rigid_body::figure_out_reference_res_for_jump ( pose::Pose const &  pose,
Size const  moving_res 
)
void protocols::stepwise::sampler::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::stepwise::sampler::rigid_body::get_base_centroid_and_rotation_matrix ( pose::Pose const &  pose,
Size const  i,
Vector centroid,
Matrix M 
)
void protocols::stepwise::sampler::rigid_body::get_euler_angles ( Real alpha,
Real beta,
Real gamma,
Matrix  M1,
Matrix  M2,
bool const  verbose 
)
void protocols::stepwise::sampler::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::stepwise::sampler::rigid_body::get_specific_atom_coordinate ( Vector atom_pos,
kinematics::Stub const &  moving_res_base_stub 
)
void protocols::stepwise::sampler::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 
)
kinematics::Stub protocols::stepwise::sampler::rigid_body::initialize_stub ( conformation::Residue const &  rsd)
void protocols::stepwise::sampler::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::stepwise::sampler::rigid_body::rotate ( pose::Pose pose,
Matrix const  M,
pose::Pose const &  ref_pose,
utility::vector1< Size > const &  moving_res 
)
void protocols::stepwise::sampler::rigid_body::set_to_origin ( pose::Pose pose,
Size const  seq_num,
utility::vector1< Size > const &  move_res_list,
bool  verbose = false 
)
void protocols::stepwise::sampler::rigid_body::set_to_origin ( pose::Pose pose,
Size const  seq_num,
bool  verbose 
)
PoseCOP protocols::stepwise::sampler::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::stepwise::sampler::rigid_body::translate ( pose::Pose pose,
Vector const  shift,
pose::Pose const &  ref_pose,
utility::vector1< Size > const &  moving_res 
)
void protocols::stepwise::sampler::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::stepwise::sampler::rigid_body::translate_and_rotate_residue_to_origin ( pose::Pose pose,
Size const  i 
)