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StepWiseUtil.hh File Reference
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/kinematics/FoldTree.fwd.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/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>

Namespaces

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

Constant Groups

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

Typedefs

typedef numeric::xyzMatrix< RealMatrix
 

Functions

Size protocols::swa::make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
 
bool protocols::swa::Is_close_chain_break (pose::Pose const &pose)
 
bool protocols::swa::Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
 
void protocols::swa::Output_boolean (std::string const &tag, bool boolean)
 
void protocols::swa::Output_boolean (bool boolean)
 
void protocols::swa::Output_movemap (kinematics::MoveMap const &mm, Size const total_residue)
 
void protocols::swa::Figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const &fixed_res, bool const move_takeoff_torsions, bool const move_jumps_between_chains)
 
void protocols::swa::pdbslice (core::pose::Pose &new_pose, core::pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)
 
void protocols::swa::pdbslice (core::pose::Pose &pose, utility::vector1< core::Size > const &slice_res)
 
id::AtomID_Map< id::AtomIDprotocols::swa::create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &superimpose_res)
 
id::AtomID_Map< id::AtomIDprotocols::swa::create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)
 
utility::vector1< Size > const protocols::swa::convert_to_working_res (utility::vector1< Size > const &res_vector, utility::vector1< Size > const &working_res)
 
core::scoring::constraints::ConstraintSetOP protocols::swa::constraint_set_slice (core::scoring::constraints::ConstraintSetOP &cst_set, utility::vector1< core::Size > const &slice_res, pose::Pose const &pose, pose::Pose const &full_pose)
 
utility::vector1< std::string > protocols::swa::load_s_and_l ()
 
std::string protocols::swa::get_file_name (std::string const &silent_file, std::string const &tag)
 
void protocols::swa::check_scorefxn_has_constraint_terms_if_pose_has_constraints (pose::Pose const &pose, core::scoring::ScoreFunctionOP &scorefxn)
 
utility::vector1< Sizeprotocols::swa::merge_vectors (utility::vector1< Size > const &vec1, utility::vector1< Size > const &vec2)
 
void protocols::swa::get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)
 
void protocols::swa::create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)
 
void protocols::swa::create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)
 
void protocols::swa::translate (pose::Pose &pose, Vector const shift, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
 
void protocols::swa::rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res, Vector const &centroid)
 
void protocols::swa::rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
 
void protocols::swa::get_base_centroid_and_rotation_matrix (pose::Pose const &pose, Size const i, Vector &centroid, Matrix &M)
 
void protocols::swa::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::swa::translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i)
 

Typedef Documentation