ccd_closure.cc File Reference

#include <protocols/loops/loop_closure/ccd/ccd_closure.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/Ramachandran.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <basic/prof.hh>
#include <basic/basic.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/random/random.fwd.hh>
#include <utility/assert.hh>
#include <utility/vector1.hh>

Go to the source code of this file.

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::loops
	protocols::loops::loop_closure
	protocols::loops::loop_closure::ccd

Constant Groups
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::loops
	protocols::loops::loop_closure
	protocols::loops::loop_closure::ccd

Typedefs
typedef numeric::xyzMatrix< Real >	protocols::loops::loop_closure::ccd::Matrix

Functions
basic::Tracer	protocols::loops::loop_closure::ccd::tccd ("protocols.loops.loop_closure.ccd.ccd_closure")
void	protocols::loops::loop_closure::ccd::load_coords_and_torsions (pose::Pose const &pose, vector1< vector1< Vector > > &coords, vector1< vector1< Real > > &torsions)
	copy mainchain atoms xyz and torsions from pose to coords and torsions More...
void	protocols::loops::loop_closure::ccd::copy_torsions_to_pose (pose::Pose &pose, int const loop_begin, int const loop_end, vector1< vector1< Real > > const &torsions)
	copy torsions into pose between residue loop_begin and loop_end More...
void	protocols::loops::loop_closure::ccd::get_overlap_pos (vector1< vector1< Vector > > const &coords, vector1< vector1< Real > > const &torsions, int const cutpoint, int const direction, Real const bond_angle1, Real const bond_length, Real const bond_angle2, Matrix &M)
void	protocols::loops::loop_closure::ccd::check_overlap_pos (vector1< vector1< Vector > > const &coords, vector1< vector1< Real > > const &torsions, int const cutpoint, int const direction, Real const bond_angle1, Real const ASSERT_ONLY(bond_length), Real const bond_angle2, Matrix const &M_in)
	check whether xyz coords of overlap position match internal coords More...
void	protocols::loops::loop_closure::ccd::index_pair_in_range (int &pos, int &atom, int const nbb)
void	protocols::loops::loop_closure::ccd::get_torsion_axis (vector1< vector1< Vector > > const &coords, int const seqpos, int const torsion, Vector &axis_atom, Vector &axis_vector)
void	protocols::loops::loop_closure::ccd::refold_loop_torsion (Real const alpha, int const pos, int const torsion, int const dir, int const cutpoint, vector1< vector1< Vector > > &coords, Matrix &M)
void	protocols::loops::loop_closure::ccd::calculate_ccd_angle (Matrix const &F, Matrix const &M, vector1< vector1< Vector > > const &coords, int const pos, int const torsion, int const direction, Real &angle, Real &dev)
void	protocols::loops::loop_closure::ccd::check_torsions (int const loop_begin, int const loop_end, int const cutpoint, vector1< vector1< Real > > const &torsions, vector1< vector1< Vector > > const &coords)
int	protocols::loops::loop_closure::ccd::fast_ccd_loop_closure (pose::Pose &pose, kinematics::MoveMap const &mm, int const loop_begin, int const loop_end, int const cutpoint, int const ii_cycles, Real const tolerance, bool const rama_check, Real const max_rama_score_increase, Real const max_total_delta_helix, Real const max_total_delta_strand, Real const max_total_delta_loop, Real &forward_deviation, Real &backward_deviation, Real &torsion_delta, Real &rama_delta)
void	protocols::loops::loop_closure::ccd::ccd_moves (int const total_moves, core::pose::Pose &pose, core::kinematics::MoveMap const &mm, int const loop_begin, int const loop_end, int const cutpoint)

Detailed Description

Author

Phil Bradley

Definition in file ccd_closure.cc.