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protocols::loops::loop_closure::ccd Namespace Reference

Classes

class  CcdLoopClosureMover
 
class  CcdMover
 
class  FASelectSlidingWindowLoopClosure
 
class  LoopClosure
 
class  ShortLoopClosure
 
class  SlidingWindowLoopClosure
 
class  WidthFirstSlidingWindowLoopClosure
 

Typedefs

typedef numeric::xyzMatrix< RealMatrix
 
typedef
utility::pointer::owning_ptr
< CcdLoopClosureMover
CcdLoopClosureMoverOP
 
typedef
utility::pointer::owning_ptr
< CcdLoopClosureMover const > 
CcdLoopClosureMoverCOP
 
typedef
utility::pointer::owning_ptr
< CcdMover
CcdMoverOP
 
typedef
utility::pointer::owning_ptr
< CcdMover const > 
CcdMoverCOP
 
typedef
utility::pointer::owning_ptr
< FASelectSlidingWindowLoopClosure
FASelectSlidingWindowLoopClosureOP
 
typedef
utility::pointer::owning_ptr
< FASelectSlidingWindowLoopClosure
const > 
FASelectSlidingWindowLoopClosureCOP
 
typedef
utility::pointer::owning_ptr
< LoopClosure
LoopClosureOP
 
typedef
utility::pointer::owning_ptr
< LoopClosure const > 
LoopClosureCOP
 
typedef
utility::pointer::owning_ptr
< ShortLoopClosure
ShortLoopClosureOP
 
typedef
utility::pointer::owning_ptr
< ShortLoopClosure const > 
ShortLoopClosureCOP
 
typedef
utility::pointer::owning_ptr
< SlidingWindowLoopClosure
SlidingWindowLoopClosureOP
 
typedef
utility::pointer::owning_ptr
< SlidingWindowLoopClosure
const > 
SlidingWindowLoopClosureCOP
 

Functions

basic::Tracer tccd ("protocols.loops.loop_closure.ccd.ccd_closure")
 
void 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 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 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 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 index_pair_in_range (int &pos, int &atom, int const nbb)
 
void get_torsion_axis (vector1< vector1< Vector > > const &coords, int const seqpos, int const torsion, Vector &axis_atom, Vector &axis_vector)
 
void 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 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 check_torsions (int const loop_begin, int const loop_end, int const cutpoint, vector1< vector1< Real > > const &torsions, vector1< vector1< Vector > > const &coords)
 
int 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 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)
 
std::ostream & operator<< (std::ostream &os, CcdLoopClosureMover const &mover)
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure")
 
const Real REALLY_BAD_SCORE (1000000000.0)
 
static
numeric::random::RandomGenerator 
RG (9781212)
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.LoopClosure")
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.ShortLoopClosure")
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure")
 
std::string const VDW_FRAG_STORE ("closure_loop_vdw")
 
std::string const SCORE_FRAG_STORE ("closure_loop_score")
 
std::string const RMSD_FRAG_STORE ("closure_loop_rmsd")
 

Variables

std::string const VDW_FRAG_STORE
 
std::string const SCORE_FRAG_STORE
 
std::string const RMSD_FRAG_STORE
 

Typedef Documentation

Function Documentation

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::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 
)

References core::pose::Pose::aa(), core::id::BB, protocols::rigid::c2n, calculate_ccd_angle(), check_overlap_pos(), copy_torsions_to_pose(), core::chemical::AtomICoor::d(), core::kinematics::MoveMap::get(), get_overlap_pos(), core::chemical::ResidueConnection::icoor(), load_coords_and_torsions(), core::conformation::Residue::lower_connect(), core::conformation::Residue::mainchain_atoms(), protocols::rigid::n2c, core::scoring::rama, refold_loop_torsion(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::io::serialization::size(), tccd(), core::chemical::AtomICoor::theta(), core::pose::Pose::total_residue(), and core::conformation::Residue::upper_connect().

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::antibody2::CloseOneCDRLoop::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::rbsegment_relax::CCDMoveWrapper::apply(), protocols::loops::loop_closure::ccd::CcdMover::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::antibody2::H3RefineCCD::finalize_setup(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::antibody::CDRH3Modeler::scored_frag_close(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

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_ONLYbond_length,
Real const  bond_angle2,
Matrix const &  M_in 
)

check whether xyz coords of overlap position match internal coords

References core::scoring::packstat::old::angles, core::kinematics::distance(), and core::io::serialization::size().

Referenced by ccd_moves(), and fast_ccd_loop_closure().

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 
)
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

References core::id::BB, and core::pose::Pose::set_torsion().

Referenced by ccd_moves(), and fast_ccd_loop_closure().

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::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::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::index_pair_in_range ( int pos,
int atom,
int const  nbb 
)
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

References core::conformation::Residue::atom(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::kinmatch::xyz().

Referenced by ccd_moves(), and fast_ccd_loop_closure().

std::ostream& protocols::loops::loop_closure::ccd::operator<< ( std::ostream &  os,
CcdLoopClosureMover const &  mover 
)
const Real protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE ( 1000000000.  0)
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 
)
static numeric::random::RandomGenerator protocols::loops::loop_closure::ccd::RG ( 9781212  )
static
std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE ( "closure_loop_rmsd"  )
std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE ( "closure_loop_score"  )
basic::Tracer protocols::loops::loop_closure::ccd::tccd ( "protocols.loops.loop_closure.ccd.ccd_closure"  )
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.LoopClosure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.ShortLoopClosure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure"  )
static
std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE ( "closure_loop_vdw"  )

Variable Documentation

std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE
std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE
std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE