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protocols::jumping Namespace Reference

Classes

class  DisulfTemplate
 
class  BaseDisulfPairingLibrary
 
class  DisulfPairingLibrary
 
class  StandardDisulfPairingLibrary
 
class  DisulfPairing
 
class  JumpSample
 
class  Interval
 two numbers, i.e., jump start end residue, or cut-regions... More...
 
class  BaseJumpSetup
 virtual base class: can create a set of jumps and cuts More...
 
class  JumpSetup
 
class  JumpsFromAllPairings
 
class  JumpSelector
 
class  MembraneJump
 
class  PairingTemplate
 
class  BasePairingLibrary
 returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors. More...
 
class  PairingLibrary
 
class  SpecificGeometryLibrary
 
class  StandardPairingLibrary
 
class  RandomSheetBuilder
 select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ More...
 
class  ResiduePairJumpSingle
 a single residue component of a ResiduePairJump class More...
 
class  ResiduePairJump
 
class  ResiduePairJumpSetup
 
class  SameStrand
 tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, More...
 
class  SheetBuilder
 select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ More...
 

Typedefs

typedef utility::vector1
< DisulfPairing > 		DisulfPairingsList
 
typedef utility::vector1
< DisulfPairing > 		DisulfPairingList
 
typedef utility::vector1
< jumping::Interval > 		JumpList
 
typedef
utility::pointer::owning_ptr
< BaseJumpSetup > 		BaseJumpSetupOP
 
typedef
utility::pointer::owning_ptr
< BaseJumpSetup const > 		BaseJumpSetupCOP
 
typedef
utility::pointer::owning_ptr
< JumpSetup > 		JumpSetupOP
 
typedef
utility::pointer::owning_ptr
< JumpSetup const > 		JumpSetupCOP
 
typedef
utility::pointer::owning_ptr
< JumpSelector > 		JumpSelectorOP
 
typedef
utility::pointer::owning_ptr
< JumpSelector const > 		JumpSelectorCOP
 
typedef
utility::pointer::owning_ptr
< MembraneJump > 		MembraneJumpOP
 
typedef
utility::pointer::owning_ptr
< BasePairingLibrary > 		BasePairingLibraryOP
 
typedef
utility::pointer::owning_ptr
< BasePairingLibrary const > 		BasePairingLibraryCOP
 
typedef
utility::pointer::owning_ptr
< PairingLibrary > 		PairingLibraryOP
 
typedef
utility::pointer::owning_ptr
< PairingLibrary const > 		PairingLibraryCOP
 
typedef
utility::pointer::owning_ptr
< StandardPairingLibrary > 		StandardPairingLibraryOP
 
typedef
utility::pointer::owning_ptr
< StandardPairingLibrary const > 		StandardPairingLibraryCOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJumpSingle > 		ResiduePairJumpSingleOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJumpSingle const > 		ResiduePairJumpSingleCOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJump > 		ResiduePairJumpOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJump const > 		ResiduePairJumpCOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJumpSetupSingle > 		ResiduePairJumpSetupSingleOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJumpSetupSingle
const > 		ResiduePairJumpSetupSingleCOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJumpSetup > 		ResiduePairJumpSetupOP
 
typedef
utility::pointer::owning_ptr
< ResiduePairJumpSetup const > 		ResiduePairJumpSetupCOP
 
typedef
utility::pointer::owning_ptr
< SameStrand > 		SameStrandOP
 
typedef
utility::pointer::owning_ptr
< SameStrand const > 		SameStrandCOP
 
typedef utility::vector1
< PointPosition > 		PointList
 

Enumerations

enum  cstType {
  disAB = 1, angleA, angleB, dihedralA,
  dihedralAB, dihedralB, num_cstType = dihedralB
}
 
enum  dofType { rot1 = 1, rot2, cstJump, num_dofType = cstJump }
 

Functions

static
numeric::random::RandomGenerator 		RG (12345)
 
void dis_get_coordinate_system (numeric::xyzMatrix_double const &p, numeric::xyzMatrix_double &m)
 
void dis_get_ncac (FArray2A_float pos, numeric::xyzMatrix_double &p)
 
numeric::xyzMatrix_double dis_get_ncac (FArray2A_float pos)
 
RT dis_RT_from_epos (FArray2A_float Epos1, FArray2A_float Epos2)
 
void read_pairing_list (std::string disulf_pairing_file, DisulfPairingsList &disulf_pairings)
 
void read_disulf_pairing_list (std::istream &is, DisulfPairingsList &disulf_pairings)
 add pairings in pairing_file to list "pairings" More...
 
std::ostream & operator<< (std::ostream &out, DisulfPairing const &)
 list of pairings More...
 
std::ostream & operator<< (std::ostream &out, DisulfPairingsList const &p)
 
static basic::Tracer tr ("protocols.jumping")
 
std::ostream & operator<< (std::ostream &os, JumpSample const &t)
 output operator More...
 
static basic::Tracer tr ("protocols.jumping")
 
void dump_tags_ (FArray1D_int const &tags, Size nres, std::ostream &out)
 
void fill_tags_ (FArray1D_int &tags, Size fill_pos, int tag, Size nres)
 
static
numeric::random::RandomGenerator 		RG (489134)
 
static basic::Tracer tr ("protocols.jumping.MembraneJump")
 
static
numeric::random::RandomGenerator 		RG (750107)
 
static
numeric::random::RandomGenerator 		RG (9238)
 
void get_coordinate_system (numeric::xyzMatrix_double const &p, numeric::xyzMatrix_double &m)
 
void get_ncac (FArray2A_float pos, numeric::xyzMatrix_double &p)
 
numeric::xyzMatrix_double get_ncac (FArray2A_float pos)
 
RT RT_from_epos (FArray2A_float Epos1, FArray2A_float Epos2)
 
static basic::Tracer tr ("protocols.jumping")
 
std::ostream & operator<< (std::ostream &os, SameStrand const &t)
 output operator More...
 
static basic::Tracer tr ("protocols.jumping")
 
void close_chainbreaks (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol, Pose &open_pose, protocols::checkpoint::CheckPointer &checkpoint, const std::string &decoy_tag, core::kinematics::FoldTree const &final_fold_tree_in)
 
bool remove_cut (Size cutpoint, Pose &pose, FoldTree const &final_fold_tree)
 
bool remove_cut (Size cutpoint, FoldTree &new_fold_tree, FoldTree const &final_fold_tree)
 
void safe_secstruct (pose::Pose &pose)
 
core::fragment::JumpingFrameOP generate_empty_jump_frame (Size startpos, Size endpos, Size length)
 
core::fragment::JumpingFrameOP generate_jump_frame (Size startpos, Size endpos, bool bWithTorsion)
 
void get_CA_vectors (PointList const &ca1, PointList const &ca2, Vector &a, Vector &b, Vector &c)
 
void get_pairing_geometry (pose::Pose const &pose, Size const res1, Size const res2, Real &orientation, Real &pleating1, Real &pleating2)
 
void get_pleating (pose::Pose const &pose, Size const pos1, Size const pos2, Size &orientation, Size &pleating)
 
void assign_ss_dssp (core::pose::Pose &pose)
 Assign secondary structure using DSSP. More...
 
bool remove_cut (core::Size cutpoint, core::pose::Pose &pose, core::kinematics::FoldTree const &final_fold_tree=core::kinematics::FoldTree())
 
bool remove_cut (core::Size cutpoint, core::kinematics::FoldTree &fold_tree, core::kinematics::FoldTree const &final_fold_tree=core::kinematics::FoldTree())
 
void close_chainbreaks (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol, core::pose::Pose &pose, checkpoint::CheckPointer &checkpoint, const std::string &decoy_tag, core::kinematics::FoldTree const &final_fold_tree=core::kinematics::FoldTree())
 

Typedef Documentation

typedef utility::pointer::owning_ptr< BaseJumpSetup const > protocols::jumping::BaseJumpSetupCOP

Definition at line 34 of file JumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< BaseJumpSetup > protocols::jumping::BaseJumpSetupOP

Definition at line 30 of file JumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< BasePairingLibrary const > protocols::jumping::BasePairingLibraryCOP

Definition at line 35 of file PairingLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< BasePairingLibrary > protocols::jumping::BasePairingLibraryOP

Definition at line 31 of file PairingLibrary.fwd.hh.

typedef utility::vector1<DisulfPairing> protocols::jumping::DisulfPairingList

Definition at line 37 of file DisulfPairingsList.fwd.hh.

typedef utility::vector1<DisulfPairing> protocols::jumping::DisulfPairingsList

Definition at line 33 of file DisulfPairingsList.fwd.hh.

typedef utility::vector1< jumping::Interval > protocols::jumping::JumpList

Definition at line 59 of file JumpSample.hh.

typedef utility::pointer::owning_ptr< JumpSelector const > protocols::jumping::JumpSelectorCOP

Definition at line 40 of file JumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< JumpSelector > protocols::jumping::JumpSelectorOP

Definition at line 39 of file JumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< JumpSetup const > protocols::jumping::JumpSetupCOP

Definition at line 37 of file JumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< JumpSetup > protocols::jumping::JumpSetupOP

Definition at line 36 of file JumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< MembraneJump > protocols::jumping::MembraneJumpOP

Definition at line 28 of file MembraneJump.fwd.hh.

typedef utility::pointer::owning_ptr< PairingLibrary const > protocols::jumping::PairingLibraryCOP

Definition at line 39 of file PairingLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< PairingLibrary > protocols::jumping::PairingLibraryOP

Definition at line 38 of file PairingLibrary.fwd.hh.

typedef utility::vector1< PointPosition > protocols::jumping::PointList

some legacy code

Definition at line 340 of file util.cc.

typedef utility::pointer::owning_ptr< ResiduePairJump const > protocols::jumping::ResiduePairJumpCOP

Definition at line 39 of file ResiduePairJump.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJump > protocols::jumping::ResiduePairJumpOP

Definition at line 35 of file ResiduePairJump.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJumpSetup const > protocols::jumping::ResiduePairJumpSetupCOP

Definition at line 39 of file ResiduePairJumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJumpSetup > protocols::jumping::ResiduePairJumpSetupOP

Definition at line 35 of file ResiduePairJumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJumpSetupSingle const > protocols::jumping::ResiduePairJumpSetupSingleCOP

Definition at line 32 of file ResiduePairJumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJumpSetupSingle > protocols::jumping::ResiduePairJumpSetupSingleOP

Definition at line 28 of file ResiduePairJumpSetup.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJumpSingle const > protocols::jumping::ResiduePairJumpSingleCOP

Definition at line 32 of file ResiduePairJump.fwd.hh.

typedef utility::pointer::owning_ptr< ResiduePairJumpSingle > protocols::jumping::ResiduePairJumpSingleOP

Definition at line 28 of file ResiduePairJump.fwd.hh.

typedef utility::pointer::owning_ptr< SameStrand const > protocols::jumping::SameStrandCOP

Definition at line 32 of file SameStrand.fwd.hh.

typedef utility::pointer::owning_ptr< SameStrand > protocols::jumping::SameStrandOP

Definition at line 28 of file SameStrand.fwd.hh.

typedef utility::pointer::owning_ptr< StandardPairingLibrary const > protocols::jumping::StandardPairingLibraryCOP

Definition at line 43 of file PairingLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< StandardPairingLibrary > protocols::jumping::StandardPairingLibraryOP

Definition at line 42 of file PairingLibrary.fwd.hh.

Enumeration Type Documentation

enum protocols::jumping::cstType
Enumerator
disAB 
angleA 
angleB 
dihedralA 
dihedralAB 
dihedralB 
num_cstType 

Definition at line 134 of file ResiduePairJump.hh.

enum protocols::jumping::dofType
Enumerator
rot1 
rot2 
cstJump 
num_dofType 

Definition at line 144 of file ResiduePairJump.hh.

Function Documentation

void protocols::jumping::assign_ss_dssp ( core::pose::Pose &  pose)

Assign secondary structure using DSSP.

Definition at line 475 of file util.cc.

References core::scoring::dssp::Dssp::insert_ss_into_pose().

void protocols::jumping::close_chainbreaks ( loops::loop_closure::ccd::SlidingWindowLoopClosureOP  closure_protocol,
core::pose::Pose &  pose,
checkpoint::CheckPointer &  checkpoint,
const std::string &  decoy_tag,
core::kinematics::FoldTree const &  final_fold_tree = core::kinematics::FoldTree() 
)
void protocols::jumping::close_chainbreaks ( loops::loop_closure::ccd::SlidingWindowLoopClosureOP  closure_protocol,
Pose &  open_pose,
protocols::checkpoint::CheckPointer &  checkpoint,
const std::string &  decoy_tag,
core::kinematics::FoldTree const &  final_fold_tree_in 
)

Definition at line 82 of file util.cc.

References protocols::checkpoint::CheckPointer::checkpoint(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get_bb(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::pose::symmetry::is_symmetric(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_cutpoint(), protocols::checkpoint::CheckPointer::recover_checkpoint(), remove_cut(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), core::kinematics::FoldTree::simple_tree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and tr().

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), and protocols::loop_build::LoopMover_SlidingWindow::model_loop().

void protocols::jumping::dis_get_coordinate_system ( numeric::xyzMatrix_double const &  p,
numeric::xyzMatrix_double &  m 
)

Definition at line 114 of file DisulfPairingLibrary.cc.

Referenced by dis_RT_from_epos().

void protocols::jumping::dis_get_ncac ( FArray2A_float  pos,
numeric::xyzMatrix_double &  p 
)

Definition at line 132 of file DisulfPairingLibrary.cc.

References core::pack::dunbrack::c.

Referenced by dis_RT_from_epos().

numeric::xyzMatrix_double protocols::jumping::dis_get_ncac ( FArray2A_float  pos)

Definition at line 149 of file DisulfPairingLibrary.cc.

References core::pack::dunbrack::c.

RT protocols::jumping::dis_RT_from_epos ( FArray2A_float  Epos1,
FArray2A_float  Epos2 
)

Definition at line 165 of file DisulfPairingLibrary.cc.

References dis_get_coordinate_system(), dis_get_ncac(), core::kinematics::RT::set_rotation(), and core::kinematics::RT::set_translation().

void protocols::jumping::dump_tags_ ( FArray1D_int const &  tags,
Size  nres,
std::ostream &  out 
)

Definition at line 164 of file JumpSetup.cc.

Referenced by protocols::jumping::JumpSelector::create_jump_sample().

void protocols::jumping::fill_tags_ ( FArray1D_int &  tags,
Size  fill_pos,
int  tag,
Size  nres 
)

Definition at line 185 of file JumpSetup.cc.

Referenced by protocols::jumping::JumpSelector::create_jump_sample().

core::fragment::JumpingFrameOP protocols::jumping::generate_empty_jump_frame ( Size  startpos,
Size  endpos,
Size  length 
)

Definition at line 306 of file util.cc.

Referenced by protocols::jumping::DisulfPairingLibrary::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::PairingLibrary::generate_jump_frags(), and generate_jump_frame().

core::fragment::JumpingFrameOP protocols::jumping::generate_jump_frame ( Size  startpos,
Size  endpos,
bool  bWithTorsion 
)

Definition at line 318 of file util.cc.

References generate_empty_jump_frame(), protocols::loops::start, and protocols::loops::stop.

void protocols::jumping::get_CA_vectors ( PointList const &  ca1,
PointList const &  ca2,
Vector &  a,
Vector &  b,
Vector &  c 
)

Definition at line 343 of file util.cc.

Referenced by get_pairing_geometry().

void protocols::jumping::get_coordinate_system ( numeric::xyzMatrix_double const &  p,
numeric::xyzMatrix_double &  m 
)

Definition at line 98 of file PairingLibrary.cc.

Referenced by RT_from_epos().

void protocols::jumping::get_ncac ( FArray2A_float  pos,
numeric::xyzMatrix_double &  p 
)

Definition at line 116 of file PairingLibrary.cc.

References core::pack::dunbrack::c.

Referenced by RT_from_epos().

numeric::xyzMatrix_double protocols::jumping::get_ncac ( FArray2A_float  pos)

Definition at line 133 of file PairingLibrary.cc.

References core::pack::dunbrack::c.

void protocols::jumping::get_pairing_geometry ( pose::Pose const &  pose,
Size const  res1,
Size const  res2,
Real &  orientation,
Real &  pleating1,
Real &  pleating2 
)

Definition at line 367 of file util.cc.

References get_CA_vectors(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), tr(), and core::pose::Pose::xyz().

Referenced by get_pleating().

void protocols::jumping::get_pleating ( pose::Pose const &  pose,
Size const  pos1,
Size const  pos2,
Size &  orientation,
Size &  pleating 
)

Definition at line 427 of file util.cc.

References get_pairing_geometry(), and tr().

Referenced by protocols::jumping::JumpSample::steal_orientation_and_pleating().

std::ostream & protocols::jumping::operator<< ( std::ostream &  out,
DisulfPairing const &  p 
)

list of pairings

Definition at line 100 of file DisulfPairingsList.cc.

References protocols::jumping::DisulfPairing::pos1, protocols::jumping::DisulfPairing::pos2, protocols::jumping::DisulfPairing::seq_sep, and protocols::jumping::DisulfPairing::ss_type.

std::ostream& protocols::jumping::operator<< ( std::ostream &  os,
SameStrand const &  t 
)
inline

output operator

Definition at line 103 of file SameStrand.hh.

References protocols::jumping::SameStrand::show().

std::ostream & protocols::jumping::operator<< ( std::ostream &  out,
DisulfPairingsList const &  p 
)

Definition at line 106 of file DisulfPairingsList.cc.

std::ostream & protocols::jumping::operator<< ( std::ostream &  os,
JumpSample const &  t 
)

output operator

Definition at line 578 of file JumpSample.cc.

References protocols::jumping::JumpSample::cuts_, protocols::jumping::JumpSample::jumps_, and protocols::jumping::JumpSample::size().

void protocols::jumping::read_disulf_pairing_list ( std::istream &  disulf_pairing_stream,
DisulfPairingsList &  disulf_pairings 
)

add pairings in pairing_file to list "pairings"

Definition at line 80 of file DisulfPairingsList.cc.

References protocols::match::upstream::b, and core::pack::dunbrack::c.

Referenced by read_pairing_list().

void protocols::jumping::read_pairing_list ( std::string  disulf_pairing_file,
DisulfPairingsList &  disulf_pairings 
)

Definition at line 68 of file DisulfPairingsList.cc.

References read_disulf_pairing_list(), and tr().

Referenced by protocols::jumping::MembraneJump::init().

bool protocols::jumping::remove_cut ( core::Size  cutpoint,
core::pose::Pose &  pose,
core::kinematics::FoldTree const &  final_fold_tree = core::kinematics::FoldTree() 
)
bool protocols::jumping::remove_cut ( core::Size  cutpoint,
core::kinematics::FoldTree &  fold_tree,
core::kinematics::FoldTree const &  final_fold_tree = core::kinematics::FoldTree() 
)
bool protocols::jumping::remove_cut ( Size  cutpoint,
Pose &  pose,
FoldTree const &  final_fold_tree 
)

Definition at line 194 of file util.cc.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::idealize_position(), and tr().

Referenced by close_chainbreaks().

bool protocols::jumping::remove_cut ( Size  cutpoint,
FoldTree &  new_fold_tree,
FoldTree const &  final_fold_tree 
)

Definition at line 209 of file util.cc.

References tr().

static numeric::random::RandomGenerator protocols::jumping::RG ( 750107  )
static
static numeric::random::RandomGenerator protocols::jumping::RG ( 9238  )
static
static numeric::random::RandomGenerator protocols::jumping::RG ( 12345  )
static

Referenced by protocols::jumping::SheetBuilder::choose_next_pairing(), protocols::jumping::JumpSelector::create_jump_sample(), protocols::jumping::RandomSheetBuilder::create_new_random_topol(), protocols::jumping::SameStrand::do_same_strand(), protocols::jumping::PairingLibrary::get_random_beta_sheet_jump(), protocols::jumping::PairingLibrary::get_random_tmh_jump(), protocols::jumping::JumpSelector::select_random(), protocols::jumping::PairingLibrary::set_tmh_jump(), and protocols::jumping::MembraneJump::setup_fold_tree().

static numeric::random::RandomGenerator protocols::jumping::RG ( 489134  )
static
RT protocols::jumping::RT_from_epos ( FArray2A_float  Epos1,
FArray2A_float  Epos2 
)

Definition at line 149 of file PairingLibrary.cc.

References get_coordinate_system(), get_ncac(), core::kinematics::RT::set_rotation(), and core::kinematics::RT::set_translation().

Referenced by protocols::jumping::PairingLibrary::read_from_file().

void protocols::jumping::safe_secstruct ( pose::Pose &  pose)

Definition at line 284 of file util.cc.

References core::pose::Pose::fold_tree(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::abinitio::KinematicControl::prepare_pose_for_sampling().

static basic::Tracer protocols::jumping::tr ( "protocols.jumping.MembraneJump"  )
static
static basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )
static
static basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )
static
static basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )
static
static basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )
static

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), protocols::jumping::SheetBuilder::builder_loop(), close_chainbreaks(), protocols::jumping::SheetBuilder::create_jump_sample(), protocols::jumping::JumpSelector::create_jump_sample(), protocols::jumping::RandomSheetBuilder::create_new_random_topol(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), protocols::jumping::JumpSample::generate_random_tree_from_jumps(), get_pairing_geometry(), get_pleating(), protocols::jumping::JumpSample::JumpSample(), protocols::jumping::ResiduePairJumpSetup::read_file(), protocols::jumping::JumpSetup::read_file(), protocols::jumping::JumpSelector::read_file(), remove_cut(), protocols::jumping::JumpSample::steal_orientation_and_pleating(), and protocols::jumping::JumpSample::transfer_jumps().

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