Classes | Typedefs | Enumerations | Functions
protocols::jumping Namespace Reference


class  DisulfTemplate
class  BaseDisulfPairingLibrary
class  DisulfPairingLibrary
class  StandardDisulfPairingLibrary
 The StandardDisulfPairingsLibrary initializes itself in its constructor from the sampling/disulfide_jump_database_wip.dat file in the database. Users should not in any circumstance invoke any of its non-const methods that are defined in the subclass. This class ought to be reworked to ensure that it is threadsafe. More...
class  DisulfPairing
class  ChainbreakDistFunc
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
 This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn't be. More...
class  RandomSheetBuilder
 select jumps to build a given topology @detail this class encapsulates the functionality of choose_random_pairings in 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 @detail 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 @detail this class encapsulates the functionality of choose_random_pairings in of Rosetta++ More...


typedef utility::vector1< DisulfPairingDisulfPairingsList
typedef utility::vector1< DisulfPairingDisulfPairingList
typedef utility::vector1< jumping::IntervalJumpList
typedef utility::pointer::shared_ptr< BaseJumpSetupBaseJumpSetupOP
typedef utility::pointer::shared_ptr< BaseJumpSetup const > BaseJumpSetupCOP
typedef utility::pointer::shared_ptr< JumpSetupJumpSetupOP
typedef utility::pointer::shared_ptr< JumpSetup const > JumpSetupCOP
typedef utility::pointer::shared_ptr< JumpSelectorJumpSelectorOP
typedef utility::pointer::shared_ptr< JumpSelector const > JumpSelectorCOP
typedef utility::pointer::shared_ptr< MembraneJumpMembraneJumpOP
typedef utility::pointer::shared_ptr< BasePairingLibraryBasePairingLibraryOP
typedef utility::pointer::shared_ptr< BasePairingLibrary const > BasePairingLibraryCOP
typedef utility::pointer::shared_ptr< PairingLibraryPairingLibraryOP
typedef utility::pointer::shared_ptr< PairingLibrary const > PairingLibraryCOP
typedef utility::pointer::shared_ptr< StandardPairingLibraryStandardPairingLibraryOP
typedef utility::pointer::shared_ptr< StandardPairingLibrary const > StandardPairingLibraryCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSingleResiduePairJumpSingleOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSingle const > ResiduePairJumpSingleCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpResiduePairJumpOP
typedef utility::pointer::shared_ptr< ResiduePairJump const > ResiduePairJumpCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetupSingle > ResiduePairJumpSetupSingleOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetupSingle const > ResiduePairJumpSetupSingleCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetupResiduePairJumpSetupOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetup const > ResiduePairJumpSetupCOP
typedef utility::pointer::shared_ptr< SameStrandSameStrandOP
typedef utility::pointer::shared_ptr< SameStrand const > SameStrandCOP
using PointList = utility::vector1< PointPosition >


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


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, core::Size nres, std::ostream &out)
void fill_tags_ (FArray1D_int &tags, core::Size fill_pos, int tag, core::Size nres)
static basic::Tracer tr ("protocols.jumping.MembraneJump")
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 (core::Size cutpoint, Pose &pose, FoldTree const &final_fold_tree)
bool remove_cut (core::Size cutpoint, FoldTree &new_fold_tree, FoldTree const &final_fold_tree)
void safe_secstruct (pose::Pose &pose)
core::fragment::JumpingFrameOP generate_empty_jump_frame (core::Size startpos, core::Size endpos, core::Size length)
core::fragment::JumpingFrameOP generate_jump_frame (core::Size startpos, core::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, core::Size const res1, core::Size const res2, Real &orientation, Real &pleating1, Real &pleating2)
void get_pleating (pose::Pose const &pose, core::Size const pos1, core::Size const pos2, core::Size &orientation, core::Size &pleating)
void assign_ss_dssp (core::pose::Pose &pose)
 Assign secondary structure using DSSP. More...

Typedef Documentation

◆ BaseJumpSetupCOP

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

◆ BaseJumpSetupOP

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

◆ BasePairingLibraryCOP

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

◆ BasePairingLibraryOP

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

◆ DisulfPairingList

◆ DisulfPairingsList

◆ JumpList

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

◆ JumpSelectorCOP

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

◆ JumpSelectorOP

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

◆ JumpSetupCOP

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

◆ JumpSetupOP

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

◆ MembraneJumpOP

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

◆ PairingLibraryCOP

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

◆ PairingLibraryOP

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

◆ PointList

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

some legacy code

◆ ResiduePairJumpCOP

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

◆ ResiduePairJumpOP

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

◆ ResiduePairJumpSetupCOP

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

◆ ResiduePairJumpSetupOP

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

◆ ResiduePairJumpSetupSingleCOP

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

◆ ResiduePairJumpSetupSingleOP

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

◆ ResiduePairJumpSingleCOP

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

◆ ResiduePairJumpSingleOP

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

◆ SameStrandCOP

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

◆ SameStrandOP

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

◆ StandardPairingLibraryCOP

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

◆ StandardPairingLibraryOP

Enumeration Type Documentation

◆ cstType


◆ dofType


Function Documentation

◆ assign_ss_dssp()

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

Assign secondary structure using DSSP.

References protocols::simple_filters::dssp().

◆ close_chainbreaks()

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 

◆ dis_get_coordinate_system()

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

Referenced by dis_RT_from_epos().

◆ dis_get_ncac() [1/2]

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

Referenced by dis_RT_from_epos().

◆ dis_get_ncac() [2/2]

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

◆ dis_RT_from_epos()

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

◆ dump_tags_()

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

◆ fill_tags_()

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

◆ generate_empty_jump_frame()

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

◆ generate_jump_frame()

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

◆ get_CA_vectors()

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

◆ get_coordinate_system()

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

Referenced by RT_from_epos().

◆ get_ncac() [1/2]

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

Referenced by RT_from_epos().

◆ get_ncac() [2/2]

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

◆ get_pairing_geometry()

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

◆ get_pleating()

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

References get_pairing_geometry(), and tr().

◆ operator<<() [1/4]

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

output operator

◆ operator<<() [2/4]

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

output operator

References protocols::hybridization::t.

◆ operator<<() [3/4]

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

◆ operator<<() [4/4]

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

◆ read_disulf_pairing_list()

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

add pairings in pairing_file to list "pairings"

References core::pose::motif::a(), protocols::match::upstream::b, and tr().

Referenced by read_pairing_list().

◆ read_pairing_list()

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

◆ remove_cut() [1/2]

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

◆ remove_cut() [2/2]

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

◆ RT_from_epos()

RT protocols::jumping::RT_from_epos ( FArray2A_float  Epos1,
FArray2A_float  Epos2 

◆ safe_secstruct()

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

◆ tr() [1/5]

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

◆ tr() [2/5]

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

◆ tr() [3/5]

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

◆ tr() [4/5]

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

◆ tr() [5/5]

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