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protocols::jumping Namespace Reference

Classes

class  BaseDisulfPairingLibrary
 
class  BaseJumpSetup
 virtual base class: can create a set of jumps and cuts More...
 
class  BasePairingLibrary
 returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors. More...
 
class  ChainbreakDistFunc
 
class  DisulfPairing
 
class  DisulfPairingLibrary
 
class  DisulfTemplate
 
class  Interval
 two numbers, i.e., jump start end residue, or cut-regions... More...
 
class  JumpSample
 
class  JumpSelector
 
class  JumpSetup
 
class  JumpsFromAllPairings
 
class  MembraneJump
 
class  PairingLibrary
 
class  PairingTemplate
 
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  ResiduePairJump
 
class  ResiduePairJumpSetup
 
class  ResiduePairJumpSingle
 a single residue component of a ResiduePairJump class More...
 
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...
 
class  SpecificGeometryLibrary
 
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  StandardPairingLibrary
 This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn't be. More...
 

Typedefs

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

Enumerations

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

Functions

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...
 
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::shared_ptr< BaseJumpSetup const > protocols::jumping::BaseJumpSetupCOP
typedef utility::pointer::shared_ptr< BaseJumpSetup > protocols::jumping::BaseJumpSetupOP
typedef utility::pointer::shared_ptr< BasePairingLibrary const > protocols::jumping::BasePairingLibraryCOP
typedef utility::pointer::shared_ptr< BasePairingLibrary > protocols::jumping::BasePairingLibraryOP
typedef utility::vector1< jumping::Interval > protocols::jumping::JumpList
typedef utility::pointer::shared_ptr< JumpSelector const > protocols::jumping::JumpSelectorCOP
typedef utility::pointer::shared_ptr< JumpSelector > protocols::jumping::JumpSelectorOP
typedef utility::pointer::shared_ptr< JumpSetup const > protocols::jumping::JumpSetupCOP
typedef utility::pointer::shared_ptr< JumpSetup > protocols::jumping::JumpSetupOP
typedef utility::pointer::shared_ptr< MembraneJump > protocols::jumping::MembraneJumpOP
typedef utility::pointer::shared_ptr< PairingLibrary const > protocols::jumping::PairingLibraryCOP
typedef utility::pointer::shared_ptr< PairingLibrary > protocols::jumping::PairingLibraryOP
using protocols::jumping::PointList = typedef utility::vector1<PointPosition>

some legacy code

typedef utility::pointer::shared_ptr< ResiduePairJump const > protocols::jumping::ResiduePairJumpCOP
typedef utility::pointer::shared_ptr< ResiduePairJump > protocols::jumping::ResiduePairJumpOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetup const > protocols::jumping::ResiduePairJumpSetupCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetup > protocols::jumping::ResiduePairJumpSetupOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetupSingle const > protocols::jumping::ResiduePairJumpSetupSingleCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSetupSingle > protocols::jumping::ResiduePairJumpSetupSingleOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSingle const > protocols::jumping::ResiduePairJumpSingleCOP
typedef utility::pointer::shared_ptr< ResiduePairJumpSingle > protocols::jumping::ResiduePairJumpSingleOP
typedef utility::pointer::shared_ptr< SameStrand const > protocols::jumping::SameStrandCOP
typedef utility::pointer::shared_ptr< SameStrand > protocols::jumping::SameStrandOP
typedef utility::pointer::shared_ptr< StandardPairingLibrary const > protocols::jumping::StandardPairingLibraryCOP

Enumeration Type Documentation

Enumerator
disAB 
angleA 
angleB 
dihedralA 
dihedralAB 
dihedralB 
num_cstType 
Enumerator
rot1 
rot2 
cstJump 
num_dofType 

Function Documentation

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

Assign secondary structure using DSSP.

References protocols::simple_filters::dssp(), and 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 
)
void protocols::jumping::dis_get_coordinate_system ( numeric::xyzMatrix_double const &  p,
numeric::xyzMatrix_double &  m 
)

Referenced by dis_RT_from_epos().

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

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

Referenced by dis_RT_from_epos().

RT protocols::jumping::dis_RT_from_epos ( FArray2A_float  Epos1,
FArray2A_float  Epos2 
)
void protocols::jumping::dump_tags_ ( FArray1D_int const &  tags,
core::Size  nres,
std::ostream &  out 
)
void protocols::jumping::fill_tags_ ( FArray1D_int &  tags,
core::Size  fill_pos,
int  tag,
core::Size  nres 
)
core::fragment::JumpingFrameOP protocols::jumping::generate_empty_jump_frame ( core::Size  startpos,
core::Size  endpos,
core::Size  length 
)
core::fragment::JumpingFrameOP protocols::jumping::generate_jump_frame ( core::Size  startpos,
core::Size  endpos,
bool  bWithTorsion 
)
void protocols::jumping::get_CA_vectors ( PointList const &  ca1,
PointList const &  ca2,
Vector a,
Vector b,
Vector c 
)

Referenced by get_pairing_geometry().

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

Referenced by RT_from_epos().

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

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

Referenced by RT_from_epos().

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

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

output operator

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

std::ostream & protocols::jumping::operator<< ( std::ostream &  out,
DisulfPairingsList const &  p 
)
std::ostream & protocols::jumping::operator<< ( std::ostream &  os,
JumpSample const &  t 
)
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, core::pack::dunbrack::c, and tr().

Referenced by read_pairing_list().

void protocols::jumping::read_pairing_list ( std::string  disulf_pairing_file,
DisulfPairingsList &  disulf_pairings 
)
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 ( core::Size  cutpoint,
Pose pose,
FoldTree const &  final_fold_tree 
)
bool protocols::jumping::remove_cut ( core::Size  cutpoint,
FoldTree &  new_fold_tree,
FoldTree const &  final_fold_tree 
)

References tr().

RT protocols::jumping::RT_from_epos ( FArray2A_float  Epos1,
FArray2A_float  Epos2 
)
void protocols::jumping::safe_secstruct ( pose::Pose pose)
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