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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

some legacy code

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 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 
)

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

Referenced by dis_RT_from_epos().

numeric::xyzMatrix_double protocols::jumping::dis_get_ncac ( FArray2A_float  pos)
RT protocols::jumping::dis_RT_from_epos ( FArray2A_float  Epos1,
FArray2A_float  Epos2 
)
void protocols::jumping::dump_tags_ ( FArray1D_int const &  tags,
Size  nres,
std::ostream &  out 
)
void protocols::jumping::fill_tags_ ( FArray1D_int &  tags,
Size  fill_pos,
int  tag,
Size  nres 
)
core::fragment::JumpingFrameOP protocols::jumping::generate_empty_jump_frame ( Size  startpos,
Size  endpos,
Size  length 
)
core::fragment::JumpingFrameOP protocols::jumping::generate_jump_frame ( Size  startpos,
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 
)

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

Referenced by RT_from_epos().

numeric::xyzMatrix_double protocols::jumping::get_ncac ( FArray2A_float  pos)
void protocols::jumping::get_pairing_geometry ( pose::Pose const &  pose,
Size const  res1,
Size const  res2,
Real orientation,
Real pleating1,
Real pleating2 
)
void protocols::jumping::get_pleating ( pose::Pose const &  pose,
Size const  pos1,
Size const  pos2,
Size orientation,
Size pleating 
)
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 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 
)
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 
)
bool protocols::jumping::remove_cut ( Size  cutpoint,
FoldTree &  new_fold_tree,
FoldTree const &  final_fold_tree 
)

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
static numeric::random::RandomGenerator protocols::jumping::RG ( 489134  )
static
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