Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
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
< JumpSetup
JumpSetupOP
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"
std::ostream & operator<< (std::ostream &out, DisulfPairing const &)
 list of pairings
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
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)
std::ostream & operator<< (std::ostream &os, SameStrand const &t)
 output operator
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.
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,
Pose open_pose,
protocols::checkpoint::CheckPointer checkpoint,
const std::string &  decoy_tag,
core::kinematics::FoldTree const &  final_fold_tree_in 
)
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::dis_get_coordinate_system ( numeric::xyzMatrix_double const &  p,
numeric::xyzMatrix_double &  m 
)

Referenced by dis_RT_from_epos().

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

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

output operator

References protocols::jumping::JumpSample::size().

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

output operator

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

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, core::pack::dunbrack::c, and make_table_of_pilot_apps::d.

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 
)
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]
static numeric::random::RandomGenerator protocols::jumping::RG ( 750107  ) [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]
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