Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
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  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 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 More...
 
class  SpecificGeometryLibrary
 
class  StandardDisulfPairingLibrary
 
class  StandardPairingLibrary
 

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

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)
 
std::ostream & operator<< (std::ostream &os, JumpSample const &t)
 output operator More...
 
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)
 
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 More...
 
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())
 

Variables

static
numeric::random::RandomGenerator 
RG (12345)
 
static basic::Tracer tr ("protocols.jumping")
 
static basic::Tracer tr ("protocols.jumping")
 
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)
 
static basic::Tracer tr ("protocols.jumping")
 
static basic::Tracer tr ("protocols.jumping")
 

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

References c.

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

References 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 
)
void protocols::jumping::get_coordinate_system ( numeric::xyzMatrix_double const &  p,
numeric::xyzMatrix_double m 
)
void protocols::jumping::get_ncac ( FArray2A_float  pos,
numeric::xyzMatrix_double p 
)

References c.

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

References c.

Referenced by RT_from_epos().

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, c, getline(), and o.

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 runtime_assert, and tr.

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

Variable Documentation

numeric::random::RandomGenerator protocols::jumping::RG(750107)
static
numeric::random::RandomGenerator protocols::jumping::RG(9238)
static
numeric::random::RandomGenerator protocols::jumping::RG(12345)
static
numeric::random::RandomGenerator protocols::jumping::RG(489134)
static
basic::Tracer protocols::jumping::tr("protocols.jumping.MembraneJump")
static
basic::Tracer protocols::jumping::tr("protocols.jumping")
static
basic::Tracer protocols::jumping::tr("protocols.jumping")
static
basic::Tracer protocols::jumping::tr("protocols.jumping")
static
basic::Tracer protocols::jumping::tr("protocols.jumping")
static