Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
protocols::abinitio Namespace Reference

Classes

class  PcaEvaluator
class  ShowViolation
class  ComputeTotalDistCst
class  Stage1Sampler
class  AbrelaxApplication
 application level code for Abrelax, Foldconstraints and JumpingFoldconstraints More...
class  AbrelaxMover
class  AllResiduesChanged
 (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values More...
class  hConvergenceCheck
class  ClassicAbinitio
class  ConstraintFragmentSampler
class  DomainAssembly
 insert fragments in a linker region. Very similar to what's in looprelax_main More...
class  DomainAssemblyCreator
class  DoubleLayerKinematicAbinitio
class  FoldConstraints
 extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles() More...
class  FragmentSampler
class  IterativeAbrelax
class  IterativeBase
class  IterativeCentroid
class  IterativeFullatom
class  JumpingFoldConstraints
class  KinematicAbinitio
class  JumpingFoldConstraintsWrapper
class  KinematicControl
class  CoordinateConstraintKC
class  KinematicTaskControl
class  LoopJumpFoldCst
class  MembraneAbinitio
class  PairingStatEntry
class  PairingStatistics
class  Protocol
class  ResolutionSwitcher
class  AlternativePairings
class  StrandConstraints
class  Template
class  TemplateJumpSetup
class  FixTemplateJumpSetup
class  StructureStore
class  Templates

Typedefs

typedef std::pair
< core::pose::Pose, core::Real
PoseWithScore
typedef
utility::pointer::owning_ptr
< AbrelaxMover
AbrelaxMoverOP
typedef
utility::pointer::owning_ptr
< AbrelaxMover const > 
AbrelaxMoverCOP
typedef
utility::pointer::owning_ptr
< hConvergenceCheck
hConvergenceCheckOP
typedef
utility::pointer::owning_ptr
< ClassicAbinitio
ClassicAbinitioOP
typedef
utility::pointer::owning_ptr
< ClassicAbinitio const > 
ClassicAbinitioCOP
typedef
utility::pointer::owning_ptr
< ConstraintFragmentSampler
ConstraintFragmentSamplerOP
typedef
utility::pointer::owning_ptr
< DoubleLayerKinematicAbinitio
DoubleLayerKinematicAbinitioOP
typedef
utility::pointer::owning_ptr
< DoubleLayerKinematicAbinitio
const > 
DoubleLayerKinematicAbinitioCOP
typedef
utility::pointer::owning_ptr
< FoldConstraints
FoldConstraintsOP
typedef
utility::pointer::owning_ptr
< FoldConstraints const > 
FoldConstraintsCOP
typedef
utility::pointer::owning_ptr
< FragmentSampler
FragmentSamplerOP
typedef
utility::pointer::owning_ptr
< FragmentSampler const > 
FragmentSamplerCOP
typedef
utility::pointer::owning_ptr
< KinematicAbinitio
KinematicAbinitioOP
typedef
utility::pointer::owning_ptr
< KinematicAbinitio const > 
KinematicAbinitioCOP
typedef
utility::pointer::owning_ptr
< KinematicControl
KinematicControlOP
typedef
utility::pointer::owning_ptr
< KinematicControl const > 
KinematicControlCOP
typedef
utility::pointer::owning_ptr
< KinematicTaskControl
KinematicTaskControlOP
typedef
utility::pointer::owning_ptr
< KinematicTaskControl const > 
KinematicTaskControlCOP
typedef
utility::pointer::owning_ptr
< LoopJumpFoldCst
LoopJumpFoldCstOP
typedef
utility::pointer::owning_ptr
< LoopJumpFoldCst const > 
LoopJumpFoldCstCOP
typedef
utility::pointer::owning_ptr
< MembraneAbinitio
MembraneAbinitioOP
typedef
utility::pointer::owning_ptr
< MembraneAbinitio const > 
MembraneAbinitioCOP
typedef
utility::pointer::owning_ptr
< PairingStatistics
PairingStatisticsOP
typedef
utility::pointer::owning_ptr
< PairingStatistics const > 
PairingStatisticsCOP
typedef utility::vector1
< PairingStatEntry
StatEntries
typedef
utility::pointer::owning_ptr
< Protocol
ProtocolOP
typedef
utility::pointer::owning_ptr
< Protocol const > 
ProtocolCOP
typedef
utility::pointer::owning_ptr
< ResolutionSwitcher
ResolutionSwitcherOP
typedef
utility::pointer::owning_ptr
< ResolutionSwitcher const > 
ResolutionSwitcherCOP
typedef utility::vector1< SizeSizeList
typedef
utility::pointer::owning_ptr
< Template
TemplateOP
typedef
utility::pointer::owning_ptr
< Template const > 
TemplateCOP
typedef
utility::pointer::owning_ptr
< TemplateJumpSetup
TemplateJumpSetupOP
typedef
utility::pointer::owning_ptr
< TemplateJumpSetup const > 
TemplateJumpSetupCOP
typedef
utility::pointer::owning_ptr
< Templates
TemplatesOP
typedef
utility::pointer::owning_ptr
< Templates const > 
TemplatesCOP

Enumerations

enum  StageID {
  ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3,
  STAGE_3a, STAGE_3b, STAGE_4, END_ABINITIO,
  LOOP_CLOSURE, SWITCH_TO_FULLATOM, RELAX, LAST_STAGE
}

Functions

bool sort_PoseWithScore (const PoseWithScore &left, const PoseWithScore &right)
void register_options_broker ()
 Registers options that are relevant to the application. This function must be called prior to Broker_main() or Loopbuild_Threading_main().
void common_setup ()
void Broker_main ()
 Initiates AbrelaxMover using the job distribution (jd2)
bool contains_stageid (utility::vector1< ClassicAbinitio::StageID > vec, ClassicAbinitio::StageID query)
static basic::Tracer TR ("protocols.protein_interface_design.movers.DomainAssembly")
Size noe_stage (Size total_res, Real factor)
bool contains_stageid (utility::vector1< abinitio::StageID > vec, abinitio::StageID query)
static
numeric::random::RandomGenerator 
RG (42089)
void get_core (toolbox::DecoySetEvaluation &eval, core::Real cutoff, loops::Loops &rigid)
void find_sampling_cuts (kinematics::FoldTree const &sampling, kinematics::FoldTree const &final, utility::vector1< Size > &sample_cuts)
static
numeric::random::RandomGenerator 
RG (5651234)
std::ostream & operator<< (std::ostream &out, PairingStatistics const &ps)
std::istream & operator>> (std::istream &is, PairingStatEntry &ps)
std::ostream & operator<< (std::ostream &out, StatEntries const &ps)
std::istream & operator>> (std::istream &is, StatEntries &pslist)
std::istream & operator>> (std::istream &is, PairingStatistics &ps)
std::ostream & operator<< (std::ostream &out, PairingStatEntry const &ps)
std::istream & operator<< (std::istream &, StatEntries &)
bool copy_side_chains (core::pose::Pose &pose, utility::vector1< bool > &needToRepack, core::pose::Pose const &fa_input_pose)
Size register_cutoff (5)
Size residue_cutoff (5)
std::ostream & operator<< (std::ostream &out, AlternativePairings const &alt_pairs)
std::ostream & operator<< (std::ostream &out, StrandConstraints const &st)
void dump_movemap (kinematics::MoveMap const &mm, Size nres, std::ostream &out)
static
numeric::random::RandomGenerator 
RG (1259812489)
static
numeric::random::RandomGenerator 
RG (12598234)
int run_boinc_debug ()

Typedef Documentation


Enumeration Type Documentation

Enumerator:
ALL_STAGES 
STAGE_1 
STAGE_2 
STAGE_3 
STAGE_3a 
STAGE_3b 
STAGE_4 
END_ABINITIO 
LOOP_CLOSURE 
SWITCH_TO_FULLATOM 
RELAX 
LAST_STAGE 

Function Documentation

void protocols::abinitio::Broker_main ( )
void protocols::abinitio::common_setup ( )
bool protocols::abinitio::contains_stageid ( utility::vector1< abinitio::StageID >  vec,
abinitio::StageID  query 
)
bool protocols::abinitio::contains_stageid ( utility::vector1< ClassicAbinitio::StageID >  vec,
ClassicAbinitio::StageID  query 
)
bool protocols::abinitio::copy_side_chains ( core::pose::Pose pose,
utility::vector1< bool > &  needToRepack,
core::pose::Pose const &  fa_input_pose 
)
void protocols::abinitio::dump_movemap ( kinematics::MoveMap const &  mm,
Size  nres,
std::ostream &  out 
)
void protocols::abinitio::find_sampling_cuts ( kinematics::FoldTree const &  sampling,
kinematics::FoldTree const &  final,
utility::vector1< Size > &  sample_cuts 
)
void protocols::abinitio::get_core ( toolbox::DecoySetEvaluation &  eval,
core::Real  cutoff,
loops::Loops &  rigid 
)
Size protocols::abinitio::noe_stage ( Size  total_res,
Real  factor 
)
std::ostream& protocols::abinitio::operator<< ( std::ostream &  out,
PairingStatEntry const &  ps 
) [inline]
std::istream& protocols::abinitio::operator<< ( std::istream &  ,
StatEntries &   
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
StrandConstraints const &  st 
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
AlternativePairings const &  alt_pairs 
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
PairingStatistics const &  ps 
)
std::ostream & protocols::abinitio::operator<< ( std::ostream &  out,
StatEntries const &  ps 
)
std::istream& protocols::abinitio::operator>> ( std::istream &  is,
StatEntries &  pslist 
)
std::istream& protocols::abinitio::operator>> ( std::istream &  is,
PairingStatistics &  ps 
)
std::istream& protocols::abinitio::operator>> ( std::istream &  is,
PairingStatEntry &  ps 
)

References tr().

Size protocols::abinitio::register_cutoff ( )
void protocols::abinitio::register_options_broker ( )

Registers options that are relevant to the application. This function must be called prior to Broker_main() or Loopbuild_Threading_main().

References core::pack::interaction_graph::debug.

Size protocols::abinitio::residue_cutoff ( )
static numeric::random::RandomGenerator protocols::abinitio::RG ( 12598234  ) [static]
static numeric::random::RandomGenerator protocols::abinitio::RG ( 5651234  ) [static]
static numeric::random::RandomGenerator protocols::abinitio::RG ( 1259812489  ) [static]
static numeric::random::RandomGenerator protocols::abinitio::RG ( 42089  ) [static]
int protocols::abinitio::run_boinc_debug ( )
bool protocols::abinitio::sort_PoseWithScore ( const PoseWithScore &  left,
const PoseWithScore &  right 
)
static basic::Tracer protocols::abinitio::TR ( "protocols.protein_interface_design.movers.DomainAssembly"  ) [static]
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