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protocols::minimization_packing Namespace Reference

Namespaces

 symmetry
 

Classes

class  BoltzmannRotamerMover
 
class  BoltzmannRotamerMoverCreator
 
class  ChainGroupDiscriminator
 
class  DisulfideOptimizationMover
 A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues. More...
 
class  DisulfideOptimizationMoverCreator
 
class  EnergyCutRotamerTrialsMinMover
 Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant. More...
 
class  EnergyCutRotamerTrialsMover
 
class  GreenPacker
 
class  GroupDiscriminator
 Interface class used to break a pose down into a set of component "groups" where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings. More...
 
class  MinimalRotamer
 
class  MinMover
 A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set. More...
 
class  MinMoverCreator
 
class  MinPackMover
 a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing. More...
 
class  MinPackMoverCreator
 
class  PackRotamersMover
 A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing. More...
 
class  PackRotamersMoverCreator
 
class  PackRotamersMoverLazy
 a mover that packs the side-chains using a rotamer library in a lazy fashion. More...
 
class  PackRotamersMoverLazyCreator
 
class  PertMinMover
 Random perturbation, followed by minimization. More...
 
class  PertMinMoverCreator
 
class  RepackSidechainsMover
 A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() More...
 
class  RepackSidechainsMoverCreator
 
class  RotamerizeMover
 a mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set. More...
 
class  RotamerTrialsMinMover
 
class  RotamerTrialsMinMoverCreator
 
class  RotamerTrialsMover
 
class  RotamerTrialsMoverCreator
 
class  SaneMinMover
 
class  SaneMinMoverCreator
 
class  SetReturningPackRotamersMover
 
class  TaskAwareMinMover
 
class  TaskAwareMinMoverCreator
 
class  UserDefinedGroupDiscriminator
 

Typedefs

typedef
utility::pointer::shared_ptr
< BoltzmannRotamerMover
BoltzmannRotamerMoverOP
 
typedef
utility::pointer::shared_ptr
< BoltzmannRotamerMover const > 
BoltzmannRotamerMoverCOP
 
typedef
utility::pointer::shared_ptr
< DisulfideOptimizationMover
DisulfideOptimizationMoverOP
 
typedef
utility::pointer::shared_ptr
< DisulfideOptimizationMover
const > 
DisulfideOptimizationMoverCOP
 
typedef
utility::pointer::shared_ptr
< MinimalRotamer
MinimalRotamerOP
 
typedef
utility::pointer::shared_ptr
< MinimalRotamer const > 
MinimalRotamerCOP
 
typedef
utility::pointer::shared_ptr
< GroupDiscriminator
GroupDiscriminatorOP
 
typedef
utility::pointer::shared_ptr
< GroupDiscriminator const > 
GroupDiscriminatorCOP
 
typedef
utility::pointer::shared_ptr
< UserDefinedGroupDiscriminator
UserDefinedGroupDiscriminatorOP
 
typedef
utility::pointer::shared_ptr
< GreenPacker
GreenPackerOP
 
typedef
utility::pointer::shared_ptr
< GreenPacker const > 
GreenPackerCOP
 
typedef
utility::pointer::shared_ptr
< MinMover
MinMoverOP
 
typedef
utility::pointer::shared_ptr
< MinMover const > 
MinMoverCOP
 
typedef
utility::pointer::shared_ptr
< MinPackMover
MinPackMoverOP
 
typedef
utility::pointer::shared_ptr
< MinPackMover const > 
MinPackMoverCOP
 
typedef
utility::pointer::shared_ptr
< PackRotamersMover
PackRotamersMoverOP
 
typedef
utility::pointer::shared_ptr
< PackRotamersMover const > 
PackRotamersMoverCOP
 
typedef
utility::pointer::shared_ptr
< PackRotamersMoverLazy
PackRotamersMoverLazyOP
 
typedef
utility::pointer::shared_ptr
< PackRotamersMoverLazy const > 
PackRotamersMoverLazyCOP
 
typedef
utility::pointer::shared_ptr
< PertMinMover
PertMinMoverOP
 
typedef
utility::pointer::shared_ptr
< PertMinMover const > 
PertMinMoverCOP
 
typedef
utility::pointer::shared_ptr
< RepackSidechainsMover
RepackSidechainsMoverOP
 
typedef
utility::pointer::shared_ptr
< RepackSidechainsMover const > 
RepackSidechainsMoverCOP
 
typedef
utility::pointer::shared_ptr
< RotamerizeMover
RotamerizeMoverOP
 
typedef
utility::pointer::shared_ptr
< RotamerizeMover const > 
RotamerizeMoverCOP
 
typedef
utility::pointer::shared_ptr
< RotamerTrialsMinMover
RotamerTrialsMinMoverOP
 
typedef
utility::pointer::shared_ptr
< RotamerTrialsMinMover const > 
RotamerTrialsMinMoverCOP
 
typedef
utility::pointer::shared_ptr
< EnergyCutRotamerTrialsMinMover
EnergyCutRotamerTrialsMinMoverOP
 
typedef
utility::pointer::shared_ptr
< EnergyCutRotamerTrialsMinMover
const > 
EnergyCutRotamerTrialsMinMoverCOP
 
typedef
utility::pointer::shared_ptr
< RotamerTrialsMover
RotamerTrialsMoverOP
 
typedef
utility::pointer::shared_ptr
< RotamerTrialsMover const > 
RotamerTrialsMoverCOP
 
typedef
utility::pointer::shared_ptr
< EnergyCutRotamerTrialsMover
EnergyCutRotamerTrialsMoverOP
 
typedef
utility::pointer::shared_ptr
< EnergyCutRotamerTrialsMover
const > 
EnergyCutRotamerTrialsMoverCOP
 
typedef
utility::pointer::shared_ptr
< SaneMinMover
SaneMinMoverOP
 
typedef
utility::pointer::shared_ptr
< SaneMinMover const > 
SaneMinMoverCOP
 
typedef
utility::pointer::shared_ptr
< SetReturningPackRotamersMover
SetReturningPackRotamersMoverOP
 
typedef
utility::pointer::shared_ptr
< SetReturningPackRotamersMover
const > 
SetReturningPackRotamersMoverCOP
 
typedef
utility::pointer::shared_ptr
< TaskAwareMinMover
TaskAwareMinMoverOP
 
typedef
utility::pointer::shared_ptr
< TaskAwareMinMover const > 
TaskAwareMinMoverCOP
 

Functions

std::ostream & operator<< (std::ostream &os, BoltzmannRotamerMover const &mover)
 
std::ostream & operator<< (std::ostream &os, DisulfideOptimizationMover const &mover)
 private methods /// More...
 
static basic::Tracer TR ("protocols.minimization_packing.GreenPacker")
 
static basic::Tracer TR ("protocols.minimization_packing.MinMover")
 
std::ostream & operator<< (std::ostream &os, MinMover const &mover)
 
static basic::Tracer TR ("protocols.minimization_packing.MinPackMover")
 
static basic::Tracer TR ("protocols.minimization_packing.PackRotamersMover")
 
std::ostream & operator<< (std::ostream &os, PackRotamersMover const &mover)
 
static basic::Tracer TR ("protocols.minimization_packing.PackRotamersMoverLazy")
 
std::ostream & operator<< (std::ostream &os, PertMinMover const &mover)
 
static basic::Tracer TR ("protocols.minimization_packing.RepackSidechainsMover")
 
static basic::Tracer TR ("protocols.moves.RotamerizeMover")
 
std::ostream & operator<< (std::ostream &os, RotamerTrialsMinMover const &mover)
 
std::ostream & operator<< (std::ostream &os, RotamerTrialsMover const &mover)
 
static basic::Tracer TR ("protocols.minimization_packing.SaneMinMover")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< GreenPacker const > protocols::minimization_packing::GreenPackerCOP
typedef utility::pointer::shared_ptr< GreenPacker > protocols::minimization_packing::GreenPackerOP
typedef utility::pointer::shared_ptr< GroupDiscriminator const > protocols::minimization_packing::GroupDiscriminatorCOP
typedef utility::pointer::shared_ptr< MinimalRotamer const > protocols::minimization_packing::MinimalRotamerCOP
typedef utility::pointer::shared_ptr< MinimalRotamer > protocols::minimization_packing::MinimalRotamerOP
typedef utility::pointer::shared_ptr< MinMover const > protocols::minimization_packing::MinMoverCOP
typedef utility::pointer::shared_ptr< MinMover > protocols::minimization_packing::MinMoverOP
typedef utility::pointer::shared_ptr< MinPackMover const > protocols::minimization_packing::MinPackMoverCOP
typedef utility::pointer::shared_ptr< MinPackMover > protocols::minimization_packing::MinPackMoverOP
typedef utility::pointer::shared_ptr< PackRotamersMover const > protocols::minimization_packing::PackRotamersMoverCOP
typedef utility::pointer::shared_ptr< PertMinMover const > protocols::minimization_packing::PertMinMoverCOP
typedef utility::pointer::shared_ptr< PertMinMover > protocols::minimization_packing::PertMinMoverOP
typedef utility::pointer::shared_ptr< RotamerizeMover const > protocols::minimization_packing::RotamerizeMoverCOP
typedef utility::pointer::shared_ptr< RotamerTrialsMover const > protocols::minimization_packing::RotamerTrialsMoverCOP
typedef utility::pointer::shared_ptr< SaneMinMover const > protocols::minimization_packing::SaneMinMoverCOP
typedef utility::pointer::shared_ptr< SaneMinMover > protocols::minimization_packing::SaneMinMoverOP
typedef utility::pointer::shared_ptr< TaskAwareMinMover const > protocols::minimization_packing::TaskAwareMinMoverCOP

Function Documentation

std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
PertMinMover const &  mover 
)
std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
RotamerTrialsMinMover const &  mover 
)
std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
RotamerTrialsMover const &  mover 
)
std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
DisulfideOptimizationMover const &  mover 
)
std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
PackRotamersMover const &  mover 
)
std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
BoltzmannRotamerMover const &  mover 
)
std::ostream & protocols::minimization_packing::operator<< ( std::ostream &  os,
MinMover const &  mover 
)
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.SaneMinMover"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.PackRotamersMoverLazy"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.RepackSidechainsMover"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.MinPackMover"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.moves.RotamerizeMover"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.GreenPacker"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.PackRotamersMover"  )
static
static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.MinMover"  )
static