protocols::minimization_packing Namespace Reference

Namespaces
	symmetry

Classes
class	BoltzmannRotamerMover
class	BoltzmannRotamerMoverCreator
class	DisulfideOptimizationMover
	A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues. More...
class	DisulfideOptimizationMoverCreator
class	MinimalRotamer
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	UserDefinedGroupDiscriminator
class	ChainGroupDiscriminator
class	GreenPacker
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	EnergyCutRotamerTrialsMinMover
	Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant. More...
class	RotamerTrialsMinMoverCreator
class	RotamerTrialsMover
class	EnergyCutRotamerTrialsMover
class	RotamerTrialsMoverCreator
class	SaneMinMover
class	SaneMinMoverCreator
class	SetReturningPackRotamersMover
class	TaskAwareMinMover
class	TaskAwareMinMoverCreator

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

BoltzmannRotamerMoverCOP

typedef utility::pointer::shared_ptr< BoltzmannRotamerMover const > protocols::minimization_packing::BoltzmannRotamerMoverCOP

BoltzmannRotamerMoverOP

typedef utility::pointer::shared_ptr< BoltzmannRotamerMover > protocols::minimization_packing::BoltzmannRotamerMoverOP

DisulfideOptimizationMoverCOP

typedef utility::pointer::shared_ptr< DisulfideOptimizationMover const > protocols::minimization_packing::DisulfideOptimizationMoverCOP

DisulfideOptimizationMoverOP

typedef utility::pointer::shared_ptr< DisulfideOptimizationMover > protocols::minimization_packing::DisulfideOptimizationMoverOP

EnergyCutRotamerTrialsMinMoverCOP

typedef utility::pointer::shared_ptr< EnergyCutRotamerTrialsMinMover const > protocols::minimization_packing::EnergyCutRotamerTrialsMinMoverCOP

EnergyCutRotamerTrialsMinMoverOP

typedef utility::pointer::shared_ptr< EnergyCutRotamerTrialsMinMover > protocols::minimization_packing::EnergyCutRotamerTrialsMinMoverOP

EnergyCutRotamerTrialsMoverCOP

typedef utility::pointer::shared_ptr< EnergyCutRotamerTrialsMover const > protocols::minimization_packing::EnergyCutRotamerTrialsMoverCOP

EnergyCutRotamerTrialsMoverOP

typedef utility::pointer::shared_ptr< EnergyCutRotamerTrialsMover > protocols::minimization_packing::EnergyCutRotamerTrialsMoverOP

GreenPackerCOP

typedef utility::pointer::shared_ptr< GreenPacker const > protocols::minimization_packing::GreenPackerCOP

GreenPackerOP

typedef utility::pointer::shared_ptr< GreenPacker > protocols::minimization_packing::GreenPackerOP

GroupDiscriminatorCOP

typedef utility::pointer::shared_ptr< GroupDiscriminator const > protocols::minimization_packing::GroupDiscriminatorCOP

GroupDiscriminatorOP

typedef utility::pointer::shared_ptr< GroupDiscriminator > protocols::minimization_packing::GroupDiscriminatorOP

MinimalRotamerCOP

typedef utility::pointer::shared_ptr< MinimalRotamer const > protocols::minimization_packing::MinimalRotamerCOP

MinimalRotamerOP

typedef utility::pointer::shared_ptr< MinimalRotamer > protocols::minimization_packing::MinimalRotamerOP

MinMoverCOP

typedef utility::pointer::shared_ptr< MinMover const > protocols::minimization_packing::MinMoverCOP

MinMoverOP

typedef utility::pointer::shared_ptr< MinMover > protocols::minimization_packing::MinMoverOP

MinPackMoverCOP

typedef utility::pointer::shared_ptr< MinPackMover const > protocols::minimization_packing::MinPackMoverCOP

MinPackMoverOP

typedef utility::pointer::shared_ptr< MinPackMover > protocols::minimization_packing::MinPackMoverOP

PackRotamersMoverCOP

typedef utility::pointer::shared_ptr< PackRotamersMover const > protocols::minimization_packing::PackRotamersMoverCOP

PackRotamersMoverLazyCOP

typedef utility::pointer::shared_ptr< PackRotamersMoverLazy const > protocols::minimization_packing::PackRotamersMoverLazyCOP

PackRotamersMoverLazyOP

typedef utility::pointer::shared_ptr< PackRotamersMoverLazy > protocols::minimization_packing::PackRotamersMoverLazyOP

PackRotamersMoverOP

typedef utility::pointer::shared_ptr< PackRotamersMover > protocols::minimization_packing::PackRotamersMoverOP

PertMinMoverCOP

typedef utility::pointer::shared_ptr< PertMinMover const > protocols::minimization_packing::PertMinMoverCOP

PertMinMoverOP

typedef utility::pointer::shared_ptr< PertMinMover > protocols::minimization_packing::PertMinMoverOP

RepackSidechainsMoverCOP

typedef utility::pointer::shared_ptr< RepackSidechainsMover const > protocols::minimization_packing::RepackSidechainsMoverCOP

RepackSidechainsMoverOP

typedef utility::pointer::shared_ptr< RepackSidechainsMover > protocols::minimization_packing::RepackSidechainsMoverOP

RotamerizeMoverCOP

typedef utility::pointer::shared_ptr< RotamerizeMover const > protocols::minimization_packing::RotamerizeMoverCOP

RotamerizeMoverOP

typedef utility::pointer::shared_ptr< RotamerizeMover > protocols::minimization_packing::RotamerizeMoverOP

RotamerTrialsMinMoverCOP

typedef utility::pointer::shared_ptr< RotamerTrialsMinMover const > protocols::minimization_packing::RotamerTrialsMinMoverCOP

RotamerTrialsMinMoverOP

typedef utility::pointer::shared_ptr< RotamerTrialsMinMover > protocols::minimization_packing::RotamerTrialsMinMoverOP

RotamerTrialsMoverCOP

typedef utility::pointer::shared_ptr< RotamerTrialsMover const > protocols::minimization_packing::RotamerTrialsMoverCOP

RotamerTrialsMoverOP

typedef utility::pointer::shared_ptr< RotamerTrialsMover > protocols::minimization_packing::RotamerTrialsMoverOP

SaneMinMoverCOP

typedef utility::pointer::shared_ptr< SaneMinMover const > protocols::minimization_packing::SaneMinMoverCOP

SaneMinMoverOP

typedef utility::pointer::shared_ptr< SaneMinMover > protocols::minimization_packing::SaneMinMoverOP

SetReturningPackRotamersMoverCOP

typedef utility::pointer::shared_ptr< SetReturningPackRotamersMover const > protocols::minimization_packing::SetReturningPackRotamersMoverCOP

SetReturningPackRotamersMoverOP

typedef utility::pointer::shared_ptr< SetReturningPackRotamersMover > protocols::minimization_packing::SetReturningPackRotamersMoverOP

TaskAwareMinMoverCOP

typedef utility::pointer::shared_ptr< TaskAwareMinMover const > protocols::minimization_packing::TaskAwareMinMoverCOP

TaskAwareMinMoverOP

typedef utility::pointer::shared_ptr< TaskAwareMinMover > protocols::minimization_packing::TaskAwareMinMoverOP

UserDefinedGroupDiscriminatorOP

typedef utility::pointer::shared_ptr< UserDefinedGroupDiscriminator > protocols::minimization_packing::UserDefinedGroupDiscriminatorOP

Function Documentation

operator<<() [1/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		BoltzmannRotamerMover const &	mover
	)

References protocols::minimization_packing::BoltzmannRotamerMover::show().

operator<<() [2/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		DisulfideOptimizationMover const &	mover
	)

private methods ///

References protocols::minimization_packing::DisulfideOptimizationMover::show().

operator<<() [3/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		MinMover const &	mover
	)

References protocols::minimization_packing::MinMover::show().

operator<<() [4/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		PackRotamersMover const &	mover
	)

References protocols::minimization_packing::PackRotamersMover::show().

operator<<() [5/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		PertMinMover const &	mover
	)

References protocols::minimization_packing::PertMinMover::show().

operator<<() [6/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		RotamerTrialsMinMover const &	mover
	)

References protocols::minimization_packing::RotamerTrialsMinMover::show().

operator<<() [7/7]

std::ostream & protocols::minimization_packing::operator<<	(	std::ostream &	os,
		RotamerTrialsMover const &	mover
	)

References protocols::minimization_packing::RotamerTrialsMover::show().

TR() [1/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.GreenPacker"  )

static

Referenced by protocols::minimization_packing::BoltzmannRotamerMover::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::minimization_packing::PertMinMover::apply(), protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::minimization_packing::SaneMinMover::apply(), protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::minimization_packing::GreenPacker::apply(), protocols::minimization_packing::MinPackMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::minimization_packing::MinMover::apply_dof_tasks_to_movemap(), protocols::minimization_packing::GreenPacker::find_reference_and_current_rotamer_correspondence(), protocols::minimization_packing::PertMinMover::min(), protocols::minimization_packing::MinMover::minimize(), protocols::minimization_packing::MinMover::parse_dof_task_type(), protocols::minimization_packing::MinMover::parse_dof_tasks(), protocols::minimization_packing::MinMover::parse_movemap_factory(), protocols::minimization_packing::RotamerTrialsMinMover::parse_my_tag(), protocols::minimization_packing::DisulfideOptimizationMover::parse_my_tag(), protocols::minimization_packing::PackRotamersMover::setup(), and protocols::minimization_packing::RotamerizeMover::setup().

TR() [2/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.MinMover"  )

static

TR() [3/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.MinPackMover"  )

static

TR() [4/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.PackRotamersMover"  )

static

TR() [5/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.PackRotamersMoverLazy"  )

static

TR() [6/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.RepackSidechainsMover"  )

static

TR() [7/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.minimization_packing.SaneMinMover"  )

static

TR() [8/8]

static basic::Tracer protocols::minimization_packing::TR ( "protocols.moves.RotamerizeMover"  )

static