protocols::loop_modeling Namespace Reference

Framework for loop structure prediction. More...

Namespaces
	refiners
	Algorithms for lowering loop region scores during sampling.
	samplers
	Algorithms for generating new loop conformations.
	utilities
	Generally useful loop-sampling meta-algorithms.

Classes
class	LoopBuilder
	Build loops from scratch. More...
class	LoopBuilderCreator
struct	ToolboxKeys
	Key names for data shared between loop movers. More...
class	LoopMover
	Base class for loop-sampling algorithms. More...
class	LoopProtocol
	Monte Carlo search for low energy loop conformations. More...
class	LoopProtocolCreator

Typedefs
typedef utility::pointer::shared_ptr< LoopBuilder >	LoopBuilderOP
typedef utility::pointer::shared_ptr< LoopBuilder const >	LoopBuilderCOP
typedef utility::pointer::shared_ptr< LoopMover >	LoopMoverOP
typedef utility::pointer::shared_ptr< LoopMover const >	LoopMoverCOP
typedef utility::vector1< LoopMoverOP >	LoopMoverOPs
typedef utility::vector1< LoopMoverCOP >	LoopMoverCOPs
typedef utility::pointer::shared_ptr< LoopProtocol >	LoopProtocolOP
typedef utility::pointer::shared_ptr< LoopProtocol const >	LoopProtocolCOP
typedef vector1< core::Size >	IndexList
typedef vector1< LoopMoverOP >	LoopMovers

Enumerations
enum	FoldTreeRequest { FTR_LOOPS_WITH_CUTS = 0x01 , FTR_SIMPLE_TREE = 0x02 , FTR_DONT_CARE = 0xFF }
	Represent the types of fold tree supported by LoopMover. More...

Functions
static basic::Tracer	TR ("protocols.loop_modeling.LoopBuilder")
static basic::Tracer	TR ("protocols.loop_modeling.LoopMover")
std::string	LoopMover_subelement_ct_name (std::string const &name)
FoldTreeRequest	operator| (FoldTreeRequest a, FoldTreeRequest b)
	Implement the bitwise or operator for fold tree requests. More...
FoldTreeRequest	operator& (FoldTreeRequest a, FoldTreeRequest b)
	Implement the bitwise and operator for fold tree requests. More...
static basic::Tracer	TR ("protocols.loop_modeling.LoopProtocol")

Detailed Description

Framework for loop structure prediction.

The most important classes in this namespace are LoopModeler, LoopProtocol and LoopMover. LoopMover provides an interface for loop sampling algorithms. Methods are provided for specifying which loops need to be sampled and for setting up a compatible fold tree. Some important LoopMover subclasses include RepackingRefiner, MinimizationRefiner, and KicMover. The LoopProtocol class provides a framework for combining any number of loop movers into a single Monte Carlo simulation. Aspects of the simulation like the number of iterations, the score function, and the temperature can be easily controlled. LoopModeler combines initial loop building, centroid refinement, and fullatom refinement into a complete loop modeling simulation. It also provides a lot of configurability, especially from rosetta scripts.

Below is an excerpt from protocols::relax::loop::LoopRelaxMover that shows some of the classes from this namespace in action. This code creates a protocol featuring KIC moves followed by a rotamer trials and local minimization. Full repacking is done once every 20 iterations. The number of iterations can be controlled from the command line, and a concise progress update will be reported after every iteration.

LoopProtocolOP protocol = new LoopProtocol;
 
core::Size repack_period = 20;
if (option[OptionKeys::loops::repack_period].user()) {
  repack_period = option[OptionKeys::loops::repack_period]();
}
 
protocol->add_mover(new KicMover);
protocol->add_mover(new RepackingRefiner(repack_period));
protocol->add_mover(new RotamerTrialsRefiner);
protocol->add_mover(new FullatomMinimizationRefiner);
 
core::Size outer_cycles = 3;
core::Size inner_cycles = 10 * loops->loop_size();
 
if (option[OptionKeys::loops::outer_cycles].user()) {
  outer_cycles = option[ OptionKeys::loops::outer_cycles ]();
}
if (option[OptionKeys::loops::max_inner_cycles].user()) {
  core::Size max_cycles = option[OptionKeys::loops::max_inner_cycles]();
  inner_cycles = std::max(inner_cycles, max_cycles);
}
if (option[OptionKeys::loops::fast]) {
  outer_cycles = 3;
  inner_cycles = 12;
}
 
protocol->set_loops(*loops);
protocol->set_score_function(fa_scorefxn_);
protocol->set_iterations(outer_cycles, inner_cycles, 2);
protocol->apply(pose);

Typedef Documentation

IndexList

typedef vector1<core::Size> protocols::loop_modeling::IndexList

LoopBuilderCOP

typedef utility::pointer::shared_ptr<LoopBuilder const> protocols::loop_modeling::LoopBuilderCOP

LoopBuilderOP

typedef utility::pointer::shared_ptr<LoopBuilder> protocols::loop_modeling::LoopBuilderOP

LoopMoverCOP

typedef utility::pointer::shared_ptr<LoopMover const> protocols::loop_modeling::LoopMoverCOP

LoopMoverCOPs

typedef utility::vector1<LoopMoverCOP> protocols::loop_modeling::LoopMoverCOPs

LoopMoverOP

typedef utility::pointer::shared_ptr<LoopMover> protocols::loop_modeling::LoopMoverOP

LoopMoverOPs

typedef utility::vector1<LoopMoverOP> protocols::loop_modeling::LoopMoverOPs

LoopMovers

typedef vector1<LoopMoverOP> protocols::loop_modeling::LoopMovers

LoopProtocolCOP

typedef utility::pointer::shared_ptr<LoopProtocol const> protocols::loop_modeling::LoopProtocolCOP

LoopProtocolOP

typedef utility::pointer::shared_ptr<LoopProtocol> protocols::loop_modeling::LoopProtocolOP

Enumeration Type Documentation

FoldTreeRequest

enum protocols::loop_modeling::FoldTreeRequest

Represent the types of fold tree supported by LoopMover.

This enum supports the bitwise and and or operators. Strictly speaking, this is an abuse of enum because both operators can return values that are not contained in the enum. But this design meets two key requirements. First, programmers have to work with the enumerated values. Second, bitwise logic can be used to easily combine flags and to determine how composite requests should be satisfied.

Enumerator
FTR_LOOPS_WITH_CUTS
FTR_SIMPLE_TREE
FTR_DONT_CARE

Function Documentation

LoopMover_subelement_ct_name()

std::string protocols::loop_modeling::LoopMover_subelement_ct_name

(

std::string const &

name

)

Referenced by protocols::loop_modeling::LoopMover::define_composition_schema().

operator&()

FoldTreeRequest protocols::loop_modeling::operator& ( FoldTreeRequest  a, FoldTreeRequest  b  )

inline

Implement the bitwise and operator for fold tree requests.

References core::pose::motif::a(), and protocols::match::upstream::b.

operator|()

FoldTreeRequest protocols::loop_modeling::operator| ( FoldTreeRequest  a, FoldTreeRequest  b  )

inline

Implement the bitwise or operator for fold tree requests.

References core::pose::motif::a(), and protocols::match::upstream::b.

TR() [1/3]

static basic::Tracer protocols::loop_modeling::TR ( "protocols.loop_modeling.LoopBuilder"  )

static

Referenced by protocols::loop_modeling::LoopBuilder::do_apply().

TR() [2/3]

static basic::Tracer protocols::loop_modeling::TR ( "protocols.loop_modeling.LoopMover"  )

static

TR() [3/3]

static basic::Tracer protocols::loop_modeling::TR ( "protocols.loop_modeling.LoopProtocol"  )

static

Referenced by protocols::loop_modeling::LoopProtocol::attempt_loop_move(), protocols::loop_modeling::LoopProtocol::do_apply(), protocols::loop_modeling::LoopProtocol::finish_protocol(), protocols::loop_modeling::LoopProtocol::ramp_temperature(), and protocols::loop_modeling::LoopProtocol::start_protocol().