protocols::loop_modeling::openers Namespace Reference

Unused algorithms for created open loop conformations. More...

Classes
class	BondAngleOpener
class	IdealGeometryOpener
class	LoopOpener
class	NullOpener
class	OpenerCollection
class	RamachandranOpener

Typedefs
typedef owning_ptr < BondAngleOpener >	BondAngleOpenerOP
typedef owning_ptr < BondAngleOpener const >	BondAngleOpenerCOP
typedef owning_ptr < IdealGeometryOpener >	IdealGeometryOpenerOP
typedef owning_ptr < IdealGeometryOpener const >	IdealGeometryOpenerCOP
typedef owning_ptr< LoopOpener >	LoopOpenerOP
typedef owning_ptr< LoopOpener const >	LoopOpenerCOP
typedef utility::pointer::owning_ptr < NullOpener >	NullOpenerOP
typedef utility::pointer::owning_ptr < NullOpener const >	NullOpenerCOP
typedef owning_ptr < OpenerCollection >	OpenerCollectionOP
typedef owning_ptr < OpenerCollection const >	OpenerCollectionCOP
typedef owning_ptr < RamachandranOpener >	RamachandranOpenerOP
typedef owning_ptr < RamachandranOpener const >	RamachandranOpenerCOP

Detailed Description

Unused algorithms for created open loop conformations.

This namespace was originally intended to provide a general set of algorithms for sampling new backbone torsions. The idea is that these algorithms not concern themselves with whether or not the backbone was closed so that they could sample freely. Then an algorithm like KIC or CCD would be used to ensure closure.

The problem is that these methods ended up being too slow for kinematic closure, presumably because they were causing the AtomTree to recalculate its coordinates too often. (I'm not totally sure about that, though.) So instead, KIC uses custom perturber classes that operate directly on its internal matrix representation of the closure problem.

So these algorithms would only be used by CCD, but CCD has not yet been ported to the new loop modeling framework. For now, then, these algorithms are not being used.

Typedef Documentation

typedef owning_ptr<BondAngleOpener const> protocols::loop_modeling::openers::BondAngleOpenerCOP

typedef owning_ptr<BondAngleOpener> protocols::loop_modeling::openers::BondAngleOpenerOP

typedef owning_ptr<IdealGeometryOpener const> protocols::loop_modeling::openers::IdealGeometryOpenerCOP

typedef owning_ptr<IdealGeometryOpener> protocols::loop_modeling::openers::IdealGeometryOpenerOP

typedef owning_ptr<LoopOpener const> protocols::loop_modeling::openers::LoopOpenerCOP

typedef owning_ptr<LoopOpener> protocols::loop_modeling::openers::LoopOpenerOP

typedef utility::pointer::owning_ptr<NullOpener const> protocols::loop_modeling::openers::NullOpenerCOP

typedef utility::pointer::owning_ptr<NullOpener> protocols::loop_modeling::openers::NullOpenerOP

typedef owning_ptr<OpenerCollection const> protocols::loop_modeling::openers::OpenerCollectionCOP

typedef owning_ptr<OpenerCollection> protocols::loop_modeling::openers::OpenerCollectionOP

typedef owning_ptr<RamachandranOpener const> protocols::loop_modeling::openers::RamachandranOpenerCOP

typedef owning_ptr<RamachandranOpener> protocols::loop_modeling::openers::RamachandranOpenerOP