Rosetta Protocols  2014.35
Classes | Typedefs
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< LoopOpenerLoopOpenerOP
 
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