Conformational Updates

Conformational updates for proteins and related utilities. More...

Classes
class	prf::BGS
	Biased Gaussian Steps. More...
class	prf::Pivot
	Pivot move twists the protein about one backbone degree of freedom. More...
class	prf::Rot
	Rotation of a single side chain torsional degree of freedom. More...
class	prf::Rotation
	Rigid body rotation of a whole chain. More...
class	prf::Translation
	Rigid body translation of a whole chain. More...
class	prf::Update
	The base class for all conformational updates. More...

Detailed Description

These classes represent different ways to propose a new conformation of a protein chain during a Monte Carlo simulation. An update could be a single angle update, representing a certain kind of change in one of the degrees of freedom, or a concerted update of a series of angles. An update class should conform to the interface defined by the base class called Update. Any class that inherits from Update and provides sensible actions for the different virtual member functions of Update (by overriding the virtual functions) can be used in a Monte Carlo simulation with ProFASi. In fact, it is quite likely that if an update class provides the information that the virtual functions in the base class ask for, the energy classes of ProFASi will automatically know how to evaluate increments in energy due to the update in an optimized manner. This module also contains other entities related to conformational updates, such as probability calculators for such updates.