prf::Hydrophobicity Class Reference

Effective hydrophobic attraction between non-polar side chains. More...

#include <Hydrophobicity.hh>

Inheritance diagram for prf::Hydrophobicity:

Public Member Functions
double	evaluate ()
double	deltaE (Update *)
	do a new delta calculation optimized for the given kind of update
void	Accept (Update *)
	Accept a proposed update.
void	rangeEstimate (double &x1, double &x2)
	Estimate a range in which values of this observable are expected.
double	contact_frac (int i, int j, double(*distf)(int, int))
	i and j refer to the list of hydrophobic residues in the whole system.
double	hp_contact_frac (int iaa, int jaa, double(*distf)(int, int))
	iaa and jaa refer to the ligand indices relative to the whole system
Public Member Functions inherited from prf::Energy
void	Connect (Population *pl)
	Connect the energy term with one population.
virtual void	set_pars (std::string pars)
	Set some adjustible parameters.
void	refresh ()
	Overrides the virtual member from the Observable class.
double	value ()
	return result from last calculation
double	deltaE ()
	return result from the last energy change calculation
double	delta (Update *)
	Quick estimate of the change in an Observable due to an update.
virtual double	deltaEwithlimit (Update *updt, double maxde)
	Calculate energy change for an update, but with a stop condition.
virtual void	Revert (Update *)
	Reject a proposed update.
int	init_obs ()
	All observables must implement one initialize routine.
Public Member Functions inherited from prf::Observable
void	set (std::string cmd)
	Give the object an instruction to process during initialization.
double	operator() ()
	Retrieve the value of the observable.
double	Value ()
	Retrieve the value of the observable.
void	disable_stats ()
	Stop collecting statistical data like averages and histograms.
void	enable_stats ()
	Start collecting statistical data like averages and histograms.
Public Member Functions inherited from prf::Named
	Named ()
	Create an object with name "unnamed".
	Named (const char *st)
	Create an object with name st given as a C string.
	Named (std::string st)
	Create an object with a name given as a string.
std::string	Name () const
	Retrive the name of an object.
void	Name (std::string gnm)
	Assign a new name to an object.

Detailed Description

This class represents the hydrophobicity interaction in the model. In its current version, hydrophobicity is a simple pair-wise additive potential. A degree of contact between two hydrophobic side chains is calculated based on the proximity of a pre-determined set of atoms from each side chain. This degree of contact is multiplied by a strength assigned to pairs of side chain, which are in rough correspondence with their size. Like other terms, the implementation of the class takes care of the optimization. Contribution from each pair of hydrophobic side-chains is saved in a contribution matrix. For each update, the affected contributions are determined, and reevaluated, and compared with the value stored in the matrix. Contributions from hydrophobic pairs that are nearest and second-nearest neighbours in sequence are supressed by factors 0.0 and 0.5 respectively.

Member Function Documentation

void prf::Hydrophobicity::Accept ( Update *  updt )

virtual

PROFASI uses many local contribution matrices and backup variables to quickly evaluate the change caused to any energy term by a given update. Those backup variables and the contribution matrices need to be kept in sync with the current system configuration. So, each energy class has an accept and a reject method, which are called when an update is accepted or rejected. What is done inside these functions depends on the energy term and optimization trick used therein.

Reimplemented from prf::Energy.

double prf::Hydrophobicity::evaluate ( )

virtual

do a new ab initio calculation

Reimplemented from prf::Energy.

void prf::Hydrophobicity::rangeEstimate ( double &  x1, double &  x2  )

virtual

The default is between 0 and 1. So, for observables with values always between 0 and 1, you need not over-write this virtual function. Sometimes the observable will have a different fixed range, determined by its definition. Sometimes the range can not be determined perfectly. In such a case, let this function just return something reasonable.

Reimplemented from prf::Energy.

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The documentation for this class was generated from the following files:

• model/Energy/Hydrophobicity.hh
• model/Energy/Hydrophobicity.cc