PROFASI  Version 1.5
Public Member Functions | List of all members
prf::HBMS Class Reference

The Backbone-Sidechain hydrogen bond term. More...

#include <HydrogenBond.hh>

Inheritance diagram for prf::HBMS:
Inheritance graph
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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.
 
- 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.
 

Additional Inherited Members

- Protected Member Functions inherited from prf::HydrogenBond
double hb_pair (Dipole &don, Dipole &acc, int excl1, int excl2)
 Bare hydrogen bond function between two dipoles.
 

Detailed Description

This class represents the hydrogen bonds between the NH and CO dipoles of the backbones with charged side chains of all proteins in the system. Only amino acids D, E, K and R make side-chain backbone hydrogen bonds in the model. The term is significantly weaker than the HBMM term. The implementation here takes care of the optimization of this energy term. For a side chain update on a charged side-chain, only the interaction of that side chain with all the backbones is recalculated, and compared with a backup matrix. When a backbone or rigid body update is made, interaction of all side chains in other protein objects with that backbone, as well as interactions of all side chains attached to that backbone with all other backbones, are recalculated.

Member Function Documentation

void prf::HBMS::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::HBMS::evaluate ( )
virtual

do a new ab initio calculation

Reimplemented from prf::Energy.

void prf::HBMS::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.


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

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2