PROFASI
Version 1.5
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The Backbone-Sidechain hydrogen bond term. More...
#include <HydrogenBond.hh>
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. | |
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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. | |
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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. | |
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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 | |
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double | hb_pair (Dipole &don, Dipole &acc, int excl1, int excl2) |
Bare hydrogen bond function between two dipoles. | |
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.
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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.
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virtual |
do a new ab initio calculation
Reimplemented from prf::Energy.
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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.