PROFASI
Version 1.5
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Effective hydrophobic attraction between non-polar side chains. More...
#include <Hydrophobicity.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. | |
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 | |
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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. | |
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.
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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.