#include <OligoOrient.hh>
Inherits prf::Observable.
Inheritance diagram for prf::OligoOrient:
Public Member Functions | |
| void | refresh (int curT) |
| Necessary before an observable value is used. | |
| int | init_obs () |
| All observables must implement one initialize routine. | |
| void | setAngleCut (double x) |
| Angle cut-off below which to strands should be regarded as parallel. | |
| void | minHB (double mbnd) |
| Minimum energy of backbone-backbone hydrogen bonds. | |
| void | minBeta (double mbt) |
| Minimum beta strand content for each peptide. | |
| void | rangeEstimate (double &x1, double &x2) |
| Estimate a range in which values of this observable are expected. | |
The Observable makes no sense for single peptide runs, and it may not make sense to use it for every oligomerisation simulation. It was originally made for the study of the 7 residue peptide Abeta(16-22), but for longer systems, the alignment or otherwise of end-to-end vectors might mean much less.
Normally one is interested in the content of both parallel and anti-parallel pairs. So, this class actually finds both. But as an observable it only returns the number of parallel pairs in the function Value(). But value2() returns the anti-parallel pair content. To create an Observable object out of the number of anti-parallel pairs, a dummy class OligoNminus is provided below, which depends on this class to get its value.
| void OligoOrient::refresh | ( | int | curT | ) | [virtual] |
This is done because complex observables like RMSD are not evaluated at every step. A call to refresh() would make sure that the Observable has its most current value. The optional argument tindx was introduced in version 1.1 when management of histograms was relocated from ObsHandler class to the Observable class. The argument tells the Observable object about a "temperature index" which it can use to put the current data in the appropriate histogram block.
Reimplemented from prf::Observable.
| int OligoOrient::init_obs | ( | ) | [virtual] |
Even if it seems that one particular observable might need additional arguments during initialization, it is advantageous to have a uniform syntax for all of them. So, when additional arguments are needed, one should provide them in a separate function called before initialization, and then call init_obs without arguments. The name init_obs instead of a more natural "init" or "initialize" is because an Observable often inherits from other classes which represent its character more fundamentally. So, the names such as "init" are kept free for such base classes.
Reimplemented from prf::Observable.
| void prf::OligoOrient::setAngleCut | ( | double | x | ) | [inline] |
Should be liberal. The default is 30 degrees. Values are to be passed in radians, not degrees.
| void prf::OligoOrient::minHB | ( | double | mbnd | ) | [inline] |
Minimum energy of inter-chain backbone-backbone hydrogen bonds for a pair to be considered bonded in a dimer, or as a part of a larger oligomer. The default is 4.6, corresponding to 2-3 hydrogen bonds.
| void prf::OligoOrient::minBeta | ( | double | mbt | ) | [inline] |
Peptides with less beta strand content than what is provided here will not be considered in the calculations. If nothing is provided, the default value is 0.5.
| void OligoOrient::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::Observable.