Ramachandran plot class. More...
#include <ramachandran.h>
Public Types | |
| enum | TYPE { Gly, Pro, NonGlyPro, NonGly, All } |
| enumeration of built-in Ramachandran tables | |
Public Member Functions | |
| Ramachandran () | |
| null constructor | |
| Ramachandran (TYPE type) | |
| constructor: from standard plot More... | |
| void | init (TYPE type) |
| initialise: from standard plot More... | |
| void | set_thresholds (ftype prob_favored=0.01, ftype prob_allowed=0.0005) |
| change threshholds to different values More... | |
| ftype | probability (const ftype &phi, const ftype &psi) const |
| get probability for a particular pair of angles | |
| bool | favored (const ftype &phi, const ftype &psi) const |
| test if a pair of angles are in the favored region | |
| bool | allowed (const ftype &phi, const ftype &psi) const |
| test if a pair of angles are in the allowed region | |
Additional Inherited Members | |
 Private Member Functions inherited from clipper::Prob_phi_2d | |
| void | init (const int &size) |
| initialise: with sampling | |
| void | accumulate (const ftype32 table[]) |
| accumulate new table of samples to probability | |
| void | accumulate (const ftype &phi1, const ftype &phi2, ftype wgt=1.0) |
| accumulate new sample to probability More... | |
| void | normalise () |
| normalise to integrate to 1/(2pi)^2 More... | |
| ftype | probability (const ftype &phi1, const ftype &phi2) const |
| get probability for a particular pair of angles More... | |
| String | format () const |
| formatted string representation (as C++ code) | |
| const ftype & | data (const int &i, const int &j) const |
| 2d read access | |
| ftype & | data (const int &i, const int &j) |
| 2d write access | |
Detailed Description
Ramachandran plot class.
This class provides a reference Ramachandran plot for Gly, Pro, other, and combinations of those types of residues. The source data comes from the best residues from the 'top500' best-determined structures list of D. C. and J. S. Richardson, http://kinemage.biochem.duke.edu/index.html
The Ramachandran plot is normalised in inverse radians squared, so the mean value of a probability is 1/(2 pi)2.
Constructor & Destructor Documentation
| clipper::Ramachandran::Ramachandran | ( | TYPE | type) |
constructor: from standard plot
Construct a Ramachandran plot of a given type.
- Parameters
-
type The residue type of the plot. Options include: Ramachandran::Gly, Ramachandran::Pro, Ramachandran::NonGlyPro, Ramachandran::NonGly, Ramachandran::All
Member Function Documentation
| void clipper::Ramachandran::init | ( | TYPE | type) |
initialise: from standard plot
Construct a Ramachandran plot of a given type.
- Parameters
-
type The residue type of the plot. Options include: Ramachandran::Gly, Ramachandran::Pro, Ramachandran::NonGlyPro, Ramachandran::NonGly, Ramachandran::All
| void clipper::Ramachandran::set_thresholds | ( | ftype | prob_favored = 0.01, |
| ftype | prob_allowed = 0.0005 |
||
| ) |
change threshholds to different values
Set thresholds for favorable and allowed regions of the Ramachandran plot. The US spelling is used because it is the same length as 'allowed'. I should get out more. Sorry.
- Parameters
-
prob_favored The probability threshold for the favored region. prob_allowed The probability threshold for the allowed region.
The documentation for this class was generated from the following files:
- ramachandran.h
- ramachandran.cpp
