Clipper
ramachandran.h
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4//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
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43
44
45#ifndef CLIPPER_RAMACHANDRAN
46#define CLIPPER_RAMACHANDRAN
47
48
49#include "clipper_types.h"
50
51
52namespace clipper {
53
55
58 {
59 public:
61 void init( const int& size );
63 void accumulate( const ftype32 table[] );
65 void accumulate( const ftype& phi1, const ftype& phi2, ftype wgt = 1.0 );
67 void normalise();
69 ftype probability( const ftype& phi1, const ftype& phi2 ) const;
71 String format() const;
73 const ftype& data( const int& i, const int& j ) const
74 { return data_[n*i+j]; }
76 ftype& data( const int& i, const int& j )
77 { return data_[n*i+j]; }
78 private:
79 int n;
80 std::vector<ftype> data_;
81 };
82
83
85
93 class Ramachandran : private Prob_phi_2d
94 {
95 public:
97 enum TYPE { Gly, Pro, NonGlyPro, NonGly, All, Gly5, Pro5, NonGlyPro5, NonGly5, All5,
98 All2, Gly2, Pro2, PrePro2, IleVal2, NoGPIVpreP2 };
102 Ramachandran( TYPE type );
104 void init( TYPE type );
106 void set_thresholds( ftype prob_favored = 0.01,
107 ftype prob_allowed = 0.0005 );
109 ftype probability( const ftype& phi, const ftype& psi ) const
110 { return Prob_phi_2d::probability( phi, psi ); }
112 bool favored( const ftype& phi, const ftype& psi ) const
113 { return ( probability( phi, psi ) > p_favored ); }
115 bool allowed( const ftype& phi, const ftype& psi ) const
116 { return ( probability( phi, psi ) > p_allowed ); }
117 private:
118 ftype p_favored, p_allowed;
119 };
120
121
122} // namespace clipper
123
124
125#endif
2-d angular probability distibution class
Definition: ramachandran.h:58
const ftype & data(const int &i, const int &j) const
2d read access
Definition: ramachandran.h:73
void init(const int &size)
initialise: with sampling
Definition: ramachandran.cpp:37251
ftype probability(const ftype &phi1, const ftype &phi2) const
get probability for a particular pair of angles
Definition: ramachandran.cpp:37294
void normalise()
normalise to integrate to 1/(2pi)^2
Definition: ramachandran.cpp:37285
ftype & data(const int &i, const int &j)
2d write access
Definition: ramachandran.h:76
void accumulate(const ftype32 table[])
accumulate new table of samples to probability
Definition: ramachandran.cpp:37258
String format() const
formatted string representation (as C++ code)
Definition: ramachandran.cpp:37315
Ramachandran plot class.
Definition: ramachandran.h:94
ftype probability(const ftype &phi, const ftype &psi) const
get probability for a particular pair of angles
Definition: ramachandran.h:109
void init(TYPE type)
initialise: from standard plot
Definition: ramachandran.cpp:37341
bool allowed(const ftype &phi, const ftype &psi) const
test if a pair of angles are in the allowed region
Definition: ramachandran.h:115
TYPE
enumeration of built-in Ramachandran tables
Definition: ramachandran.h:97
Ramachandran()
null constructor
Definition: ramachandran.h:100
bool favored(const ftype &phi, const ftype &psi) const
test if a pair of angles are in the favored region
Definition: ramachandran.h:112
void set_thresholds(ftype prob_favored=0.01, ftype prob_allowed=0.0005)
change threshholds to different values
Definition: ramachandran.cpp:37432
String extension with simple parsing methods.
Definition: clipper_types.h:65
ftype64 ftype
ftype definition for floating point representation
Definition: clipper_precision.h:58