Clipper
ramachandran.h
Go to the documentation of this file.
1 
4 //C Copyright (C) 2000-2006 Kevin Cowtan and University of York
5 //L
6 //L This library is free software and is distributed under the terms
7 //L and conditions of version 2.1 of the GNU Lesser General Public
8 //L Licence (LGPL) with the following additional clause:
9 //L
10 //L `You may also combine or link a "work that uses the Library" to
11 //L produce a work containing portions of the Library, and distribute
12 //L that work under terms of your choice, provided that you give
13 //L prominent notice with each copy of the work that the specified
14 //L version of the Library is used in it, and that you include or
15 //L provide public access to the complete corresponding
16 //L machine-readable source code for the Library including whatever
17 //L changes were used in the work. (i.e. If you make changes to the
18 //L Library you must distribute those, but you do not need to
19 //L distribute source or object code to those portions of the work
20 //L not covered by this licence.)'
21 //L
22 //L Note that this clause grants an additional right and does not impose
23 //L any additional restriction, and so does not affect compatibility
24 //L with the GNU General Public Licence (GPL). If you wish to negotiate
25 //L other terms, please contact the maintainer.
26 //L
27 //L You can redistribute it and/or modify the library under the terms of
28 //L the GNU Lesser General Public License as published by the Free Software
29 //L Foundation; either version 2.1 of the License, or (at your option) any
30 //L later version.
31 //L
32 //L This library is distributed in the hope that it will be useful, but
33 //L WITHOUT ANY WARRANTY; without even the implied warranty of
34 //L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
35 //L Lesser General Public License for more details.
36 //L
37 //L You should have received a copy of the CCP4 licence and/or GNU
38 //L Lesser General Public License along with this library; if not, write
39 //L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
40 //L The GNU Lesser General Public can also be obtained by writing to the
41 //L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
42 //L MA 02111-1307 USA
43 
44 
45 #ifndef CLIPPER_RAMACHANDRAN
46 #define CLIPPER_RAMACHANDRAN
47 
48 
49 #include "clipper_types.h"
50 
51 
52 namespace 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 };
101  Ramachandran( TYPE type );
103  void init( TYPE type );
105  void set_thresholds( ftype prob_favored = 0.01,
106  ftype prob_allowed = 0.0005 );
108  ftype probability( const ftype& phi, const ftype& psi ) const
109  { return Prob_phi_2d::probability( phi, psi ); }
111  bool favored( const ftype& phi, const ftype& psi ) const
112  { return ( probability( phi, psi ) > p_favored ); }
114  bool allowed( const ftype& phi, const ftype& psi ) const
115  { return ( probability( phi, psi ) > p_allowed ); }
116  private:
117  ftype p_favored, p_allowed;
118  };
119 
120 
121 } // namespace clipper
122 
123 
124 #endif
TYPE
enumeration of built-in Ramachandran tables
Definition: ramachandran.h:97
ftype & data(const int &i, const int &j)
2d write access
Definition: ramachandran.h:76
const ftype & data(const int &i, const int &j) const
2d read access
Definition: ramachandran.h:73
void accumulate(const ftype32 table[])
accumulate new table of samples to probability
Definition: ramachandran.cpp:392
bool favored(const ftype &phi, const ftype &psi) const
test if a pair of angles are in the favored region
Definition: ramachandran.h:111
2-d angular probability distibution class
Definition: ramachandran.h:57
ftype probability(const ftype &phi, const ftype &psi) const
get probability for a particular pair of angles
Definition: ramachandran.h:108
ftype64 ftype
ftype definition for floating point representation
Definition: clipper_precision.h:58
String format() const
formatted string representation (as C++ code)
Definition: ramachandran.cpp:449
bool allowed(const ftype &phi, const ftype &psi) const
test if a pair of angles are in the allowed region
Definition: ramachandran.h:114
String extension with simple parsing methods.
Definition: clipper_types.h:64
void normalise()
normalise to integrate to 1/(2pi)^2
Definition: ramachandran.cpp:419
ftype probability(const ftype &phi1, const ftype &phi2) const
get probability for a particular pair of angles
Definition: ramachandran.cpp:428
void set_thresholds(ftype prob_favored=0.01, ftype prob_allowed=0.0005)
change threshholds to different values
Definition: ramachandran.cpp:512
Ramachandran plot class.
Definition: ramachandran.h:93
void init(TYPE type)
initialise: from standard plot
Definition: ramachandran.cpp:475
Ramachandran()
null constructor
Definition: ramachandran.h:99
void init(const int &size)
initialise: with sampling
Definition: ramachandran.cpp:385