Clipper
cell.h
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 /* This code is derived from the 'dm' source code */
44 
45 
46 #ifndef CLIPPER_CELL
47 #define CLIPPER_CELL
48 
49 
50 #include "clipper_types.h"
51 
52 
53 namespace clipper
54 {
55 
56 
58 
64  {
65  public:
67  inline Metric_tensor() {}
68  Metric_tensor( const ftype& a, const ftype& b, const ftype& c, const ftype& alph, const ftype& beta, const ftype& gamm );
71  inline ftype lengthsq( const Vec3<>& v ) const
72  { return ( v[0]*(v[0]*m00 + v[1]*m01 + v[2]*m02) +
73  v[1]*(v[1]*m11 + v[2]*m12) + v[2]*(v[2]*m22) ); }
75  inline ftype lengthsq( const Vec3<int>& v ) const
76  { ftype h = ftype(v[0]); ftype k = ftype(v[1]); ftype l = ftype(v[2]);
77  return h*(h*m00 + k*m01 + l*m02) + k*(k*m11 + l*m12) + l*(l*m22); }
78 
79  String format() const;
80  private:
81  ftype m00, m11, m22, m01, m02, m12;
82  };
83 
84 
86 
91  class Cell_descr
92  {
93  public:
94  inline Cell_descr() {}
95  Cell_descr( const ftype& a, const ftype& b, const ftype& c,
97  const ftype& alpha=90.0f, const ftype& beta=90.0f,
98  const ftype& gamma=90.0f );
99  inline const ftype& a() const { return a_; }
100  inline const ftype& b() const { return b_; }
101  inline const ftype& c() const { return c_; }
102  inline const ftype& alpha() const { return alpha_; }
103  inline const ftype& beta() const { return beta_; }
104  inline const ftype& gamma() const { return gamma_; }
105  ftype alpha_deg() const;
106  ftype beta_deg() const;
107  ftype gamma_deg() const;
108  String format() const;
109 
110  protected:
111  ftype a_,b_,c_,alpha_,beta_,gamma_;
112  };
113 
114 
116 
121  class Cell : public Cell_descr
122  {
123  public:
125  inline Cell() { vol = 0.0; }
127  explicit Cell( const Cell_descr& cell_ ) { init( cell_ ); }
129  void init( const Cell_descr& cell_ );
130 
132  bool is_null() const;
133 
134  ftype a_star() const;
135  ftype b_star() const;
136  ftype c_star() const;
137  ftype alpha_star() const;
138  ftype beta_star() const;
139  ftype gamma_star() const;
140  // inherited functions listed for documentation purposes
141  //-- const ftype& a() const;
142  //-- const ftype& b() const;
143  //-- const ftype& c() const;
144  //-- const ftype& alpha() const;
145  //-- const ftype& beta() const;
146  //-- const ftype& gamma() const;
147  //-- ftype alpha_deg() const;
148  //-- ftype beta_deg() const;
149  //-- ftype gamma_deg() const;
150  //-- String format() const;
151 
153  inline const Cell_descr& descr() const { return (*this); }
155  inline const ftype& volume() const { return vol; }
157  bool equals( const Cell& other, const ftype tol=1.0 ) const;
159  inline const Mat33<>& matrix_orth() const { return orthmat; }
161  inline const Mat33<>& matrix_frac() const { return fracmat; }
163  inline const Metric_tensor& metric_real() const { return realmetric; }
165  inline const Metric_tensor& metric_reci() const { return recimetric; }
166 
167  void debug() const;
168 
169  private:
170  Cell_descr descr_;
171  ftype vol;
172  Mat33<> orthmat;
173  Mat33<> fracmat;
174  Metric_tensor realmetric;
175  Metric_tensor recimetric;
176  };
177 
178 
179 } // namespace clipper
180 
181 #endif
clipper::Cell_descr::Cell_descr
Cell_descr(const ftype &a, const ftype &b, const ftype &c, const ftype &alpha=90.0f, const ftype &beta=90.0f, const ftype &gamma=90.0f)
constructor: from cell parameters
Definition: cell.cpp:57
clipper::Cell::volume
const ftype & volume() const
return cell volume
Definition: cell.h:155
clipper
clipper::Mat33
3x3-matrix class
Definition: clipper_types.h:182
clipper::Cell::b_star
ftype b_star() const
get b*
Definition: cell.cpp:157
clipper::Cell::alpha_star
ftype alpha_star() const
get alpha*
Definition: cell.cpp:163
clipper::ftype
ftype64 ftype
ftype definition for floating point representation
Definition: clipper_precision.h:58
clipper::Metric_tensor::lengthsq
ftype lengthsq(const Vec3<> &v) const
apply metric to vector
Definition: cell.h:71
clipper::Cell
Cell object.
Definition: cell.h:121
clipper::Cell::a_star
ftype a_star() const
get a*
Definition: cell.cpp:154
clipper::Cell::metric_reci
const Metric_tensor & metric_reci() const
return reciprocal space metric tensor
Definition: cell.h:165
clipper::Metric_tensor::Metric_tensor
Metric_tensor(const ftype &a, const ftype &b, const ftype &c, const ftype &alph, const ftype &beta, const ftype &gamm)
constructor: takes parameters of normal or inverse cell
Definition: cell.cpp:93
clipper::Cell::is_null
bool is_null() const
test if object has been initialised
Definition: cell.cpp:151
clipper::Cell_descr
cell description (automatically converts to radians)
Definition: cell.h:91
clipper::Metric_tensor
Metric tensor.
Definition: cell.h:63
clipper::Cell_descr::gamma_deg
ftype gamma_deg() const
get gamma in degrees
Definition: cell.cpp:76
clipper::Cell::init
void init(const Cell_descr &cell_)
initialiser
Definition: cell.cpp:113
clipper::Cell::matrix_orth
const Mat33 & matrix_orth() const
return orthogonalisation matrix
Definition: cell.h:159
clipper::Cell::equals
bool equals(const Cell &other, const ftype tol=1.0) const
test equality with another cell
Definition: cell.cpp:181
clipper::String
String extension with simple parsing methods.
Definition: clipper_types.h:64
clipper::Metric_tensor::format
String format() const
return formatted String representation
Definition: cell.cpp:103
clipper::Cell_descr::alpha_deg
ftype alpha_deg() const
get alpha in degrees
Definition: cell.cpp:68
clipper::Cell_descr::beta_deg
ftype beta_deg() const
get alpha in degrees
Definition: cell.cpp:72
clipper::Vec3<>
clipper::Cell::metric_real
const Metric_tensor & metric_real() const
return real space metric tensor
Definition: cell.h:163
clipper::Metric_tensor::lengthsq
ftype lengthsq(const Vec3< int > &v) const
apply metric to int vector
Definition: cell.h:75
clipper::Cell::matrix_frac
const Mat33 & matrix_frac() const
return fractionalisation matrix
Definition: cell.h:161
clipper::Cell::gamma_star
ftype gamma_star() const
get gamma*
Definition: cell.cpp:171
clipper::Cell::Cell
Cell(const Cell_descr &cell_)
constructor: takes a Cell descriptor
Definition: cell.h:127
clipper::Cell::c_star
ftype c_star() const
get c*
Definition: cell.cpp:160
clipper::Cell::beta_star
ftype beta_star() const
get beta*
Definition: cell.cpp:167
clipper::Cell::descr
const Cell_descr & descr() const
return cell dimensions
Definition: cell.h:153
clipper::Cell::Cell
Cell()
null constructor: must initialise later
Definition: cell.h:125
clipper::Cell_descr::format
String format() const
return formatted String representation
Definition: cell.cpp:80