Clipper
spacegroup.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:
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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
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26//L
27//L You can redistribute it and/or modify the library under the terms of
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43/* some code & data converted from CCP4 library symlib.f (various authors) */
44
45
46#ifndef CLIPPER_SPACEGROUP
47#define CLIPPER_SPACEGROUP
48
49
50#include "symop.h"
51#include "spacegroup_data.h"
52
53
54namespace clipper {
55
56 // forward definitions
57 class HKL;
58 class HKL_class;
59 class Coord_frac;
60
61
63
74 {
75 public:
76 enum TYPE { Hall, HM, XHM, Symops, Number, Unknown };
78 Spgr_descr();
80 explicit Spgr_descr( const String& symb, TYPE type = Unknown );
82 explicit Spgr_descr( const int& num );
84 int spacegroup_number() const;
86 String symbol_hall() const;
88 String symbol_hm() const;
90 String symbol_xhm() const;
92 String symbol_hm_ext() const;
94 static void set_preferred( const char& c );
95
97 class Symop_codes : public std::vector<Symop_code>
98 {
99 public:
101 void init_hall( const String& symb );
103 void init_symops( const String& symb );
105 Symop_codes expand() const;
115 Symop_codes laue_ops() const;
117 Symop_codes pgrp_ops() const;
123 Symop_codes product( const Symop_codes& ops2 ) const;
125 unsigned int hash() const;
126 };
127
129 explicit Spgr_descr( const Symop_codes& ops );
131 const Symop_codes& generator_ops() const { return generators_; }
133 const unsigned int& hash() const { return hash_; }
134
135 protected:
136 unsigned int hash_;
138
139 static char pref_12, pref_hr;
140 };
141
142
143 // ObjectCache data type
145 {
146 public:
147 typedef Spgr_descr Key;
148 Spgr_cacheobj( const Key& spgr_cachekey );
149 bool matches( const Key& spgr_cachekey ) const;
150 String format() const;
151 // data
153 int nsym, nsymn, nsymi, nsymc, nsymp;
154 int lgrp;
155 std::vector<Symop> symops;
156 std::vector<Isymop> isymops;
157 Vec3<> asu_min_, asu_max_;
158 static Mutex mutex;
159 };
160
161
163
172 class Spacegroup : public Spgr_descr
173 {
174 public:
176 enum TYPE { Null, P1 };
178 enum AXIS { A=0, B=1, C=2 };
182 explicit Spacegroup( TYPE type );
184 explicit Spacegroup( const Spgr_descr& spgr_descr );
186 void init( const Spgr_descr& spgr_descr );
187
189 bool is_null() const;
190
191 // methods
193 inline const Spgr_descr& descr() const { return (*this); }
195 inline const int& num_symops() const { return nsym; }
197 inline const int& num_primops() const { return num_primitive_symops(); }
199 inline const int& num_primitive_symops() const { return nsymp; }
201 inline const int& num_centering_symops() const { return nsymc; }
203 inline const int& num_inversion_symops() const { return nsymi; }
205 inline const int& num_primitive_noninversion_symops() const { return nsymn;}
207 inline const Symop& symop( const int& sym_no ) const
208 { return symops[sym_no]; }
210 inline const Symop& primitive_symop( const int& sym_no ) const
211 { return symops[sym_no]; }
213 inline const Symop& inversion_symop( const int& sym_no ) const
214 { return symops[nsymn*sym_no]; }
216 inline const Symop& centering_symop( const int& sym_no ) const
217 { return symops[nsymp*sym_no]; }
219 int order_of_symmetry_about_axis( const AXIS axis ) const;
220
222 HKL_class hkl_class( const HKL& hkl ) const;
224 bool recip_asu( const HKL& hkl ) const;
225
227 int product_op( const int& s1, int& s2 ) const;
229 int inverse_op( const int& s ) const;
230
232 Coord_frac asu_max() const;
234 Coord_frac asu_min() const;
235
238
239 // inherited functions listed for documentation purposes
240 //-- int spacegroup_number() const;
241 //-- String symbol_hall() const;
242 //-- String symbol_hm() const;
244 String symbol_laue() const;
245
247 static Spacegroup p1() { return Spacegroup( P1 ); }
249 static Spacegroup null() { return Spacegroup( Null ); }
250
251 void debug() const;
252
253 private:
255 const Symop* symops;
256 const Isymop* isymops;
257 data::ASUfn asufn;
258 int nsym, nsymn, nsymi, nsymc, nsymp;
259 };
260
261
262} // namespace clipper
263
264#endif
fractional (cell) coordinates
Definition: coords.h:343
reflection class
Definition: coords.h:87
reflection 'Miller' index
Definition: coords.h:146
Integerised symmetry matrix.
Definition: symop.h:109
Mutex class: used for locking and unlocking shared resources.
Definition: clipper_thread.h:64
ObjectCache reference class.
Definition: clipper_memory.h:155
Spacegroup object.
Definition: spacegroup.h:173
const Symop & centering_symop(const int &sym_no) const
get n'th centering symop (0...3 max)
Definition: spacegroup.h:216
int product_op(const int &s1, int &s2) const
get symop number corresponding to the product of two symops
Definition: spacegroup.cpp:922
const int & num_primitive_symops() const
get number of primitive symops (inc identity and inversion)
Definition: spacegroup.h:199
int inverse_op(const int &s) const
get symop number corresponding to the inverse of a symop
Definition: spacegroup.cpp:930
const Symop & primitive_symop(const int &sym_no) const
get n'th primitive symop (identical to symop(sym_no))
Definition: spacegroup.h:210
bool invariant_under_change_of_hand() const
test if change of hand preserves spacegroup
Definition: spacegroup.cpp:953
Coord_frac asu_min() const
get map ASU, lower bound
Definition: spacegroup.cpp:948
static Spacegroup null()
Return null spacegroup.
Definition: spacegroup.h:249
AXIS
enumeration for cell axes
Definition: spacegroup.h:178
HKL_class hkl_class(const HKL &hkl) const
get 'class' of reflection: multiplicity, allowed phase, absence
Definition: spacegroup.cpp:913
int order_of_symmetry_about_axis(const AXIS axis) const
get the order of rotational symmetry about a given axis
Definition: spacegroup.cpp:892
const int & num_primops() const
get number of primitive symops (identical to num_primitive_symops())
Definition: spacegroup.h:197
Spacegroup()
null constructor
Definition: spacegroup.h:180
TYPE
enumeration for fast construction of Null or P1 spacegroup
Definition: spacegroup.h:176
const int & num_primitive_noninversion_symops() const
get number of primitive non-inversion symops (inc identity)
Definition: spacegroup.h:205
Coord_frac asu_max() const
get map ASU, upper bound
Definition: spacegroup.cpp:941
const Symop & symop(const int &sym_no) const
get n'th symop
Definition: spacegroup.h:207
static Spacegroup p1()
Return P1 spacegroup.
Definition: spacegroup.h:247
bool is_null() const
test if object has been initialised
Definition: spacegroup.cpp:885
bool recip_asu(const HKL &hkl) const
test if hkl is in default reciprocal ASU
Definition: spacegroup.cpp:919
const int & num_centering_symops() const
get number of centering symops (inc identity)
Definition: spacegroup.h:201
const Spgr_descr & descr() const
get spacegroup description
Definition: spacegroup.h:193
const Symop & inversion_symop(const int &sym_no) const
get n'th inversion symop (0...1 max)
Definition: spacegroup.h:213
void init(const Spgr_descr &spgr_descr)
initialiser: from spacegroup description
Definition: spacegroup.cpp:867
const int & num_symops() const
get number of symops
Definition: spacegroup.h:195
String symbol_laue() const
return the Laue group symbol
Definition: spacegroup.cpp:965
const int & num_inversion_symops() const
get number of inversion symops (inc identity)
Definition: spacegroup.h:203
Definition: spacegroup.h:145
Key spgr_cachekey_
spacegroup cachekey
Definition: spacegroup.h:152
std::vector< Isymop > isymops
symmetry operators
Definition: spacegroup.h:156
Spgr_cacheobj(const Key &spgr_cachekey)
construct entry
Definition: spacegroup.cpp:777
static Mutex mutex
thread safety
Definition: spacegroup.h:158
std::vector< Symop > symops
symmetry operators
Definition: spacegroup.h:155
int nsymp
number of syms: total, primitive
Definition: spacegroup.h:153
bool matches(const Key &spgr_cachekey) const
compare entry
Definition: spacegroup.cpp:832
int lgrp
Laue group number.
Definition: spacegroup.h:154
String format() const
string description
Definition: spacegroup.cpp:835
Vec3 asu_max_
real space ASU
Definition: spacegroup.h:157
Vector of symop codes and associated methods.
Definition: spacegroup.h:98
Symop_codes product(const Symop_codes &ops2) const
return product of this (expanded) list by another (expanded) list
Definition: spacegroup.cpp:417
Symop_codes primitive_ops() const
return primitive incl inversion ops (by computation)
Definition: spacegroup.cpp:318
void init_symops(const String &symb)
initialise from symops
Definition: spacegroup.cpp:260
Symop_codes laue_ops() const
return Laue ops
Definition: spacegroup.cpp:342
Symop_codes expand() const
expand (incomplete) list of symops
Definition: spacegroup.cpp:268
void init_hall(const String &symb)
initialise from Hall symbol
Definition: spacegroup.cpp:93
unsigned int hash() const
return hash code of symop list
Definition: spacegroup.cpp:430
Symop_codes generator_ops() const
return minimal list of generator ops
Definition: spacegroup.cpp:374
Symop_codes centering_ops() const
return lattice centering ops (by computation)
Definition: spacegroup.cpp:332
Symop_codes inversion_ops() const
return inversion ops (by computation)
Definition: spacegroup.cpp:306
Symop_codes primitive_noninversion_ops() const
return primitive non-inversion ops (by computation)
Definition: spacegroup.cpp:293
Symop_codes pgrp_ops() const
return point group ops
Definition: spacegroup.cpp:352
Symop_codes patterson_ops() const
return Patterson ops
Definition: spacegroup.cpp:361
spacegroup description
Definition: spacegroup.h:74
Spgr_descr()
null constructor
Definition: spacegroup.cpp:459
String symbol_hm_ext() const
return the extension H-M symbol
Definition: spacegroup.cpp:636
String symbol_hall() const
return the Hall symbol
Definition: spacegroup.cpp:601
String symbol_hm() const
return the H-M symbol
Definition: spacegroup.cpp:611
int spacegroup_number() const
return the spacegroup number
Definition: spacegroup.cpp:591
const unsigned int & hash() const
return the hash code for the spacegroup
Definition: spacegroup.h:133
String symbol_xhm() const
return the extended H-M symbol
Definition: spacegroup.cpp:621
Symop_codes generators_
codes for symop generators
Definition: spacegroup.h:137
static char pref_hr
preferred origin and hex/romb symbols
Definition: spacegroup.h:139
const Symop_codes & generator_ops() const
return the generators for the spacegroup
Definition: spacegroup.h:131
unsigned int hash_
hash code of spacegroup
Definition: spacegroup.h:136
static void set_preferred(const char &c)
set preferred default spacegroup choice
Definition: spacegroup.cpp:658
String extension with simple parsing methods.
Definition: clipper_types.h:65
Crystallographic symmetry operator.
Definition: symop.h:93
3-vector class
Definition: clipper_types.h:106