Clipper
Main Page
Related Pages
Namespaces
Classes
Files
File List
clipper
core
atomsf.h
Go to the documentation of this file.
1
5
//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
6
//L
7
//L This library is free software and is distributed under the terms
8
//L and conditions of version 2.1 of the GNU Lesser General Public
9
//L Licence (LGPL) with the following additional clause:
10
//L
11
//L `You may also combine or link a "work that uses the Library" to
12
//L produce a work containing portions of the Library, and distribute
13
//L that work under terms of your choice, provided that you give
14
//L prominent notice with each copy of the work that the specified
15
//L version of the Library is used in it, and that you include or
16
//L provide public access to the complete corresponding
17
//L machine-readable source code for the Library including whatever
18
//L changes were used in the work. (i.e. If you make changes to the
19
//L Library you must distribute those, but you do not need to
20
//L distribute source or object code to those portions of the work
21
//L not covered by this licence.)'
22
//L
23
//L Note that this clause grants an additional right and does not impose
24
//L any additional restriction, and so does not affect compatibility
25
//L with the GNU General Public Licence (GPL). If you wish to negotiate
26
//L other terms, please contact the maintainer.
27
//L
28
//L You can redistribute it and/or modify the library under the terms of
29
//L the GNU Lesser General Public License as published by the Free Software
30
//L Foundation; either version 2.1 of the License, or (at your option) any
31
//L later version.
32
//L
33
//L This library is distributed in the hope that it will be useful, but
34
//L WITHOUT ANY WARRANTY; without even the implied warranty of
35
//L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
36
//L Lesser General Public License for more details.
37
//L
38
//L You should have received a copy of the CCP4 licence and/or GNU
39
//L Lesser General Public License along with this library; if not, write
40
//L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
41
//L The GNU Lesser General Public can also be obtained by writing to the
42
//L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
43
//L MA 02111-1307 USA
44
45
46
#ifndef CLIPPER_ATOMSF
47
#define CLIPPER_ATOMSF
48
49
50
#include "coords.h"
51
52
53
namespace
clipper
54
{
55
57
72
class
AtomShapeFn
73
{
74
public
:
75
enum
TYPE { X, Y, Z, Uiso, Occ, U11, U22, U33, U12, U13, U23 };
77
AtomShapeFn
() {}
79
AtomShapeFn
(
const
Atom
& atom );
81
AtomShapeFn
(
const
Coord_orth
& xyz,
const
String
& element,
const
ftype
u_iso = 0.0,
const
ftype
occ = 1.0 );
83
AtomShapeFn
(
const
Coord_orth
& xyz,
const
String
& element,
const
U_aniso_orth
& u_aniso,
const
ftype
occ = 1.0 );
85
void
init
(
const
Atom
& atom );
87
void
init
(
const
Coord_orth
& xyz,
const
String
& element,
const
ftype
u_iso = 0.0,
const
ftype
occ = 1.0 );
89
void
init
(
const
Coord_orth
& xyz,
const
String
& element,
const
U_aniso_orth
& u_aniso,
const
ftype
occ = 1.0 );
90
92
ftype
f
(
const
Coord_reci_orth
& rfl )
const
;
94
ftype
rho
(
const
Coord_orth
& xyz )
const
;
95
97
bool
rho_grad
(
const
Coord_orth
& xyz,
ftype
&
rho
, std::vector<ftype>& grad )
const
;
99
bool
rho_curv
(
const
Coord_orth
& xyz,
ftype
&
rho
, std::vector<ftype>& grad,
Matrix<ftype>
& curv )
const
;
100
102
bool
rho_grad
(
const
Coord_orth
& xyz, std::vector<ftype>& grad )
const
;
103
105
ftype
f
(
const
ftype
& invresolsq )
const
;
107
ftype
rho
(
const
ftype
& rsq )
const
;
108
110
std::vector<TYPE>&
agarwal_params
() {
return
params; }
111
private
:
113
void
init
(
const
String
& element,
const
ftype
& u_iso );
114
// members
115
Coord_orth
coord_;
116
U_aniso_orth
u_aniso_;
117
ftype
u_iso_, occ_;
118
ftype
a[6], b[6];
119
ftype
aw[6], bw[6];
120
std::vector<Mat33sym<> > uaninv;
121
bool
is_iso;
122
std::vector<TYPE> params;
123
};
124
125
127
130
class
AtomSF
:
private
AtomShapeFn
131
{
132
public
:
133
AtomSF
(
const
String
& type,
const
ftype
u_iso = 0.0,
const
ftype
occ = 1.0 );
134
AtomSF
(
const
String
& type,
const
U_aniso_orth
& u_aniso,
const
ftype
occ = 1.0 );
135
void
init(
const
String
& type,
const
ftype
u_iso = 0.0,
const
ftype
occ = 1.0 );
136
void
init(
const
String
& type,
const
U_aniso_orth
& u_aniso,
const
ftype
occ = 1.0 );
137
ftype
f_iso(
const
ftype
& s )
const
;
138
ftype
f_aniso(
const
Coord_reci_orth
& rfl )
const
;
139
ftype
rho_iso(
const
ftype
& d2 )
const
;
140
ftype
rho_aniso(
const
Coord_orth
& uvw )
const
;
141
};
142
143
144
}
// namespace clipper
145
146
#endif
Generated on Fri Sep 6 2013 19:58:35 for Clipper by
1.8.4