1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
|
/*
* compare_hkl.c
*
* Compare reflection lists
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include "utils.h"
#include "sfac.h"
#include "reflections.h"
#include "statistics.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options] <file1.hkl> <file2.hkl>\n\n", s);
printf(
"Compare intensity lists.\n"
"\n"
" -h, --help Display this help message.\n"
" -o, --output=<filename> Specify output filename for correction factor.\n"
"\n");
}
int main(int argc, char *argv[])
{
int c;
double *ref1;
double *ref2;
double *out;
UnitCell *cell;
char *outfile = NULL;
char *afile = NULL;
char *bfile = NULL;
signed int h, k, l;
double scale, R2, Rmerge;
unsigned int *c1;
unsigned int *c2;
int i;
int nc1, nc2, ncom;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"output", 1, NULL, 'o'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "ho:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'o' :
outfile = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( argc != (optind+2) ) {
ERROR("Please provide exactly two HKL files to compare.\n");
return 1;
}
afile = strdup(argv[optind++]);
bfile = strdup(argv[optind]);
cell = load_cell_from_pdb("molecule.pdb");
c1 = new_list_count();
ref1 = read_reflections(afile, c1, NULL);
if ( ref1 == NULL ) {
ERROR("Couldn't open file '%s'\n", afile);
return 1;
}
c2 = new_list_count();
ref2 = read_reflections(bfile, c2, NULL);
if ( ref2 == NULL ) {
ERROR("Couldn't open file '%s'\n", bfile);
return 1;
}
out = new_list_intensity();
/* Knock out the zero beam, in case it's present */
set_count(c1, 0, 0, 0, 0);
set_count(c2, 0, 0, 0, 0);
/* Divide by number of counts, since we're not interested in them */
divide_down(ref1, c1);
divide_down(ref2, c2);
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double i1, i2;
i1 = lookup_intensity(ref1, h, k, l);
i2 = lookup_intensity(ref2, h, k, l);
if ( (i1 != 0.0) && (i2 != 0.0) ) {
set_intensity(out, h, k, l, i1/i2);
}
}
}
}
nc1 = 0;
nc2 = 0;
ncom = 0;
for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
nc1 += c1[i];
nc2 += c2[i];
ncom += c1[i] && c2[i];
}
STATUS("%i,%i reflections: %i in common\n", nc1, nc2, ncom);
R2 = stat_r2(ref1, c1, ref2, c2, &scale);
STATUS("R2 = %5.4f %% (scale=%5.2e)\n", R2*100.0, scale);
Rmerge = stat_rmerge(ref1, c1, ref2, c2, &scale);
STATUS("Rmerge = %5.4f %% (scale=%5.2e)\n", Rmerge*100.0, scale);
if ( outfile != NULL ) {
write_reflections(outfile, NULL, out, NULL, 1, cell, 1);
}
return 0;
}
|
