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/*
* 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"
#include "symmetry.h"
/* Number of bins for Luzzati plot */
#define NBINS (10)
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"
" -y, --symmetry=<sym> The symmetry of both the input files.\n"
"\n");
}
static void plot_luzzati(const double *ref1, const double *ref2,
ReflItemList *items, double scale, UnitCell *cell)
{
double num[NBINS];
double den[NBINS];
double rmin, rmax, rstep;
int i;
FILE *fh;
if ( cell == NULL ) {
ERROR("Need the unit cell to plot the Luzzati plot.\n");
return;
}
fh = fopen("luzzati.dat", "w");
if ( fh == NULL ) {
ERROR("Couldn't open 'luzzati.dat'\n");
return;
}
for ( i=0; i<NBINS; i++ ) {
num[i] = 0.0;
den[i] = 0.0;
}
rmin = +INFINITY;
rmax = 0.0;
for ( i=0; i<num_items(items); i++ ) {
struct refl_item *it;
signed int h, k, l;
double res;
it = get_item(items, i);
h = it->h; k = it->k; l = it->l;
res = 2.0*resolution(cell, h, k, l);
if ( res > rmax ) rmax = res;
if ( res < rmin ) rmin = res;
}
rstep = (rmax-rmin) / NBINS;
for ( i=0; i<num_items(items); i++ ) {
struct refl_item *it;
signed int h, k, l;
double res;
int bin;
double i1, i2;
it = get_item(items, i);
h = it->h; k = it->k; l = it->l;
res = 2.0*resolution(cell, h, k, l);
bin = (res-rmin)/rstep;
i1 = lookup_intensity(ref1, h, k, l);
i2 = scale * lookup_intensity(ref2, h, k, l);
num[bin] += pow(i1 - i2, 2.0);
den[bin] += pow(i1, 2.0);
}
for ( i=0; i<NBINS; i++ ) {
double r2, cen;
cen = rmin + rstep*i + rstep/2.0;
r2 = sqrt(num[i]/den[i]);
fprintf(fh, "%f %f\n", cen/1.0e9, r2*100.0);
}
fclose(fh);
}
int main(int argc, char *argv[])
{
int c;
double *ref1;
double *ref2;
double *ref2_transformed;
double *out;
UnitCell *cell;
char *outfile = NULL;
char *afile = NULL;
char *bfile = NULL;
char *sym = NULL;
double scale, scale_r2, R1, R2, Rdiff, pearson;
int i, ncom;
ReflItemList *i1, *i2, *icommon;
int config_luzzati = 0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"output", 1, NULL, 'o'},
{"symmetry", 1, NULL, 'y'},
{"luzzati", 0, &config_luzzati, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "ho:y:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'o' :
outfile = strdup(optarg);
break;
case 'y' :
sym = 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;
}
if ( sym == NULL ) {
sym = strdup("1");
}
afile = strdup(argv[optind++]);
bfile = strdup(argv[optind]);
cell = load_cell_from_pdb("molecule.pdb");
ref1 = new_list_intensity();
i1 = read_reflections(afile, ref1, NULL, NULL);
if ( i1 == NULL ) {
ERROR("Couldn't open file '%s'\n", afile);
return 1;
}
ref2 = new_list_intensity();
i2 = read_reflections(bfile, ref2, NULL, NULL);
if ( i2 == NULL ) {
ERROR("Couldn't open file '%s'\n", bfile);
return 1;
}
/* List for output scale factor map */
out = new_list_intensity();
/* Find common reflections (taking symmetry into account) */
icommon = new_items();
ref2_transformed = new_list_intensity();
for ( i=0; i<num_items(i1); i++ ) {
struct refl_item *it;
signed int h, k, l;
signed int he, ke, le;
double val1, val2;
it = get_item(i1, i);
h = it->h; k = it->k; l = it->l;
if ( !find_unique_equiv(i2, h, k, l, sym, &he, &ke, &le) ) {
continue;
}
val1 = lookup_intensity(ref1, h, k, l);
val2 = lookup_intensity(ref2, he, ke, le);
set_intensity(ref2_transformed, h, k, l, val2);
set_intensity(out, h, k, l, val1/val2);
add_item(icommon, h, k, l);
}
ncom = num_items(icommon);
STATUS("%i,%i reflections: %i in common\n",
num_items(i1), num_items(i2), ncom);
R1 = stat_r1(ref1, ref2_transformed, icommon, &scale);
STATUS("R1 = %5.4f %% (scale=%5.2e)\n", R1*100.0, scale);
R2 = stat_r2(ref1, ref2_transformed, icommon, &scale_r2);
STATUS("R2 = %5.4f %% (scale=%5.2e)\n", R2*100.0, scale_r2);
Rdiff = stat_rdiff(ref1, ref2_transformed, icommon, &scale);
STATUS("Rdiff = %5.4f %% (scale=%5.2e)\n", Rdiff*100.0, scale);
pearson = stat_pearson(ref1, ref2_transformed, icommon);
STATUS("Pearson r = %5.4f\n", pearson);
if ( config_luzzati ) {
plot_luzzati(ref1, ref2_transformed, icommon, scale_r2, cell);
}
if ( outfile != NULL ) {
write_reflections(outfile, icommon, out, NULL, NULL, cell);
}
return 0;
}
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