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-rw-r--r--src/diffraction.c108
-rw-r--r--src/image.h20
-rw-r--r--src/sfac.c108
-rw-r--r--src/sfac.h22
4 files changed, 130 insertions, 128 deletions
diff --git a/src/diffraction.c b/src/diffraction.c
index de43690d..32601046 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -101,114 +101,6 @@ static double complex molecule_factor(struct molecule *mol, struct threevec q,
}
-/* Load PDB file into a memory format suitable for efficient(ish) structure
- * factor calculation */
-static struct molecule *load_molecule()
-{
- struct molecule *mol;
- FILE *fh;
- char line[1024];
- char *rval;
- int i;
-
- mol = malloc(sizeof(struct molecule));
- if ( mol == NULL ) return NULL;
- mol->n_species = 0;
-
- fh = fopen("molecule.pdb", "r");
- if ( fh == NULL ) {
- fprintf(stderr, "Couldn't open file\n");
- return NULL;
- }
-
- do {
-
- char el[4];
- int j, r;
- int done = 0;
- float x, y, z, occ, B;
- char *coords;
-
- rval = fgets(line, 1023, fh);
-
- /* Only interested in atoms */
- if ( strncmp(line, "HETATM", 6) != 0 ) continue;
-
- /* The following crimes against programming style
- * were brought to you by Wizbit Enterprises, Inc. */
- if ( line[76] == ' ' ) {
- el[0] = line[77];
- el[1] = '\0';
- } else {
- el[0] = line[76];
- el[1] = line[77];
- el[2] = '\0';
- }
-
- coords = line + 29;
- r = sscanf(coords, "%f %f %f %f %f", &x, &y, &z, &occ, &B);
- if ( r != 5 ) {
- fprintf(stderr, "WTF?\n");
- abort();
- }
-
- for ( j=0; j<mol->n_species; j++ ) {
-
- struct mol_species *spec;
- int n;
-
- spec = mol->species[j];
-
- if ( strcmp(spec->species, el) != 0 ) continue;
-
- n = mol->species[j]->n_atoms;
-
- spec->x[n] = x;
- spec->y[n] = y;
- spec->z[n] = z;
- spec->occ[n] = occ;
- spec->B[n] = B;
- mol->species[j]->n_atoms++;
-
- done = 1;
-
- }
-
- if ( !done ) {
-
- /* Need to create record for this species */
- struct mol_species *spec;
-
- spec = malloc(sizeof(struct mol_species));
-
- memcpy(spec->species, el, 4);
- spec->x[0] = x;
- spec->y[0] = y;
- spec->z[0] = z;
- spec->occ[0] = occ;
- spec->B[0] = B;
- spec->n_atoms = 1;
-
- mol->species[mol->n_species] = spec;
- mol->n_species++;
-
- }
-
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- printf("There are %i species\n", mol->n_species);
- for ( i=0; i<mol->n_species; i++ ) {
- printf("'%s': %i\n", mol->species[i]->species,
- mol->species[i]->n_atoms);
- }
-
- return mol;
-}
-
-
void get_diffraction(struct image *image, UnitCell *cell)
{
int x, y;
diff --git a/src/image.h b/src/image.h
index ec5a20d5..40e3e35e 100644
--- a/src/image.h
+++ b/src/image.h
@@ -57,26 +57,6 @@ struct threevec
};
-struct mol_species
-{
- char species[4]; /* Species name */
- int n_atoms; /* Number of atoms of this species */
-
- float x[32*1024];
- float y[32*1024];
- float z[32*1024];
- float occ[32*1024];
- float B[32*1024];
-};
-
-
-struct molecule
-{
- int n_species;
- struct mol_species *species[32];
-};
-
-
/* Structure describing an image */
struct image {
diff --git a/src/sfac.c b/src/sfac.c
index 4c3dabd3..342c9615 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -162,3 +162,111 @@ double complex get_sfac(const char *n, double s, double en)
return fq - fq0 + f1f2;
}
+
+
+/* Load PDB file into a memory format suitable for efficient(ish) structure
+ * factor calculation */
+struct molecule *load_molecule()
+{
+ struct molecule *mol;
+ FILE *fh;
+ char line[1024];
+ char *rval;
+ int i;
+
+ mol = malloc(sizeof(struct molecule));
+ if ( mol == NULL ) return NULL;
+ mol->n_species = 0;
+
+ fh = fopen("molecule.pdb", "r");
+ if ( fh == NULL ) {
+ fprintf(stderr, "Couldn't open file\n");
+ return NULL;
+ }
+
+ do {
+
+ char el[4];
+ int j, r;
+ int done = 0;
+ float x, y, z, occ, B;
+ char *coords;
+
+ rval = fgets(line, 1023, fh);
+
+ /* Only interested in atoms */
+ if ( strncmp(line, "HETATM", 6) != 0 ) continue;
+
+ /* The following crimes against programming style
+ * were brought to you by Wizbit Enterprises, Inc. */
+ if ( line[76] == ' ' ) {
+ el[0] = line[77];
+ el[1] = '\0';
+ } else {
+ el[0] = line[76];
+ el[1] = line[77];
+ el[2] = '\0';
+ }
+
+ coords = line + 29;
+ r = sscanf(coords, "%f %f %f %f %f", &x, &y, &z, &occ, &B);
+ if ( r != 5 ) {
+ fprintf(stderr, "WTF?\n");
+ abort();
+ }
+
+ for ( j=0; j<mol->n_species; j++ ) {
+
+ struct mol_species *spec;
+ int n;
+
+ spec = mol->species[j];
+
+ if ( strcmp(spec->species, el) != 0 ) continue;
+
+ n = mol->species[j]->n_atoms;
+
+ spec->x[n] = x;
+ spec->y[n] = y;
+ spec->z[n] = z;
+ spec->occ[n] = occ;
+ spec->B[n] = B;
+ mol->species[j]->n_atoms++;
+
+ done = 1;
+
+ }
+
+ if ( !done ) {
+
+ /* Need to create record for this species */
+ struct mol_species *spec;
+
+ spec = malloc(sizeof(struct mol_species));
+
+ memcpy(spec->species, el, 4);
+ spec->x[0] = x;
+ spec->y[0] = y;
+ spec->z[0] = z;
+ spec->occ[0] = occ;
+ spec->B[0] = B;
+ spec->n_atoms = 1;
+
+ mol->species[mol->n_species] = spec;
+ mol->n_species++;
+
+ }
+
+
+ } while ( rval != NULL );
+
+ fclose(fh);
+
+ printf("There are %i species\n", mol->n_species);
+ for ( i=0; i<mol->n_species; i++ ) {
+ printf("'%s': %i\n", mol->species[i]->species,
+ mol->species[i]->n_atoms);
+ }
+
+ return mol;
+}
diff --git a/src/sfac.h b/src/sfac.h
index afa84f84..81b90234 100644
--- a/src/sfac.h
+++ b/src/sfac.h
@@ -18,6 +18,28 @@
#include <complex.h>
+
+struct mol_species
+{
+ char species[4]; /* Species name */
+ int n_atoms; /* Number of atoms of this species */
+
+ float x[32*1024];
+ float y[32*1024];
+ float z[32*1024];
+ float occ[32*1024];
+ float B[32*1024];
+};
+
+
+struct molecule
+{
+ int n_species;
+ struct mol_species *species[32];
+};
+
+
extern double complex get_sfac(const char *n, double s, double en);
+extern struct molecule *load_molecule(void);
#endif /* SFAC_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-29 03:17:56 +0000