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authorThomas White <taw@physics.org>2010-10-26 14:59:19 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:03 +0100
commit4384b499f48003b047454612732ec6b70b85199f (patch)
tree08a71b6a4228e0555eedaa4aa21fc64af6b844ba /src
parent08c67e2d0e430b57b692e7fb78fd8861f4ef0efa (diff)
Make PDB parser less horrendous
Diffstat (limited to 'src')
-rw-r--r--src/sfac.c76
1 files changed, 32 insertions, 44 deletions
diff --git a/src/sfac.c b/src/sfac.c
index b5ae7ace..c56097a4 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -15,6 +15,7 @@
#include <stdio.h>
#include <complex.h>
#include <string.h>
+#include <ctype.h>
#include "utils.h"
#include "sfac.h"
@@ -318,8 +319,6 @@ struct molecule *load_molecule(const char *filename)
char line[1024];
char *rval;
int i;
- int nbits;
- char **bits;
mol = malloc(sizeof(struct molecule));
if ( mol == NULL ) return NULL;
@@ -335,9 +334,14 @@ struct molecule *load_molecule(const char *filename)
do {
- char *el;
int j, r;
int done = 0;
+ char xs[8];
+ char ys[8];
+ char zs[8];
+ char occs[6];
+ char Bs[6];
+ char el[3];
float xf, yf, zf, occf, Bf;
double x, y, z, occ, B;
@@ -360,50 +364,36 @@ struct molecule *load_molecule(const char *filename)
/* Only interested in atoms */
if ( (strncmp(line, "HETATM", 6) != 0)
- && (strncmp(line, "ATOM", 4) != 0) ) continue;
+ && (strncmp(line, "ATOM ", 6) != 0) ) continue;
chomp(line);
- nbits = assplode(line, " ", &bits, ASSPLODE_NONE);
- if ( nbits == 0 ) continue;
-
- if ( nbits == 11 ) {
-
- /* Normal case- HETATM<space+>number<space+>stuff */
- r = sscanf(bits[5], "%f", &xf);
- r += sscanf(bits[6], "%f", &yf);
- r += sscanf(bits[7], "%f", &zf);
- r += sscanf(bits[8], "%f", &occf);
- r += sscanf(bits[9], "%f", &Bf);
- if ( r != 5 ) {
- STATUS("PDB read failed (%i)\n", r);
- for ( i=0; i<nbits; i++ ) free(bits[i]);
- continue;
- }
- el = strdup(bits[10]);
-
- } else if ( nbits == 10 ) {
-
- /* Squished case- HETATMnumber<space+>stuff */
- r = sscanf(bits[4], "%f", &xf);
- r += sscanf(bits[5], "%f", &yf);
- r += sscanf(bits[6], "%f", &zf);
- r += sscanf(bits[7], "%f", &occf);
- r += sscanf(bits[8], "%f", &Bf);
- if ( r != 5 ) {
- STATUS("PDB read failed (%i)\n", r);
- for ( i=0; i<nbits; i++ ) free(bits[i]);
- continue;
- }
- el = strdup(bits[9]);
-
- } else {
- STATUS("Unrecognised line in the PDB file (%i)\n",
- nbits);
+ if ( strlen(line) != 80 ) {
+ STATUS("Line does not have the correct length (%i):\n",
+ (int)strlen(line));
STATUS("'%s'\n", line);
- for ( i=0; i<nbits; i++ ) free(bits[i]);
continue;
}
- for ( i=0; i<nbits; i++ ) free(bits[i]);
+
+ /* Separate out fixed-width fields */
+ memcpy(xs, line+30, 5); xs[7] = '\0';
+ memcpy(ys, line+38, 5); ys[7] = '\0';
+ memcpy(zs, line+46, 5); zs[7] = '\0';
+ memcpy(occs, line+54, 5); occs[5] = '\0';
+ memcpy(Bs, line+60, 5); Bs[5] = '\0';
+ memcpy(el, line+76, 2); el[2] = '\0';
+
+ /* Convert fields */
+ r = sscanf(xs, "%f", &xf);
+ r += sscanf(ys, "%f", &yf);
+ r += sscanf(zs, "%f", &zf);
+ r += sscanf(occs, "%f", &occf);
+ r += sscanf(Bs, "%f", &Bf);
+ if ( el[0] == ' ' ) {
+ el[0] = el[1];
+ el[1] = '\0';
+ } else {
+ el[1] = tolower(el[1]);
+ }
/* Promote to double precision */
x = xf; y = yf; z = zf; occ = occf; B = Bf;
@@ -454,8 +444,6 @@ struct molecule *load_molecule(const char *filename)
}
- free(el);
-
} while ( rval != NULL );
fclose(fh);