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/*******************************************************************************
* *
* Viewmol *
* *
* R E A D P D B . C *
* *
* Copyright (c) Joerg-R. Hill, Andrew Dalke, October 2003 *
* *
********************************************************************************
*
* $Id: readpdb.c,v 1.3 2003/11/07 11:14:45 jrh Exp $
* $Log: readpdb.c,v $
* Revision 1.3 2003/11/07 11:14:45 jrh
* Release 2.4
*
* Revision 1.2 2000/12/10 15:37:08 jrh
* Release 2.3
*
* Revision 1.1 1999/05/24 01:29:21 jrh
* Initial revision
*
*/
#include<ctype.h>
#include<stdlib.h>
#include<stdio.h>
#include<string.h>
#define TRUE 1
#define FALSE 0
#define MAXLENLINE 132
int main(int, char **);
int get_pdb_fields(char *, char *, char *, char *, char *, char *, char *,
double *, double *, double *, double *, double *);
void get_pdb_coordinates(char *, double *, double *, double *, double *,
double *);
extern void eof(char *, char *, int);
int main(int argc, char **argv)
{
FILE *file;
double x, y, z, occup, beta;
int first=TRUE;
char line[MAXLENLINE], *word;
char name[5], resname[5], chain[2], segname[5], resid[5], insertion[2];
register int i;
register char *p;
if ((file=fopen(argv[1], "r")) == NULL) eof("noFile", argv[1], 1);
while (fgets(line, MAXLENLINE, file) != NULL)
{
word=strtok(line, " \t");
if (!strcmp(word, "COMPND"))
{
if ((word=strstr(&line[7], "MOLECULE")) != NULL)
{
printf("$title\n");
word=strchr(word, ' ')+1;
if ((p=strchr(word, ';')) != NULL) *p='\0';
printf("%s\n", word);
}
}
else if (!strcmp(word, "ATOM") || !strcmp(word, "HETATM"))
{
(void)get_pdb_fields(line, name, resname, chain, segname, resid,
insertion, &x, &y, &z, &occup, &beta);
if (first)
{
printf("$coord 1.0\n");
first=FALSE;
}
printf("%22.14f %22.14f %22.14f %s\n", x, y, z, name);
}
else if (!strcmp(word, "CRYST1"))
{
printf("$unitcell ");
i=0;
while ((word=strtok(NULL, " \t")) != NULL && i < 6)
{
printf("%s ", word);
i++;
}
printf("\n");
}
}
printf("$end\n");
fclose(file);
exit(0);
}
int get_pdb_fields(char *record, char *name, char *resname, char *chain,
char *segname, char *resid, char *insertion, double *x,
double *y, double *z, double *occup, double *beta)
{
/* Break a pdb ATOM record into its fields. The user must provide the
necessary space to store the atom name, residue name, and segment name.
Character strings will be null-terminated. Returns the atom serial number. */
int i,len, num;
/* get serial number */
if (record[6] >= 'A' && record[6] <= 'Z') {
/* If there are too many atoms, XPLOR uses 99998, 99999, A0000,
A0001, ... */
int base = ((int)(record[6] - 'A') + 10) * 100000;
sscanf(record + 6, "%d", &num);
num += base;
} else {
sscanf(record + 6,"%d",&num);
}
/* get atom name */
strncpy(name,record + 12, 2);
name[2]='\0';
if (name[0] == ' ' || isdigit(name[0]))
{
name[0]=name[1];
name[1]='\0';
}
name[1]=tolower(name[1]);
/* get residue name */
strncpy(resname,record + 17, 4);
resname[4] = '\0';
while((len = strlen(resname)) > 0 && resname[len-1] == ' ')
resname[len-1] = '\0';
while(len > 0 && resname[0] == ' ') {
for(i=0; i < len; i++) resname[i] = resname[i+1];
len--;
}
chain[0] = record[21];
chain[1] = 0;
/* get residue id number */
strncpy(resid,record + 22, 4);
resid[4] = '\0';
while((len = strlen(resid)) > 0 && resid[len-1] == ' ')
resid[len-1] = '\0';
while(len > 0 && resid[0] == ' ') {
for(i=0; i < len; i++) resid[i] = resid[i+1];
len--;
}
insertion[0] = record[26];
insertion[1] = 0;
/* get x, y, and z coordinates */
get_pdb_coordinates(record, x, y, z, occup, beta);
/* get segment name */
if(strlen(record) >= 73) {
strncpy(segname, record + 72, 4);
segname[4] = '\0';
while((len = strlen(segname)) > 0 && segname[len-1] == ' ')
segname[len-1] = '\0';
while(len > 0 && segname[0] == ' ') {
for(i=0; i < len; i++) segname[i] = segname[i+1];
len--;
}
} else {
strcpy(segname,"");
}
return num;
}
void get_pdb_coordinates(char *record, double *x, double *y, double *z,
double *occup, double *beta)
{
/* Extract the x,y, and z coordinates from the given ATOM record. */
char numstr[9];
/* get X, Y, and Z */
memset(numstr, 0, 9 * sizeof(char));
strncpy(numstr, record + 30, 8);
*x = atof(numstr);
memset(numstr, 0, 9 * sizeof(char));
strncpy(numstr, record + 38, 8);
*y = atof(numstr);
memset(numstr, 0, 9 * sizeof(char));
strncpy(numstr, record + 46, 8);
*z = atof(numstr);
memset(numstr, 0, 9 * sizeof(char));
strncpy(numstr, record + 54, 6);
*occup = atof(numstr);
memset(numstr, 0, 9 * sizeof(char));
strncpy(numstr, record + 60, 6);
*beta = atof(numstr);
}
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