/* This function is crap.
*/
static void
parse_pdb_data (molecule *m, const char *data, const char *filename, int line)
{
const char *s = data;
char *ss;
while (*s)
{
if ((!m->label || !*m->label) &&
(!strncmp (s, "HEADER", 6) || !strncmp (s, "COMPND", 6)))
{
char *name = calloc (1, 100);
char *n2 = name;
int L = strlen(s);
if (L > 99) L = 99;
strncpy (n2, s, L);
n2 += 7;
while (isspace(*n2)) n2++;
ss = strchr (n2, '\n');
if (ss) *ss = 0;
ss = strchr (n2, '\r');
if (ss) *ss = 0;
ss = n2+strlen(n2)-1;
while (isspace(*ss) && ss > n2)
*ss-- = 0;
if (strlen (n2) > 4 &&
!strcmp (n2 + strlen(n2) - 4, ".pdb"))
n2[strlen(n2)-4] = 0;
if (m->label) free ((char *) m->label);
m->label = strdup (n2);
free (name);
}
else if (!strncmp (s, "TITLE ", 6) ||
!strncmp (s, "HEADER", 6) ||
!strncmp (s, "COMPND", 6) ||
!strncmp (s, "AUTHOR", 6) ||
!strncmp (s, "REVDAT", 6) ||
!strncmp (s, "SOURCE", 6) ||
!strncmp (s, "EXPDTA", 6) ||
!strncmp (s, "JRNL ", 6) ||
!strncmp (s, "REMARK", 6) ||
!strncmp (s, "SEQRES", 6) ||
!strncmp (s, "HET ", 6) ||
!strncmp (s, "FORMUL", 6) ||
!strncmp (s, "CRYST1", 6) ||
!strncmp (s, "ORIGX1", 6) ||
!strncmp (s, "ORIGX2", 6) ||
!strncmp (s, "ORIGX3", 6) ||
!strncmp (s, "SCALE1", 6) ||
!strncmp (s, "SCALE2", 6) ||
!strncmp (s, "SCALE3", 6) ||
!strncmp (s, "MASTER", 6) ||
!strncmp (s, "KEYWDS", 6) ||
!strncmp (s, "DBREF ", 6) ||
!strncmp (s, "HETNAM", 6) ||
!strncmp (s, "HETSYN", 6) ||
!strncmp (s, "HELIX ", 6) ||
!strncmp (s, "LINK ", 6) ||
!strncmp (s, "MTRIX1", 6) ||
!strncmp (s, "MTRIX2", 6) ||
!strncmp (s, "MTRIX3", 6) ||
!strncmp (s, "SHEET ", 6) ||
!strncmp (s, "CISPEP", 6) ||
/*
!strncmp (s, "SEQADV", 6) ||
!strncmp (s, "SITE ", 5) ||
!strncmp (s, "FTNOTE", 6) ||
!strncmp (s, "MODEL ", 5) ||
!strncmp (s, "ENDMDL", 6) ||
!strncmp (s, "SPRSDE", 6) ||
!strncmp (s, "MODRES", 6) ||
*/
!strncmp (s, "GENERATED BY", 12) ||
!strncmp (s, "TER ", 4) ||
!strncmp (s, "END ", 4) ||
!strncmp (s, "TER\n", 4) ||
!strncmp (s, "END\n", 4) ||
!strncmp (s, "\n", 1))
/* ignored. */
;
else if (!strncmp (s, "ATOM ", 7))
{
int id;
const char *end = strchr (s, '\n');
int L = end - s;
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
if (1 != sscanf (s+7, " %d ", &id))
parse_error (filename, line, s);
/* Use the "atom name" field if that is all that is available. */
strncpy (name, s+12, 3);
/* But prefer the "element" field. */
if (L > 77 && !isspace(s[77])) {
/* fprintf(stderr, " \"%s\" -> ", name); */
name[0] = s[76];
name[1] = s[77];
name[2] = 0;
/* fprintf(stderr, "\"%s\"\n", name); */
}
while (isspace(*name)) name++;
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
*ss-- = 0;
ss = name + 1;
while(*ss)
{
*ss = tolower(*ss);
ss++;
}
if (3 != sscanf (s + 32, " %f %f %f ", &x, &y, &z))
parse_error (filename, line, s);
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
progname, filename, line,
id, name, x, y, z);
*/
push_atom (m, id, name, x, y, z);
}
else if (!strncmp (s, "HETATM ", 7))
{
int id;
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
if (1 != sscanf (s+7, " %d ", &id))
parse_error (filename, line, s);
strncpy (name, s+12, 3);
while (isspace(*name)) name++;
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
*ss-- = 0;
if (3 != sscanf (s + 30, " %f %f %f ", &x, &y, &z))
parse_error (filename, line, s);
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
progname, filename, line,
id, name, x, y, z);
*/
push_atom (m, id, name, x, y, z);
}
else if (!strncmp (s, "CONECT ", 7))
{
int atoms[11];
int i = sscanf (s + 8, " %d %d %d %d %d %d %d %d %d %d %d %d ",
&atoms[0], &atoms[1], &atoms[2], &atoms[3],
&atoms[4], &atoms[5], &atoms[6], &atoms[7],
&atoms[8], &atoms[9], &atoms[10], &atoms[11]);
int j;
for (j = 1; j < i; j++)
if (atoms[j] > 0)
{
/*
fprintf (stderr, "%s: %s: %d: bond: %d %d\n",
progname, filename, line, atoms[0], atoms[j]);
*/
push_bond (m, atoms[0], atoms[j]);
}
}
else
{
char *s1 = strdup (s);
for (ss = s1; *ss && *ss != '\n'; ss++)
;
*ss = 0;
fprintf (stderr, "%s: %s: %d: unrecognised line: %s\n",
progname, filename, line, s1);
}
while (*s && *s != '\n')
s++;
if (*s == '\n')
s++;
line++;
}
}
/* This function is crap.
*/
static void
parse_pdb_data (molecule *m, const char *data, const char *filename, int line)
{
const char *s = data;
char *ss;
while (*s)
{
if ((!m->label || !*m->label) &&
(!strncmp (s, "HEADER", 6) || !strncmp (s, "COMPND", 6)))
{
char *name = (char *) calloc (1, 100);
char *n2 = name;
int L = strlen(s);
if (L > 99) L = 99;
(void) strncpy(n2, s, L);
n2 += 7;
while (isspace((int) *n2)) n2++;
ss = strchr (n2, '\n');
if (ss) *ss = 0;
ss = strchr (n2, '\r');
if (ss) *ss = 0;
ss = n2 + strlen(n2)-1;
while (isspace((int) *ss) && ss > n2)
*ss-- = 0;
if (strlen(n2) > 4 &&
!strcmp (n2 + strlen(n2) - 4, ".pdb"))
n2[strlen(n2)-4] = 0;
if (m->label) free((char *) m->label);
m->label = (char *) strdup (n2);
free(name);
}
else if (!strncmp (s, "TITLE ", 6) ||
!strncmp (s, "HEADER", 6) ||
!strncmp (s, "COMPND", 6) ||
!strncmp (s, "AUTHOR", 6) ||
!strncmp (s, "REVDAT", 6) ||
!strncmp (s, "SOURCE", 6) ||
!strncmp (s, "EXPDTA", 6) ||
!strncmp (s, "JRNL ", 6) ||
!strncmp (s, "REMARK", 6) ||
!strncmp (s, "SEQRES", 6) ||
!strncmp (s, "HET ", 6) ||
!strncmp (s, "FORMUL", 6) ||
!strncmp (s, "CRYST1", 6) ||
!strncmp (s, "ORIGX1", 6) ||
!strncmp (s, "ORIGX2", 6) ||
!strncmp (s, "ORIGX3", 6) ||
!strncmp (s, "SCALE1", 6) ||
!strncmp (s, "SCALE2", 6) ||
!strncmp (s, "SCALE3", 6) ||
!strncmp (s, "MASTER", 6) ||
!strncmp (s, "KEYWDS", 6) ||
!strncmp (s, "DBREF ", 6) ||
!strncmp (s, "HETNAM", 6) ||
!strncmp (s, "HETSYN", 6) ||
!strncmp (s, "HELIX ", 6) ||
!strncmp (s, "LINK ", 6) ||
!strncmp (s, "MTRIX1", 6) ||
!strncmp (s, "MTRIX2", 6) ||
!strncmp (s, "MTRIX3", 6) ||
!strncmp (s, "SHEET ", 6) ||
!strncmp (s, "CISPEP", 6) ||
!strncmp (s, "GENERATED BY", 12) ||
!strncmp (s, "TER ", 4) ||
!strncmp (s, "END ", 4) ||
!strncmp (s, "TER\n", 4) ||
!strncmp (s, "END\n", 4) ||
!strncmp (s, "\n", 1))
/* ignored. */
;
else if (!strncmp (s, "ATOM ", 7))
{
int id;
/* PURIFY reports a cumulative potential memory leak on the next line */
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
(void) sscanf (s+7, " %d ", &id);
(void) strncpy (name, s+12, 3);
while (isspace((int) *name)) name++;
ss = name + strlen(name)-1;
while (isspace((int) *ss) && ss > name)
*ss-- = 0;
(void) sscanf (s + 32, " %f %f %f ", &x, &y, &z);
/*
(void) fprintf (stderr, "molecule: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
filename, line,
id, name, x, y, z);
*/
push_atom (m, id, name, x, y, z);
}
else if (!strncmp (s, "HETATM ", 7))
{
int id;
/* PURIFY reports a cumulative potential memory leak on the next line */
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
(void) sscanf (s+7, " %d ", &id);
(void) strncpy (name, s+12, 3);
while (isspace((int) *name)) name++;
ss = name + strlen(name)-1;
while (isspace((int) *ss) && ss > name)
*ss-- = 0;
(void) sscanf (s + 30, " %f %f %f ", &x, &y, &z);
/*
(void) fprintf (stderr, "molecule: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
filename, line,
id, name, x, y, z);
*/
push_atom (m, id, name, x, y, z);
}
else if (!strncmp (s, "CONECT ", 7))
{
int atoms[11];
int i = sscanf (s + 8, " %d %d %d %d %d %d %d %d %d %d %d %d ",
&atoms[0], &atoms[1], &atoms[2], &atoms[3],
&atoms[4], &atoms[5], &atoms[6], &atoms[7],
&atoms[8], &atoms[9], &atoms[10], &atoms[11]);
int j;
for (j = 1; j < i; j++)
if (atoms[j] > 0)
{
/*
(void) fprintf (stderr, "molecule: %s: %d: bond: %d %d\n",
filename, line, atoms[0], atoms[j]);
*/
push_bond (m, atoms[0], atoms[j]);
}
}
else
{
char *s1 = (char *) strdup (s);
for (ss = s1; *ss && *ss != '\n'; ss++)
;
*ss = 0;
(void) fprintf (stderr, "molecule: %s: %d: unrecognised line: %s\n",
filename, line, s1);
}
while (*s && *s != '\n')
s++;
if (*s == '\n')
s++;
line++;
}
}
