};
-/* this is not very good,
- but these are only used in gmx_trjconv and gmx_editconv */
-static gmx_bool bWideFormat = FALSE;
#define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
-void set_pdb_wide_format(gmx_bool bSet)
-{
- bWideFormat = bSet;
-}
-
static void xlate_atomname_pdb2gmx(char *name)
{
int i, length;
gmx_conect conect, gmx_bool bTerSepChains)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
- char resnm[6], nm[6], pdbform[128], pukestring[100];
+ char resnm[6], nm[6], pukestring[100];
atom_id i, ii;
- int resind, resnr, type;
+ int resind, resnr;
+ enum PDB_record type;
unsigned char resic, ch;
+ char altloc;
real occup, bfac;
gmx_bool bOccup;
int nlongname = 0;
bromacs(pukestring, 99);
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : pukestring);
- if (bWideFormat)
- {
- fprintf(out, "REMARK This file does not adhere to the PDB standard\n");
- fprintf(out, "REMARK As a result of, some programs may not like it\n");
- }
if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
{
gmx_write_pdb_box(out, ePBC, box);
}
strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
+ resnm[sizeof(resnm)-1] = 0;
strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
+ nm[sizeof(nm)-1] = 0;
+
/* rename HG12 to 2HG1, etc. */
xlate_atomname_gmx2pdb(nm);
resnr = atoms->resinfo[resind].nr;
}
if (atoms->pdbinfo)
{
- type = atoms->pdbinfo[i].type;
+ type = (enum PDB_record)(atoms->pdbinfo[i].type);
+ altloc = atoms->pdbinfo[i].altloc;
+ if (!isalnum(altloc))
+ {
+ altloc = ' ';
+ }
occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
bfac = atoms->pdbinfo[i].bfac;
}
else
{
- type = 0;
- occup = 1.0;
- bfac = 0.0;
- }
- if (bWideFormat)
- {
- strcpy(pdbform,
- "%-6s%5u %-4.4s %3.3s %c%4d%c %10.5f%10.5f%10.5f%8.4f%8.4f %2s\n");
- }
- else
- {
- /* Check whether atomname is an element name */
- if ((strlen(nm) < 4) && (gmx_strcasecmp(nm, atoms->atom[i].elem) != 0))
- {
- strcpy(pdbform, get_pdbformat());
- }
- else
- {
- strcpy(pdbform, get_pdbformat4());
- if (strlen(nm) > 4)
- {
- int maxwln = 20;
- if (nlongname < maxwln)
- {
- fprintf(stderr, "WARNING: Writing out atom name (%s) longer than 4 characters to .pdb file\n", nm);
- }
- else if (nlongname == maxwln)
- {
- fprintf(stderr, "WARNING: More than %d long atom names, will not write more warnings\n", maxwln);
- }
- nlongname++;
- }
- }
- strcat(pdbform, "%6.2f%6.2f %2s\n");
+ type = epdbATOM;
+ occup = 1.0;
+ bfac = 0.0;
+ altloc = ' ';
}
- fprintf(out, pdbform, pdbtp[type], (i+1)%100000, nm, resnm, ch, resnr,
- (resic == '\0') ? ' ' : resic,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], occup, bfac, atoms->atom[i].elem);
+
+ gmx_fprintf_pdb_atomline(out,
+ type,
+ i+1,
+ nm,
+ altloc,
+ resnm,
+ ch,
+ resnr,
+ resic,
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
+ occup,
+ bfac,
+ atoms->atom[i].elem);
+
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
- fprintf(out, "ANISOU%5u %-4.4s%3.3s %c%4d%c %7d%7d%7d%7d%7d%7d\n",
+ fprintf(out, "ANISOU%5u %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
(i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
t_atom *atomn;
int j, k;
char nc = '\0';
- char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12];
+ char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
char xc[12], yc[12], zc[12], occup[12], bfac[12];
unsigned char resic;
char chainid;
}
bfac[k] = nc;
+ /* 10 blanks */
+ j += 10;
+
+ /* Element name */
+ for (k = 0; (k < 2); k++, j++)
+ {
+ elem[k] = line[j];
+ }
+ elem[k] = nc;
+ trim(elem);
+
if (atoms->atom)
{
atomn = &(atoms->atom[natom]);
atomn->m = 0.0;
atomn->q = 0.0;
atomn->atomnumber = atomnumber;
- atomn->elem[0] = '\0';
+ strncpy(atomn->elem, elem, 4);
}
x[natom][XX] = strtod(xc, NULL)*0.1;
x[natom][YY] = strtod(yc, NULL)*0.1;
return gc;
}
-const char* get_pdbformat()
+int
+gmx_fprintf_pdb_atomline(FILE * fp,
+ enum PDB_record record,
+ int atom_seq_number,
+ const char * atom_name,
+ char alternate_location,
+ const char * res_name,
+ char chain_id,
+ int res_seq_number,
+ char res_insertion_code,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor,
+ const char * element)
{
- static const char *pdbformat = "%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f";
- return pdbformat;
-}
+ char tmp_atomname[6], tmp_resname[6];
+ gmx_bool start_name_in_col13;
+ int n;
-const char* get_pdbformat4()
-{
- static const char *pdbformat4 = "%-6s%5u %-4.4s %3.3s %c%4d%c %8.3f%8.3f%8.3f";
- return pdbformat4;
+ if (record != epdbATOM && record != epdbHETATM)
+ {
+ gmx_fatal(FARGS, "Can only print PDB atom lines as ATOM or HETATM records");
+ }
+
+ /* Format atom name */
+ if (atom_name != NULL)
+ {
+ /* If the atom name is an element name with two chars, it should start already in column 13.
+ * Otherwise it should start in column 14, unless the name length is 4 chars.
+ */
+ if ( (element != NULL) && (strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
+ {
+ start_name_in_col13 = TRUE;
+ }
+ else
+ {
+ start_name_in_col13 = (strlen(atom_name) >= 4);
+ }
+ sprintf(tmp_atomname, start_name_in_col13 ? "" : " ");
+ strncat(tmp_atomname, atom_name, 4);
+ tmp_atomname[5] = '\0';
+ }
+ else
+ {
+ tmp_atomname[0] = '\0';
+ }
+
+ /* Format residue name */
+ strncpy(tmp_resname, (res_name != NULL) ? res_name : "", 4);
+ /* Make sure the string is terminated if strlen was > 4 */
+ tmp_resname[4] = '\0';
+ /* String is properly terminated, so now we can use strcat. By adding a
+ * space we can write it right-justified, and if the original name was
+ * three characters or less there will be a space added on the right side.
+ */
+ strcat(tmp_resname, " ");
+
+ /* Truncate integers so they fit */
+ atom_seq_number = atom_seq_number % 100000;
+ res_seq_number = res_seq_number % 10000;
+
+ n = fprintf(fp,
+ "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
+ pdbtp[record],
+ atom_seq_number,
+ tmp_atomname,
+ alternate_location,
+ tmp_resname,
+ chain_id,
+ res_seq_number,
+ res_insertion_code,
+ x, y, z,
+ occupancy,
+ b_factor,
+ (element != NULL) ? element : "");
+
+ return n;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff