};
-/* 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;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
typedef struct gmx_conect_t *gmx_conect;
-/* THE pdb format (for ATOM/HETATOM lines) */
-const char* get_pdbformat(void);
-const char* get_pdbformat4(void);
-
/* Enumerated type for pdb records. The other entries are ignored
* when reading a pdb file
*/
-enum {
+enum PDB_record {
epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
epdbMODEL, epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK,
epdbCONECT, epdbNR
};
+/* Write a PDB line with an ATOM or HETATM record directly to a file pointer.
+ *
+ * Returns the number of characters printed.
+ */
+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);
+
/* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
enum {
U11, U22, U33, U12, U13, U23
};
-void set_pdb_wide_format(gmx_bool bSet);
-/* If bSet, use wider format for occupancy and bfactor */
-
void pdb_use_ter(gmx_bool bSet);
/* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
This function is fundamentally broken as far as thread-safety is concerned.*/
rvec *x;
real *b = NULL;
matrix box;
- char *resnm, *atnm, pdbform[STRLEN];
+ char *resnm, *atnm;
gmx_bool bPDB, b4D;
FILE *out;
}
if ( ( b4D || bSplit ) && bPDB)
{
- strcpy(pdbform, get_pdbformat());
- strcat(pdbform, "%8.4f%8.4f\n");
-
out = gmx_ffopen(threedplotfile, "w");
fprintf(out, "HEADER %s\n", str);
if (b4D)
fprintf(out, "TER\n");
j = 0;
}
- fprintf(out, pdbform, "ATOM", i+1, "C", "PRJ", ' ', j+1,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 10*b[i]);
+ gmx_fprintf_pdb_atomline(out, epdbATOM, i+1, "C", ' ', "PRJ", ' ', j+1, ' ',
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 10*b[i], "");
if (j > 0)
{
fprintf(out, "CONECT%5d%5d\n", i, i+1);
{
FILE *fp;
int nh[edMax];
- char buf[STRLEN];
int i, Dih, Xi;
real S2Max, S2Min;
x0 *= 10.0; /* nm -> angstrom */
y0 *= 10.0; /* nm -> angstrom */
z0 *= 10.0; /* nm -> angstrom */
- sprintf(buf, "%s%%6.f%%6.2f\n", get_pdbformat());
for (i = 0; (i < 10); i++)
{
- fprintf(fp, buf, "ATOM ", atoms->nr+1+i, "CA", "LEG", ' ',
- atoms->nres+1, ' ', x0, y0, z0+(1.2*i), 0.0, -0.1*i);
+ gmx_fprintf_pdb_atomline(fp, epdbATOM, atoms->nr+1+i, "CA", ' ', "LEG", ' ', atoms->nres+1, ' ',
+ x0, y0, z0+(1.2*i), 0.0, -0.1*i, "");
}
gmx_ffclose(fp);
}
for (i = 0; i < nat; i++)
{
- fprintf(out, get_pdbformat(), "ATOM", a0 + i, "C", "BOX", 'K' + i
- / NCUCVERT, r0 + i, 10 * vert[i][XX], 10 * vert[i][YY], 10
- * vert[i][ZZ]);
- fprintf(out, "\n");
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT, r0 + i, ' ',
+ 10*vert[i][XX], 10*vert[i][YY], 10*vert[i][ZZ], 1.0, 0.0, "");
}
edge = compact_unitcell_edges();
{
for (x = 0; x <= 1; x++)
{
- fprintf(out, get_pdbformat(), "ATOM", a0 + i, "C", "BOX", 'K' + i
- / 8, r0 + i, x * 10 * box[XX][XX],
- y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ]);
- fprintf(out, "\n");
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i/8, r0+i, ' ',
+ x * 10 * box[XX][XX], y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
i++;
}
}
out = gmx_ffopen(outfile, "w");
if (bMead)
{
- set_pdb_wide_format(TRUE);
fprintf(out, "REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out, "REMARK "
int start, int homenr, t_commrec *cr,
rvec x[], matrix box)
{
- char fname[STRLEN], format[STRLEN];
+ char fname[STRLEN];
FILE *out;
int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
gmx_domdec_t *dd;
{
sprintf(fname, "%s.pdb", fn);
}
- sprintf(format, "%s\n", get_pdbformat());
out = gmx_fio_fopen(fname, "w");
ii = i;
}
gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
- fprintf(out, format, "ATOM", (ii+1)%100000,
- anm, resnm, ' ', resnr%10000, ' ',
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ]);
+ gmx_fprintf_pdb_atomline(out, epdbATOM, ii+1, anm, ' ', resnm, ' ', resnr, ' ',
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 0.0, "");
}
fprintf(out, "TER\n");
gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox)
{
rvec grid_s[2], *grid_r = NULL, cx, r;
- char fname[STRLEN], format[STRLEN], buf[22];
+ char fname[STRLEN], buf[22];
FILE *out;
int a, i, d, z, y, x;
matrix tric;
}
}
sprintf(fname, "%s_%s.pdb", fn, gmx_step_str(step, buf));
- sprintf(format, "%s%s\n", get_pdbformat(), "%6.2f%6.2f");
out = gmx_fio_fopen(fname, "w");
gmx_write_pdb_box(out, dd->bScrewPBC ? epbcSCREW : epbcXYZ, box);
a = 1;
cx[YY] = grid_r[i*2+y][YY];
cx[ZZ] = grid_r[i*2+z][ZZ];
mvmul(tric, cx, r);
- fprintf(out, format, "ATOM", a++, "CA", "GLY", ' ', 1+i,
- ' ', 10*r[XX], 10*r[YY], 10*r[ZZ], 1.0, vol);
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a++, "CA", ' ', "GLY", ' ', i+1, ' ',
+ 10*r[XX], 10*r[YY], 10*r[ZZ], 1.0, vol, "");
}
}
}
gmx_mtop_t *mtop, t_commrec *cr,
int natoms, rvec x[], matrix box)
{
- char fname[STRLEN], format[STRLEN], format4[STRLEN], buf[22];
+ char fname[STRLEN], buf[22];
FILE *out;
int i, ii, resnr, c;
char *atomname, *resname;
sprintf(fname, "%s_%s_n%d.pdb", fn, gmx_step_str(step, buf), cr->sim_nodeid);
- sprintf(format, "%s%s\n", get_pdbformat(), "%6.2f%6.2f");
- sprintf(format4, "%s%s\n", get_pdbformat4(), "%6.2f%6.2f");
-
out = gmx_fio_fopen(fname, "w");
fprintf(out, "TITLE %s\n", title);
{
b = dd->comm->zones.n + 1;
}
- fprintf(out, strlen(atomname) < 4 ? format : format4,
- "ATOM", (ii+1)%100000,
- atomname, resname, ' ', resnr%10000, ' ',
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, b);
+ gmx_fprintf_pdb_atomline(out, epdbATOM, ii+1, atomname, ' ', resname, ' ', resnr, ' ',
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, b, "");
}
fprintf(out, "TER\n");
{
#ifdef DEBUG_PME
FILE *fp, *fp2;
- char fn[STRLEN], format[STRLEN];
+ char fn[STRLEN];
real val;
sprintf(fn, "pmegrid%d.pdb", pme->nodeid);
fp = gmx_ffopen(fn, "w");
sprintf(fn, "pmegrid%d.txt", pme->nodeid);
fp2 = gmx_ffopen(fn, "w");
- sprintf(format, "%s%s\n", pdbformat, "%6.2f%6.2f");
#endif
for (ix = 0; ix < local_fft_ndata[XX]; ix++)
val = 100*pmegrid[pmeidx];
if (pmegrid[pmeidx] != 0)
{
- fprintf(fp, format, "ATOM", pmeidx, "CA", "GLY", ' ', pmeidx, ' ',
- 5.0*ix, 5.0*iy, 5.0*iz, 1.0, val);
+ gmx_fprintf_pdb_atomline(fp, epdbATOM, pmeidx, "CA", ' ', "GLY", ' ', pmeidx, ' ',
+ 5.0*ix, 5.0*iy, 5.0*iz, 1.0, val, "");
}
if (pmegrid[pmeidx] != 0)
{
ATOM 7 CB RA B 1 20.000 30.000 0.000 1.50 0.00
ATOM 8 S1 RA B 1 20.000 40.000 0.000 1.50 0.30
ATOM 9 S2 RA B 1 30.000 10.000 0.000 2.00 0.30
-ATOM 13 CB RD B 2 40.000 10.000 0.000 1.00 0.00
-ATOM 14 S1 RD B 2 40.000 20.000 0.000 0.50 0.00
-ATOM 15 S2 RD B 2 40.000 30.000 0.000 0.00 0.00
+ATOM 13 CB A RD B 2 40.000 10.000 0.000 1.00 0.00
+ATOM 14 S1 A RD B 2 40.000 20.000 0.000 0.50 0.00
+ATOM 15 S2 A RD B 2 40.000 30.000 0.000 0.00 0.00
TER
ENDMDL
]]></String>
ATOM 10 CB RC B 1A 30.000 20.000 0.000 0.00 0.00
ATOM 11 S1 RC B 1A 30.000 30.000 0.000 0.00 0.00
ATOM 12 S2 RC B 1A 30.000 40.000 0.000 0.00 0.30
-ATOM 13 CB RD B 2 40.000 10.000 0.000 1.00 0.00
-ATOM 14 S1 RD B 2 40.000 20.000 0.000 0.50 0.00
-ATOM 15 S2 RD B 2 40.000 30.000 0.000 0.00 0.00
+ATOM 13 CB A RD B 2 40.000 10.000 0.000 1.00 0.00
+ATOM 14 S1 A RD B 2 40.000 20.000 0.000 0.50 0.00
+ATOM 15 S2 A RD B 2 40.000 30.000 0.000 0.00 0.00
TER
ENDMDL
]]></String>
ATOM 7 CB RA B 1 20.000 30.000 0.000 1.50 0.00
ATOM 8 S1 RA B 1 20.000 40.000 0.000 1.50 0.30
ATOM 9 S2 RA B 1 30.000 10.000 0.000 2.00 0.30
-ATOM 13 CB RD B 2 40.000 10.000 0.000 1.00 0.00
-ATOM 14 S1 RD B 2 40.000 20.000 0.000 0.50 0.00
+ATOM 13 CB A RD B 2 40.000 10.000 0.000 1.00 0.00
+ATOM 14 S1 A RD B 2 40.000 20.000 0.000 0.50 0.00
TER
ENDMDL
]]></String>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff