static void write_constr_pdb(const char *fn, const char *title,
gmx_mtop_t *mtop,
int start, int homenr, t_commrec *cr,
rvec x[], matrix box)
{
char fname[STRLEN], format[STRLEN];
FILE *out;
int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
gmx_domdec_t *dd;
char *anm, *resnm;
dd = NULL;
if (DOMAINDECOMP(cr))
{
dd = cr->dd;
dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
start = 0;
homenr = dd_ac1;
}
if (PAR(cr))
{
sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
}
else
{
sprintf(fname, "%s.pdb", fn);
}
sprintf(format, "%s\n", get_pdbformat());
out = gmx_fio_fopen(fname, "w");
fprintf(out, "TITLE %s\n", title);
gmx_write_pdb_box(out, -1, box);
for (i = start; i < start+homenr; i++)
{
if (dd != NULL)
{
if (i >= dd->nat_home && i < dd_ac0)
{
continue;
}
ii = dd->gatindex[i];
}
else
{
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]);
}
fprintf(out, "TER\n");
gmx_fio_fclose(out);
}
void write_pdbfile_indexed(FILE *out, const char *title,
t_atoms *atoms, rvec x[],
int ePBC, matrix box, char chainid,
int model_nr, int nindex, const int index[],
gmx_conect conect, gmx_bool bTerSepChains)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
char resnm[6], nm[6];
int i, ii;
int resind, resnr;
enum PDB_record type;
unsigned char resic, ch;
char altloc;
real occup, bfac;
gmx_bool bOccup;
int chainnum, lastchainnum;
gmx_residuetype_t*rt;
const char *p_restype;
const char *p_lastrestype;
gmx_residuetype_init(&rt);
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
{
gmx_write_pdb_box(out, ePBC, box);
}
if (atoms->pdbinfo)
{
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
*/
bOccup = TRUE;
for (ii = 0; (ii < nindex) && bOccup; ii++)
{
i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
else
{
bOccup = FALSE;
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
lastchainnum = -1;
p_restype = NULL;
for (ii = 0; ii < nindex; ii++)
{
i = index[ii];
resind = atoms->atom[i].resind;
chainnum = atoms->resinfo[resind].chainnum;
p_lastrestype = p_restype;
gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
/* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
{
/* Only add TER if the previous chain contained protein/DNA/RNA. */
if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
{
fprintf(out, "TER\n");
}
lastchainnum = chainnum;
}
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;
resic = atoms->resinfo[resind].ic;
if (chainid != ' ')
{
ch = chainid;
}
else
{
ch = atoms->resinfo[resind].chainid;
if (ch == 0)
{
ch = ' ';
}
}
if (resnr >= 10000)
{
resnr = resnr % 10000;
}
if (atoms->pdbinfo)
{
type = static_cast<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 = epdbATOM;
occup = 1.0;
bfac = 0.0;
altloc = ' ';
}
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%5d %-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],
atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
}
}
fprintf(out, "TER\n");
fprintf(out, "ENDMDL\n");
if (NULL != gc)
{
/* Write conect records */
for (i = 0; (i < gc->nconect); i++)
{
fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
}
}
gmx_residuetype_destroy(rt);
}
void write_pdbfile_indexed(FILE *out,char *title,
t_atoms *atoms,rvec x[],
int ePBC,matrix box,char chain,
int model_nr, atom_id nindex, atom_id index[])
{
char resnm[6],nm[6],ch,pdbform[128],pukestring[100];
atom_id i,ii;
int resnr,type;
real occup,bfac;
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);
}
if (atoms->pdbinfo) {
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
*/
bOccup = TRUE;
for (ii=0; (ii<nindex) && bOccup; ii++) {
i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
else
bOccup = FALSE;
if (!bTER)
fprintf(out,"MODEL %8d\n",model_nr>=0 ? model_nr : 1);
for (ii=0; ii<nindex; ii++) {
i=index[ii];
resnr=atoms->atom[i].resnr;
strcpy(resnm,*atoms->resname[resnr]);
strcpy(nm,*atoms->atomname[i]);
/* rename HG12 to 2HG1, etc. */
xlate_atomname_gmx2pdb(nm);
resnr++;
if (resnr>=10000)
resnr = resnr % 10000;
if (chain)
ch=chain;
else
if (atoms->atom[i].chain)
ch=atoms->atom[i].chain;
else
ch=' ';
if (atoms->pdbinfo) {
type = atoms->pdbinfo[i].type;
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 %10.5f%10.5f%10.5f%8.4f%8.4f\n");
else {
if (strlen(nm)<4)
strcpy(pdbform,pdbformat);
else {
strcpy(pdbform,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\n");
}
fprintf(out,pdbform,pdbtp[type],(i+1)%100000,nm,resnm,ch,resnr,
10*x[i][XX],10*x[i][YY],10*x[i][ZZ],occup,bfac);
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic) {
fprintf(out,"ANISOU%5u %-4.4s%3.3s %c%4d %7d%7d%7d%7d%7d%7d\n",
(i+1)%100000,nm,resnm,ch,resnr,
atoms->pdbinfo[i].uij[0],atoms->pdbinfo[i].uij[1],
atoms->pdbinfo[i].uij[2],atoms->pdbinfo[i].uij[3],
atoms->pdbinfo[i].uij[4],atoms->pdbinfo[i].uij[5]);
}
}
fprintf(out,"TER\n");
if (!bTER)
fprintf(out,"ENDMDL\n");
}
void write_pdbfile_indexed(FILE *out, const char *title,
t_atoms *atoms, rvec x[],
int ePBC, matrix box, char chainid,
int model_nr, atom_id nindex, atom_id index[],
gmx_conect conect, gmx_bool bTerSepChains)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
char resnm[6], nm[6], pdbform[128], pukestring[100];
atom_id i, ii;
int resind, resnr, type;
unsigned char resic, ch;
real occup, bfac;
gmx_bool bOccup;
int nlongname = 0;
int chainnum, lastchainnum;
int lastresind, lastchainresind;
gmx_residuetype_t rt;
const char *p_restype;
const char *p_lastrestype;
gmx_residuetype_init(&rt);
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);
}
if (atoms->pdbinfo)
{
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
*/
bOccup = TRUE;
for (ii = 0; (ii < nindex) && bOccup; ii++)
{
i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
else
{
bOccup = FALSE;
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
lastchainresind = -1;
lastchainnum = -1;
resind = -1;
p_restype = NULL;
for (ii = 0; ii < nindex; ii++)
{
i = index[ii];
lastresind = resind;
resind = atoms->atom[i].resind;
chainnum = atoms->resinfo[resind].chainnum;
p_lastrestype = p_restype;
gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
/* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
{
/* Only add TER if the previous chain contained protein/DNA/RNA. */
if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
{
fprintf(out, "TER\n");
}
lastchainnum = chainnum;
lastchainresind = lastresind;
}
strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
/* rename HG12 to 2HG1, etc. */
xlate_atomname_gmx2pdb(nm);
resnr = atoms->resinfo[resind].nr;
resic = atoms->resinfo[resind].ic;
if (chainid != ' ')
{
ch = chainid;
}
else
{
ch = atoms->resinfo[resind].chainid;
if (ch == 0)
{
ch = ' ';
}
}
if (resnr >= 10000)
{
resnr = resnr % 10000;
}
if (atoms->pdbinfo)
{
type = atoms->pdbinfo[i].type;
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, pdbformat);
}
else
{
strcpy(pdbform, 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");
}
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);
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",
(i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
}
}
fprintf(out, "TER\n");
fprintf(out, "ENDMDL\n");
if (NULL != gc)
{
/* Write conect records */
for (i = 0; (i < gc->nconect); i++)
{
fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
}
}
gmx_residuetype_destroy(rt);
}