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 rename_atoms(const char *xlfile,const char *ffdir,
t_atoms *atoms,t_symtab *symtab,const t_restp *restp,
gmx_bool bResname,gmx_residuetype_t rt,gmx_bool bReorderNum,
gmx_bool bVerbose)
{
FILE *fp;
int nxlate,a,i,resind;
t_xlate_atom *xlatom;
int nf;
char **f;
char c,*rnm,atombuf[32],*ptr0,*ptr1;
gmx_bool bReorderedNum,bRenamed,bMatch;
nxlate = 0;
xlatom = NULL;
if (xlfile != NULL)
{
fp = libopen(xlfile);
get_xlatoms(xlfile,fp,&nxlate,&xlatom);
fclose(fp);
}
else
{
nf = fflib_search_file_end(ffdir,".arn",FALSE,&f);
for(i=0; i<nf; i++)
{
fp = fflib_open(f[i]);
get_xlatoms(f[i],fp,&nxlate,&xlatom);
fclose(fp);
sfree(f[i]);
}
sfree(f);
}
for(a=0; (a<atoms->nr); a++)
{
resind = atoms->atom[a].resind;
if (bResname)
{
rnm = *(atoms->resinfo[resind].name);
}
else
{
rnm = *(atoms->resinfo[resind].rtp);
}
strcpy(atombuf,*(atoms->atomname[a]));
bReorderedNum = FALSE;
if (bReorderNum)
{
if (isdigit(atombuf[0]))
{
c = atombuf[0];
for (i=0; ((size_t)i<strlen(atombuf)-1); i++)
{
atombuf[i] = atombuf[i+1];
}
atombuf[i] = c;
bReorderedNum = TRUE;
}
}
bRenamed = FALSE;
for(i=0; (i<nxlate) && !bRenamed; i++) {
/* Check if the base file name of the rtp and arn entry match */
if (restp == NULL ||
gmx_strcasecmp(restp[resind].filebase,xlatom[i].filebase) == 0)
{
/* Match the residue name */
bMatch = (xlatom[i].res == NULL ||
(gmx_strcasecmp("protein",xlatom[i].res) == 0 &&
gmx_residuetype_is_protein(rt,rnm)) ||
(gmx_strcasecmp("DNA",xlatom[i].res) == 0 &&
gmx_residuetype_is_dna(rt,rnm)) ||
(gmx_strcasecmp("RNA",xlatom[i].res) == 0 &&
gmx_residuetype_is_rna(rt,rnm)));
if (!bMatch)
{
ptr0 = rnm;
ptr1 = xlatom[i].res;
while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
(ptr0[0] == ptr1[0] || ptr1[0] == '?'))
{
ptr0++;
ptr1++;
}
bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
}
if (bMatch && strcmp(atombuf,xlatom[i].atom) == 0)
{
/* We have a match. */
/* Don't free the old atomname,
* since it might be in the symtab.
*/
ptr0 = strdup(xlatom[i].replace);
if (bVerbose)
{
printf("Renaming atom '%s' in residue %d %s to '%s'\n",
*atoms->atomname[a],
atoms->resinfo[resind].nr,
*atoms->resinfo[resind].name,
ptr0);
}
atoms->atomname[a] = put_symtab(symtab,ptr0);
bRenamed = TRUE;
}
}
}
if (bReorderedNum && !bRenamed)
{
atoms->atomname[a] = put_symtab(symtab,atombuf);
}
}
done_xlatom(nxlate,xlatom);
}
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);
}
