"CONECT"
};
-
#define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
static void xlate_atomname_pdb2gmx(char *name)
const t_atoms *atoms, const rvec x[],
int ePBC, const matrix box, char chainid,
int model_nr, int nindex, const int index[],
- gmx_conect conect, gmx_bool bTerSepChains,
+ gmx_conect conect,
bool usePqrFormat)
{
- gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
- 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);
+ gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
+ enum PDB_record type;
+ char altloc;
+ real occup, bfac;
+ gmx_bool bOccup;
+
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
if (box && ( (norm2(box[XX]) != 0.0f) || (norm2(box[YY]) != 0.0f) || (norm2(box[ZZ]) != 0.0f) ) )
* otherwise set them all to one
*/
bOccup = TRUE;
- for (ii = 0; (ii < nindex) && bOccup; ii++)
+ for (int ii = 0; (ii < nindex) && bOccup; ii++)
{
- i = index[ii];
+ int i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
- lastchainnum = -1;
- p_restype = nullptr;
-
- for (ii = 0; ii < nindex; ii++)
+ ResidueType rt;
+ for (int 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;
- }
-
- std::string resnm = *atoms->resinfo[resind].name;
- std::string nm = *atoms->atomname[i];
+ int i = index[ii];
+ int resind = atoms->atom[i].resind;
+ std::string resnm = *atoms->resinfo[resind].name;
+ std::string nm = *atoms->atomname[i];
/* rename HG12 to 2HG1, etc. */
nm = xlate_atomname_gmx2pdb(nm);
- resnr = atoms->resinfo[resind].nr;
- resic = atoms->resinfo[resind].ic;
+ int resnr = atoms->resinfo[resind].nr;
+ unsigned char resic = atoms->resinfo[resind].ic;
+ unsigned char ch;
if (chainid != ' ')
{
ch = chainid;
if (nullptr != gc)
{
/* Write conect records */
- for (i = 0; (i < gc->nconect); i++)
+ for (int 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(FILE *out, const char *title, const t_atoms *atoms, const rvec x[],
- int ePBC, const matrix box, char chainid, int model_nr, gmx_conect conect, gmx_bool bTerSepChains)
+ int ePBC, const matrix box, char chainid, int model_nr, gmx_conect conect)
{
int i, *index;
index[i] = i;
}
write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr,
- atoms->nr, index, conect, bTerSepChains, false);
+ atoms->nr, index, conect, false);
sfree(index);
}
}
}
-void get_pdb_atomnumber(const t_atoms *atoms, gmx_atomprop_t aps)
+void get_pdb_atomnumber(const t_atoms *atoms, AtomProperties *aps)
{
int i, atomnumber, len;
size_t k;
- char anm[6], anm_copy[6], *ptr;
+ char anm[6], anm_copy[6];
char nc = '\0';
real eval;
if ((anm[0] != ' ') && ((len <= 2) || !std::isdigit(anm[2])))
{
anm_copy[2] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
else
{
anm_copy[1] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
anm_copy[0] = anm[k];
anm_copy[1] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
}
+ std::string buf;
if (atomNumberSet)
{
atoms->atom[i].atomnumber = atomnumber;
- ptr = gmx_atomprop_element(aps, atomnumber);
+ buf = aps->elementFromAtomNumber(atomnumber);
if (debug)
{
fprintf(debug, "Atomnumber for atom '%s' is %d\n",
anm, atomnumber);
}
}
- else
- {
- ptr = nullptr;
- }
- std::strncpy(atoms->atom[i].elem, ptr == nullptr ? "" : ptr, 4);
+ buf.resize(3);
+ std::strncpy(atoms->atom[i].elem, buf.c_str(), 4);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff