{
if (r == r_start[j])
{
- bStart = TRUE;
+ bStart = true;
}
}
for (j = 0; j < nterpairs; j++)
}
}
- nn = search_resrename(nrr, rr, *pdba->resinfo[r].rtp, bStart, bEnd, FALSE);
+ nn = search_resrename(nrr, rr, *pdba->resinfo[r].rtp, bStart, bEnd, false);
if (bFFRTPTERRNM && nn == nullptr && (bStart || bEnd))
{
* Check if we need to rename it because it is terminal.
*/
nn = search_resrename(nrr, rr,
- *pdba->resinfo[r].rtp, bStart, bEnd, TRUE);
+ *pdba->resinfo[r].rtp, bStart, bEnd, true);
}
if (nn != nullptr && strcmp(*pdba->resinfo[r].rtp, nn) != 0)
printf(" %d atoms\n", natom);
/* Rename residues */
- rename_pdbres(atoms, "HOH", watres, FALSE, symtab);
- rename_pdbres(atoms, "SOL", watres, FALSE, symtab);
- rename_pdbres(atoms, "WAT", watres, FALSE, symtab);
+ rename_pdbres(atoms, "HOH", watres, false, symtab);
+ rename_pdbres(atoms, "SOL", watres, false, symtab);
+ rename_pdbres(atoms, "WAT", watres, false, symtab);
rename_atoms("xlateat.dat", nullptr,
- atoms, symtab, nullptr, TRUE, rt, TRUE, bVerbose);
+ atoms, symtab, nullptr, true, rt, true, bVerbose);
if (natom == 0)
{
/* Rename aromatics, lys, asp and histidine */
if (bTyrU)
{
- rename_bb(pdba, "TYR", "TYRU", FALSE, symtab);
+ rename_bb(pdba, "TYR", "TYRU", false, symtab);
}
if (bTrpU)
{
- rename_bb(pdba, "TRP", "TRPU", FALSE, symtab);
+ rename_bb(pdba, "TRP", "TRPU", false, symtab);
}
if (bPheU)
{
- rename_bb(pdba, "PHE", "PHEU", FALSE, symtab);
+ rename_bb(pdba, "PHE", "PHEU", false, symtab);
}
if (bLysMan)
{
- rename_bbint(pdba, "LYS", get_lystp, FALSE, symtab, nrr, rr);
+ rename_bbint(pdba, "LYS", get_lystp, false, symtab, nrr, rr);
}
if (bArgMan)
{
- rename_bbint(pdba, "ARG", get_argtp, FALSE, symtab, nrr, rr);
+ rename_bbint(pdba, "ARG", get_argtp, false, symtab, nrr, rr);
}
if (bGlnMan)
{
- rename_bbint(pdba, "GLN", get_glntp, FALSE, symtab, nrr, rr);
+ rename_bbint(pdba, "GLN", get_glntp, false, symtab, nrr, rr);
}
if (bAspMan)
{
- rename_bbint(pdba, "ASP", get_asptp, FALSE, symtab, nrr, rr);
+ rename_bbint(pdba, "ASP", get_asptp, false, symtab, nrr, rr);
}
else
{
- rename_bb(pdba, "ASPH", "ASP", FALSE, symtab);
+ rename_bb(pdba, "ASPH", "ASP", false, symtab);
}
if (bGluMan)
{
- rename_bbint(pdba, "GLU", get_glutp, FALSE, symtab, nrr, rr);
+ rename_bbint(pdba, "GLU", get_glutp, false, symtab, nrr, rr);
}
else
{
- rename_bb(pdba, "GLUH", "GLU", FALSE, symtab);
+ rename_bb(pdba, "GLUH", "GLU", false, symtab);
}
if (!bHisMan)
}
else
{
- rename_bbint(pdba, "HIS", get_histp, TRUE, symtab, nrr, rr);
+ rename_bbint(pdba, "HIS", get_histp, true, symtab, nrr, rr);
}
/* Initialize the rtp builing block names with the residue names
/* pdba is sorted in pdbnew using the pdbi index */
snew(a, natoms);
snew(pdbnew, 1);
- init_t_atoms(pdbnew, natoms, TRUE);
+ init_t_atoms(pdbnew, natoms, true);
snew(*xnew, natoms);
pdbnew->nr = pdba->nr;
pdbnew->nres = pdba->nres;
};
- FILE *fp, *top_file, *top_file2, *itp_file = nullptr;
- int natom, nres;
- t_atoms pdba_all, *pdba;
- t_atoms *atoms;
- t_resinfo *ri;
- t_blocka *block;
- int chain, nch, maxch, nwaterchain;
+ FILE *fp, *top_file2, *itp_file = nullptr;
+ t_atoms *pdba;
t_pdbchain *pdb_ch;
t_chain *chains, *cc;
char select[STRLEN];
int nincl, nmol;
char **incls;
t_mols *mols;
- char **gnames;
- int ePBC;
- matrix box;
- rvec box_space;
- int i, j, k, l, nrtp;
int *swap_index, si;
- t_restp *restp;
- t_hackblock *ah;
- t_symtab symtab;
- gpp_atomtype_t atype;
- gmx_residuetype_t*rt;
const char *top_fn;
char itp_fn[STRLEN], posre_fn[STRLEN], buf_fn[STRLEN];
char molname[STRLEN];
char *c, forcefield[STRLEN], ffdir[STRLEN];
char ffname[STRLEN], suffix[STRLEN], buf[STRLEN];
char *watermodel;
- const char *watres;
- int nrtprename;
- rtprename_t *rtprename = nullptr;
- int nah, nNtdb, nCtdb, ntdblist;
- t_hackblock *ntdb, *ctdb, **tdblist;
int nssbonds;
t_ssbond *ssbonds;
- rvec *pdbx, *x;
- bool bVsites = FALSE, bWat, bPrevWat = FALSE, bITP, bVsiteAromatics = FALSE;
+ rvec *x;
+ bool bVsites = false, bWat, bPrevWat = false, bITP, bVsiteAromatics = false;
real mHmult = 0;
t_hackblock *hb_chain;
t_restp *restp_chain;
gmx_output_env_t *oenv;
- const char *p_restype;
- int rc;
- int this_atomnum;
- int prev_atomnum;
- const char * prev_atomname;
- const char * this_atomname;
- const char * prev_resname;
- const char * this_resname;
- int prev_resnum;
- int this_resnum;
- char prev_chainid;
- char this_chainid;
- int prev_chainnumber;
- int this_chainnumber;
- int nid_used;
- int this_chainstart;
- int prev_chainstart;
- bool bMerged;
- int nchainmerges;
-
- gmx_atomprop_t aps;
t_filenm fnm[] = {
{ efSTX, "-f", "eiwit.pdb", ffREAD },
};
#define NFILE asize(fnm)
- gmx_bool bNewRTP = FALSE;
- gmx_bool bInter = FALSE, bCysMan = FALSE;
- gmx_bool bLysMan = FALSE, bAspMan = FALSE, bGluMan = FALSE, bHisMan = FALSE;
- gmx_bool bGlnMan = FALSE, bArgMan = FALSE;
- gmx_bool bTerMan = FALSE, bUnA = FALSE, bHeavyH = FALSE;
- gmx_bool bSort = TRUE, bAllowMissing = FALSE, bRemoveH = FALSE;
- gmx_bool bDeuterate = FALSE, bVerbose = FALSE, bChargeGroups = TRUE, bCmap = TRUE;
- gmx_bool bRenumRes = FALSE, bRTPresname = FALSE;
+ gmx_bool bNewRTP = false;
+ gmx_bool bInter = false, bCysMan = false;
+ gmx_bool bLysMan = false, bAspMan = false, bGluMan = false, bHisMan = false;
+ gmx_bool bGlnMan = false, bArgMan = false;
+ gmx_bool bTerMan = false, bUnA = false, bHeavyH = false;
+ gmx_bool bSort = true, bAllowMissing = false, bRemoveH = false;
+ gmx_bool bDeuterate = false, bVerbose = false, bChargeGroups = true, bCmap = true;
+ gmx_bool bRenumRes = false, bRTPresname = false;
real angle = 135.0, distance = 0.3, posre_fc = 1000;
real long_bond_dist = 0.25, short_bond_dist = 0.05;
const char *vsitestr[] = { nullptr, "none", "hydrogens", "aromatics", nullptr };
const char *ff = "select";
t_pargs pa[] = {
- { "-newrtp", FALSE, etBOOL, {&bNewRTP},
+ { "-newrtp", false, etBOOL, {&bNewRTP},
"HIDDENWrite the residue database in new format to [TT]new.rtp[tt]"},
- { "-lb", FALSE, etREAL, {&long_bond_dist},
+ { "-lb", false, etREAL, {&long_bond_dist},
"HIDDENLong bond warning distance" },
- { "-sb", FALSE, etREAL, {&short_bond_dist},
+ { "-sb", false, etREAL, {&short_bond_dist},
"HIDDENShort bond warning distance" },
- { "-chainsep", FALSE, etENUM, {chainsep},
+ { "-chainsep", false, etENUM, {chainsep},
"Condition in PDB files when a new chain should be started (adding termini)" },
- { "-merge", FALSE, etENUM, {&merge},
+ { "-merge", false, etENUM, {&merge},
"Merge multiple chains into a single [moleculetype]" },
- { "-ff", FALSE, etSTR, {&ff},
+ { "-ff", false, etSTR, {&ff},
"Force field, interactive by default. Use [TT]-h[tt] for information." },
- { "-water", FALSE, etENUM, {watstr},
+ { "-water", false, etENUM, {watstr},
"Water model to use" },
- { "-inter", FALSE, etBOOL, {&bInter},
+ { "-inter", false, etBOOL, {&bInter},
"Set the next 8 options to interactive"},
- { "-ss", FALSE, etBOOL, {&bCysMan},
+ { "-ss", false, etBOOL, {&bCysMan},
"Interactive SS bridge selection" },
- { "-ter", FALSE, etBOOL, {&bTerMan},
+ { "-ter", false, etBOOL, {&bTerMan},
"Interactive termini selection, instead of charged (default)" },
- { "-lys", FALSE, etBOOL, {&bLysMan},
+ { "-lys", false, etBOOL, {&bLysMan},
"Interactive lysine selection, instead of charged" },
- { "-arg", FALSE, etBOOL, {&bArgMan},
+ { "-arg", false, etBOOL, {&bArgMan},
"Interactive arginine selection, instead of charged" },
- { "-asp", FALSE, etBOOL, {&bAspMan},
+ { "-asp", false, etBOOL, {&bAspMan},
"Interactive aspartic acid selection, instead of charged" },
- { "-glu", FALSE, etBOOL, {&bGluMan},
+ { "-glu", false, etBOOL, {&bGluMan},
"Interactive glutamic acid selection, instead of charged" },
- { "-gln", FALSE, etBOOL, {&bGlnMan},
+ { "-gln", false, etBOOL, {&bGlnMan},
"Interactive glutamine selection, instead of neutral" },
- { "-his", FALSE, etBOOL, {&bHisMan},
+ { "-his", false, etBOOL, {&bHisMan},
"Interactive histidine selection, instead of checking H-bonds" },
- { "-angle", FALSE, etREAL, {&angle},
+ { "-angle", false, etREAL, {&angle},
"Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)" },
- { "-dist", FALSE, etREAL, {&distance},
+ { "-dist", false, etREAL, {&distance},
"Maximum donor-acceptor distance for a H-bond (nm)" },
- { "-una", FALSE, etBOOL, {&bUnA},
+ { "-una", false, etBOOL, {&bUnA},
"Select aromatic rings with united CH atoms on phenylalanine, "
"tryptophane and tyrosine" },
- { "-sort", FALSE, etBOOL, {&bSort},
+ { "-sort", false, etBOOL, {&bSort},
"HIDDENSort the residues according to database, turning this off is dangerous as charge groups might be broken in parts" },
- { "-ignh", FALSE, etBOOL, {&bRemoveH},
+ { "-ignh", false, etBOOL, {&bRemoveH},
"Ignore hydrogen atoms that are in the coordinate file" },
- { "-missing", FALSE, etBOOL, {&bAllowMissing},
+ { "-missing", false, etBOOL, {&bAllowMissing},
"Continue when atoms are missing and bonds cannot be made, dangerous" },
- { "-v", FALSE, etBOOL, {&bVerbose},
+ { "-v", false, etBOOL, {&bVerbose},
"Be slightly more verbose in messages" },
- { "-posrefc", FALSE, etREAL, {&posre_fc},
+ { "-posrefc", false, etREAL, {&posre_fc},
"Force constant for position restraints" },
- { "-vsite", FALSE, etENUM, {vsitestr},
+ { "-vsite", false, etENUM, {vsitestr},
"Convert atoms to virtual sites" },
- { "-heavyh", FALSE, etBOOL, {&bHeavyH},
+ { "-heavyh", false, etBOOL, {&bHeavyH},
"Make hydrogen atoms heavy" },
- { "-deuterate", FALSE, etBOOL, {&bDeuterate},
+ { "-deuterate", false, etBOOL, {&bDeuterate},
"Change the mass of hydrogens to 2 amu" },
- { "-chargegrp", TRUE, etBOOL, {&bChargeGroups},
+ { "-chargegrp", true, etBOOL, {&bChargeGroups},
"Use charge groups in the [REF].rtp[ref] file" },
- { "-cmap", TRUE, etBOOL, {&bCmap},
+ { "-cmap", true, etBOOL, {&bCmap},
"Use cmap torsions (if enabled in the [REF].rtp[ref] file)" },
- { "-renum", TRUE, etBOOL, {&bRenumRes},
+ { "-renum", true, etBOOL, {&bRenumRes},
"Renumber the residues consecutively in the output" },
- { "-rtpres", TRUE, etBOOL, {&bRTPresname},
+ { "-rtpres", true, etBOOL, {&bRTPresname},
"Use [REF].rtp[ref] entry names as residue names" }
};
#define NPARGS asize(pa)
gmx_fatal(FARGS, "Empty forcefield string");
}
+ int this_atomnum;
+ int prev_atomnum;
+ const char * prev_atomname;
+ const char * this_atomname;
+ const char * prev_resname;
+ const char * this_resname;
+ int prev_resnum;
+ int this_resnum;
+ char prev_chainid;
+ char this_chainid;
+ int prev_chainnumber;
+ int this_chainnumber;
+ int this_chainstart;
+ int prev_chainstart;
+
printf("\nUsing the %s force field in directory %s\n\n",
ffname, ffdir);
if (bInter)
{
/* if anything changes here, also change description of -inter */
- bCysMan = TRUE;
- bTerMan = TRUE;
- bLysMan = TRUE;
- bArgMan = TRUE;
- bAspMan = TRUE;
- bGluMan = TRUE;
- bGlnMan = TRUE;
- bHisMan = TRUE;
+ bCysMan = true;
+ bTerMan = true;
+ bLysMan = true;
+ bArgMan = true;
+ bAspMan = true;
+ bGluMan = true;
+ bGlnMan = true;
+ bHisMan = true;
}
if (bHeavyH)
switch (vsitestr[0][0])
{
case 'n': /* none */
- bVsites = FALSE;
- bVsiteAromatics = FALSE;
+ bVsites = false;
+ bVsiteAromatics = false;
break;
case 'h': /* hydrogens */
- bVsites = TRUE;
- bVsiteAromatics = FALSE;
+ bVsites = true;
+ bVsiteAromatics = false;
break;
case 'a': /* aromatics */
- bVsites = TRUE;
- bVsiteAromatics = TRUE;
+ bVsites = true;
+ bVsiteAromatics = true;
break;
default:
gmx_fatal(FARGS, "Internal inconsistency: vsitestr[0]='%s'", vsitestr[0]);
} /* end switch */
/* Open the symbol table */
+ t_symtab symtab;
open_symtab(&symtab);
/* Residue type database */
+ gmx_residuetype_t *rt;
gmx_residuetype_init(&rt);
/* Read residue renaming database(s), if present */
- std::vector<std::string> rrn = fflib_search_file_end(ffdir, ".r2b", FALSE);
+ std::vector<std::string> rrn = fflib_search_file_end(ffdir, ".r2b", false);
- nrtprename = 0;
- rtprename = nullptr;
+ int nrtprename = 0;
+ rtprename_t *rtprename = nullptr;
for (const auto &filename : rrn)
{
fp = fflib_open(filename);
}
/* Add all alternative names from the residue renaming database to the list of recognized amino/nucleic acids. */
- for (i = 0; i < nrtprename; i++)
+ const char *p_restype;
+ for (int i = 0; i < nrtprename; i++)
{
- rc = gmx_residuetype_get_type(rt, rtprename[i].gmx, &p_restype);
+ int rc = gmx_residuetype_get_type(rt, rtprename[i].gmx, &p_restype);
/* Only add names if the 'standard' gromacs/iupac base name was found */
if (rc == 0)
}
}
+
+ matrix box;
+ const char *watres;
clear_mat(box);
if (watermodel != nullptr && (strstr(watermodel, "4p") ||
strstr(watermodel, "4P")))
watres = "HOH";
}
- aps = gmx_atomprop_init();
- char *title;
- natom = read_pdball(opt2fn("-f", NFILE, fnm), opt2fn_null("-q", NFILE, fnm), &title,
- &pdba_all, &pdbx, &ePBC, box, bRemoveH, &symtab, rt, watres,
- aps, bVerbose);
+ gmx_atomprop_t aps = gmx_atomprop_init();
+ char *title;
+ int ePBC;
+ t_atoms pdba_all;
+ rvec *pdbx;
+ int natom = read_pdball(opt2fn("-f", NFILE, fnm), opt2fn_null("-q", NFILE, fnm), &title,
+ &pdba_all, &pdbx, &ePBC, box, bRemoveH, &symtab, rt, watres,
+ aps, bVerbose);
if (natom == 0)
{
}
printf("Analyzing pdb file\n");
- nwaterchain = 0;
+ int nwaterchain = 0;
modify_chain_numbers(&pdba_all, chainsep[0]);
- nchainmerges = 0;
+ int nchainmerges = 0;
this_atomname = nullptr;
this_atomnum = -1;
/* Keep the compiler happy */
prev_chainstart = 0;
- nch = 0;
- maxch = 16;
+ int numChains = 0;
+ int maxch = 16;
snew(pdb_ch, maxch);
- bMerged = false;
- for (i = 0; (i < natom); i++)
+ t_resinfo *ri;
+ bool bMerged = false;
+ for (int i = 0; (i < natom); i++)
{
ri = &pdba_all.resinfo[pdba_all.atom[i].resind];
if (bMerged)
{
- pdb_ch[nch-1].chainstart[pdb_ch[nch-1].nterpairs] =
+ pdb_ch[numChains-1].chainstart[pdb_ch[numChains-1].nterpairs] =
pdba_all.atom[i].resind - prev_chainstart;
- pdb_ch[nch-1].nterpairs++;
- srenew(pdb_ch[nch-1].chainstart, pdb_ch[nch-1].nterpairs+1);
+ pdb_ch[numChains-1].nterpairs++;
+ srenew(pdb_ch[numChains-1].chainstart, pdb_ch[numChains-1].nterpairs+1);
nchainmerges++;
}
else
{
/* set natom for previous chain */
- if (nch > 0)
+ if (numChains > 0)
{
- pdb_ch[nch-1].natom = i-pdb_ch[nch-1].start;
+ pdb_ch[numChains-1].natom = i-pdb_ch[numChains-1].start;
}
if (bWat)
{
ri->chainid = ' ';
}
/* check if chain identifier was used before */
- for (j = 0; (j < nch); j++)
+ for (int j = 0; (j < numChains); j++)
{
if (pdb_ch[j].chainid != ' ' && pdb_ch[j].chainid == ri->chainid)
{
}
}
// TODO This is too convoluted. Use a std::vector
- if (nch == maxch)
+ if (numChains == maxch)
{
maxch += 16;
srenew(pdb_ch, maxch);
}
- pdb_ch[nch].chainid = ri->chainid;
- pdb_ch[nch].chainnum = ri->chainnum;
- pdb_ch[nch].start = i;
- pdb_ch[nch].bAllWat = bWat;
+ pdb_ch[numChains].chainid = ri->chainid;
+ pdb_ch[numChains].chainnum = ri->chainnum;
+ pdb_ch[numChains].start = i;
+ pdb_ch[numChains].bAllWat = bWat;
if (bWat)
{
- pdb_ch[nch].nterpairs = 0;
+ pdb_ch[numChains].nterpairs = 0;
}
else
{
- pdb_ch[nch].nterpairs = 1;
+ pdb_ch[numChains].nterpairs = 1;
}
- snew(pdb_ch[nch].chainstart, pdb_ch[nch].nterpairs+1);
- /* modified [nch] to [0] below */
- pdb_ch[nch].chainstart[0] = 0;
- nch++;
+ snew(pdb_ch[numChains].chainstart, pdb_ch[numChains].nterpairs+1);
+ /* modified [numChains] to [0] below */
+ pdb_ch[numChains].chainstart[0] = 0;
+ numChains++;
}
}
bPrevWat = bWat;
}
- pdb_ch[nch-1].natom = natom-pdb_ch[nch-1].start;
+ pdb_ch[numChains-1].natom = natom-pdb_ch[numChains-1].start;
/* set all the water blocks at the end of the chain */
- snew(swap_index, nch);
- j = 0;
- for (i = 0; i < nch; i++)
+ snew(swap_index, numChains);
+ int j = 0;
+ for (int i = 0; i < numChains; i++)
{
if (!pdb_ch[i].bAllWat)
{
j++;
}
}
- for (i = 0; i < nch; i++)
+ for (int i = 0; i < numChains; i++)
{
if (pdb_ch[i].bAllWat)
{
printf("Moved all the water blocks to the end\n");
}
- snew(chains, nch);
+ snew(chains, numChains);
/* copy pdb data and x for all chains */
- for (i = 0; (i < nch); i++)
+ for (int i = 0; (i < numChains); i++)
{
si = swap_index[i];
chains[i].chainid = pdb_ch[si].chainid;
snew(chains[i].r_end, pdb_ch[si].nterpairs);
snew(chains[i].pdba, 1);
- init_t_atoms(chains[i].pdba, pdb_ch[si].natom, TRUE);
+ init_t_atoms(chains[i].pdba, pdb_ch[si].natom, true);
snew(chains[i].x, chains[i].pdba->nr);
for (j = 0; j < chains[i].pdba->nr; j++)
{
copy_rvec(pdbx[pdb_ch[si].start+j], chains[i].x[j]);
}
/* Re-index the residues assuming that the indices are continuous */
- k = chains[i].pdba->atom[0].resind;
- nres = chains[i].pdba->atom[chains[i].pdba->nr-1].resind - k + 1;
+ int k = chains[i].pdba->atom[0].resind;
+ int nres = chains[i].pdba->atom[chains[i].pdba->nr-1].resind - k + 1;
chains[i].pdba->nres = nres;
- for (j = 0; j < chains[i].pdba->nr; j++)
+ for (int j = 0; j < chains[i].pdba->nr; j++)
{
chains[i].pdba->atom[j].resind -= k;
}
srenew(chains[i].pdba->resinfo, nres);
- for (j = 0; j < nres; j++)
+ for (int j = 0; j < nres; j++)
{
chains[i].pdba->resinfo[j] = pdba_all.resinfo[k+j];
snew(chains[i].pdba->resinfo[j].name, 1);
printf("There are %d chains and %d blocks of water and "
"%d residues with %d atoms\n",
- nch-nwaterchain, nwaterchain,
+ numChains-nwaterchain, nwaterchain,
pdba_all.nres, natom);
printf("\n %5s %4s %6s\n", "chain", "#res", "#atoms");
- for (i = 0; (i < nch); i++)
+ for (int i = 0; (i < numChains); i++)
{
printf(" %d '%c' %5d %6d %s\n",
i+1, chains[i].chainid ? chains[i].chainid : '-',
check_occupancy(&pdba_all, opt2fn("-f", NFILE, fnm), bVerbose);
/* Read atomtypes... */
- atype = read_atype(ffdir, &symtab);
+ gpp_atomtype_t atype = read_atype(ffdir, &symtab);
/* read residue database */
printf("Reading residue database... (%s)\n", forcefield);
- std::vector<std::string> rtpf = fflib_search_file_end(ffdir, ".rtp", TRUE);
- nrtp = 0;
- restp = nullptr;
+ std::vector<std::string> rtpf = fflib_search_file_end(ffdir, ".rtp", true);
+ int nrtp = 0;
+ t_restp *restp = nullptr;
for (const auto &filename : rtpf)
{
- read_resall(filename.c_str(), &nrtp, &restp, atype, &symtab, FALSE);
+ read_resall(filename.c_str(), &nrtp, &restp, atype, &symtab, false);
}
if (bNewRTP)
{
}
/* read hydrogen database */
- nah = read_h_db(ffdir, &ah);
+ t_hackblock *ah;
+ int nah = read_h_db(ffdir, &ah);
/* Read Termini database... */
- nNtdb = read_ter_db(ffdir, 'n', &ntdb, atype);
- nCtdb = read_ter_db(ffdir, 'c', &ctdb, atype);
+ int ntdblist;
+ t_hackblock *ntdb;
+ t_hackblock *ctdb;
+ t_hackblock **tdblist;
+ int nNtdb = read_ter_db(ffdir, 'n', &ntdb, atype);
+ int nCtdb = read_ter_db(ffdir, 'c', &ctdb, atype);
top_fn = ftp2fn(efTOP, NFILE, fnm);
- top_file = gmx_fio_fopen(top_fn, "w");
+ FILE *top_file = gmx_fio_fopen(top_fn, "w");
- print_top_header(top_file, top_fn, FALSE, ffdir, mHmult);
+ print_top_header(top_file, top_fn, false, ffdir, mHmult);
nincl = 0;
nmol = 0;
incls = nullptr;
mols = nullptr;
- for (chain = 0; (chain < nch); chain++)
+ for (int chain = 0; (chain < numChains); chain++)
{
cc = &(chains[chain]);
/* set pdba, natom and nres to the current chain */
- pdba = cc->pdba;
- x = cc->x;
- natom = cc->pdba->nr;
- nres = cc->pdba->nres;
+ pdba = cc->pdba;
+ x = cc->x;
+ natom = cc->pdba->nr;
+ int nres = cc->pdba->nres;
if (cc->chainid && ( cc->chainid != ' ' ) )
{
cc->chainstart[cc->nterpairs] = pdba->nres;
j = 0;
- for (i = 0; i < cc->nterpairs; i++)
+ for (int i = 0; i < cc->nterpairs; i++)
{
find_nc_ter(pdba, cc->chainstart[i], cc->chainstart[i+1],
&(cc->r_start[j]), &(cc->r_end[j]), rt);
&symtab, bVerbose);
}
- for (i = 0; i < cc->nterpairs; i++)
+ for (int i = 0; i < cc->nterpairs; i++)
{
/* Set termini.
do now :( AF 26-7-99 */
rename_atoms(nullptr, ffdir,
- pdba, &symtab, restp_chain, FALSE, rt, FALSE, bVerbose);
+ pdba, &symtab, restp_chain, false, rt, false, bVerbose);
match_atomnames_with_rtp(restp_chain, hb_chain, pdba, x, bVerbose);
if (bSort)
{
+ t_blocka *block;
+ char **gnames;
block = new_blocka();
snew(gnames, 1);
sort_pdbatoms(restp_chain, natom, &pdba, &x, block, &gnames);
"(the index file is generated before hydrogens are added)",
ftp2fn(efNDX, NFILE, fnm));
}
- write_index(ftp2fn(efNDX, NFILE, fnm), block, gnames, FALSE, 0);
+ write_index(ftp2fn(efNDX, NFILE, fnm), block, gnames, false, 0);
}
- for (i = 0; i < block->nr; i++)
+ for (int i = 0; i < block->nr; i++)
{
sfree(gnames[i]);
}
printf("Generating any missing hydrogen atoms and/or adding termini.\n");
add_h(&pdba, &x, nah, ah,
cc->nterpairs, cc->ntdb, cc->ctdb, cc->r_start, cc->r_end, bAllowMissing,
- nullptr, nullptr, TRUE, FALSE);
+ nullptr, nullptr, true, false);
printf("Now there are %d residues with %d atoms\n",
pdba->nres, pdba->nr);
/* make up molecule name(s) */
- k = (cc->nterpairs > 0 && cc->r_start[0] >= 0) ? cc->r_start[0] : 0;
+ int k = (cc->nterpairs > 0 && cc->r_start[0] >= 0) ? cc->r_start[0] : 0;
gmx_residuetype_get_type(rt, *pdba->resinfo[k].name, &p_restype);
}
/* Check if there have been previous chains with the same id */
- nid_used = 0;
- for (k = 0; k < chain; k++)
+ int nid_used = 0;
+ for (int k = 0; k < chain; k++)
{
if (cc->chainid == chains[k].chainid)
{
}
}
- if ((nch-nwaterchain > 1) && !cc->bAllWat)
+ if ((numChains-nwaterchain > 1) && !cc->bAllWat)
{
- bITP = TRUE;
+ bITP = true;
strcpy(itp_fn, top_fn);
printf("Chain time...\n");
c = strrchr(itp_fn, '.');
}
else
{
- bITP = FALSE;
+ bITP = false;
}
srenew(mols, nmol+1);
if (bITP)
{
- print_top_comment(itp_file, itp_fn, ffdir, TRUE);
+ print_top_comment(itp_file, itp_fn, ffdir, true);
}
if (cc->bAllWat)
if (watermodel == nullptr)
{
- for (chain = 0; chain < nch; chain++)
+ for (int chain = 0; chain < numChains; chain++)
{
if (chains[chain].bAllWat)
{
gmx_residuetype_destroy(rt);
/* now merge all chains back together */
- natom = 0;
- nres = 0;
- for (i = 0; (i < nch); i++)
+ natom = 0;
+ int nres = 0;
+ for (int i = 0; (i < numChains); i++)
{
natom += chains[i].pdba->nr;
nres += chains[i].pdba->nres;
}
+ t_atoms *atoms;
snew(atoms, 1);
- init_t_atoms(atoms, natom, FALSE);
- for (i = 0; i < atoms->nres; i++)
+ init_t_atoms(atoms, natom, false);
+ for (int i = 0; i < atoms->nres; i++)
{
sfree(atoms->resinfo[i].name);
}
atoms->nres = nres;
snew(atoms->resinfo, nres);
snew(x, natom);
- k = 0;
- l = 0;
- for (i = 0; (i < nch); i++)
+ int k = 0;
+ int l = 0;
+ for (int i = 0; (i < numChains); i++)
{
- if (nch > 1)
+ if (numChains > 1)
{
printf("Including chain %d in system: %d atoms %d residues\n",
i+1, chains[i].pdba->nr, chains[i].pdba->nres);
}
- for (j = 0; (j < chains[i].pdba->nr); j++)
+ for (int j = 0; (j < chains[i].pdba->nr); j++)
{
atoms->atom[k] = chains[i].pdba->atom[j];
atoms->atom[k].resind += l; /* l is processed nr of residues */
copy_rvec(chains[i].x[j], x[k]);
k++;
}
- for (j = 0; (j < chains[i].pdba->nres); j++)
+ for (int j = 0; (j < chains[i].pdba->nres); j++)
{
atoms->resinfo[l] = chains[i].pdba->resinfo[j];
if (bRTPresname)
}
}
- if (nch > 1)
+ if (numChains > 1)
{
fprintf(stderr, "Now there are %d atoms and %d residues\n", k, l);
- print_sums(atoms, TRUE);
+ print_sums(atoms, true);
}
+ rvec box_space;
fprintf(stderr, "\nWriting coordinate file...\n");
clear_rvec(box_space);
if (box[0][0] == 0)
{
- make_new_box(atoms->nr, x, box, box_space, FALSE);
+ make_new_box(atoms->nr, x, box, box_space, false);
}
write_sto_conf(ftp2fn(efSTO, NFILE, fnm), title, atoms, x, nullptr, ePBC, box);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff