const char* get_histp(int resnr, gmx::ArrayRef<const RtpRename> rr)
{
- const char* expl[ehisNR] = { "H on ND1 only", "H on NE2 only", "H on ND1 and NE2",
- "Coupled to Heme" };
+ const char* expl[ehisNR] = {
+ "H on ND1 only", "H on NE2 only", "H on ND1 and NE2", "Coupled to Heme"
+ };
return select_res(ehisNR, resnr, hh, expl, "HISTIDINE", rr);
}
{
if (nc != 2 && nc != 5)
{
- gmx_fatal(FARGS, "Residue renaming database '%s' has %d columns instead of %d or %d",
- fname, ncol, 2, 5);
+ gmx_fatal(FARGS,
+ "Residue renaming database '%s' has %d columns instead of %d or %d",
+ fname,
+ ncol,
+ 2,
+ 5);
}
ncol = nc;
}
gmx_fatal(FARGS,
"A line in residue renaming database '%s' has %d columns, while previous "
"lines have %d columns",
- fname, nc, ncol);
+ fname,
+ nc,
+ ncol);
}
if (nc == 2)
if (newName[0] == '-')
{
- gmx_fatal(FARGS, "In the chosen force field there is no residue type for '%s'%s", name,
+ gmx_fatal(FARGS,
+ "In the chosen force field there is no residue type for '%s'%s",
+ name,
bStart ? (bEnd ? " as a standalone (starting & ending) residue" : " as a starting terminus")
: (bEnd ? " as an ending terminus" : ""));
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Changing rtp entry of residue %d %s to '%s'",
- pdba->resinfo[r].nr, *pdba->resinfo[r].name,
+ pdba->resinfo[r].nr,
+ *pdba->resinfo[r].name,
newName.c_str());
}
pdba->resinfo[r].rtp = put_symtab(symtab, newName.c_str());
.appendTextFormatted(
"Replaced %d residue%s named %s to the default %s. Use interactive "
"selection of protonated residues if that is what you need.",
- numMatchesFound, numMatchesFound > 1 ? "s" : "", oldnm, newnm);
+ numMatchesFound,
+ numMatchesFound > 1 ? "s" : "",
+ oldnm,
+ newnm);
}
}
.appendTextFormatted("Occupancy for atom %s%d-%s is %f rather than 1",
*atoms->resinfo[atoms->atom[i].resind].name,
atoms->resinfo[atoms->atom[i].resind].nr,
- *atoms->atomname[i], atoms->pdbinfo[i].occup);
+ *atoms->atomname[i],
+ atoms->pdbinfo[i].occup);
}
if (atoms->pdbinfo[i].occup == 0)
{
"there were %d atoms with zero occupancy and %d atoms with "
" occupancy unequal to one (out of %d atoms). Check your pdb "
"file.",
- nzero, nnotone, atoms->nr);
+ nzero,
+ nnotone,
+ atoms->nr);
}
else
{
"\n"
"[ position_restraints ]\n"
"; %4s%6s%8s%8s%8s\n",
- "atom", "type", "fx", "fy", "fz");
+ "atom",
+ "type",
+ "fx",
+ "fy",
+ "fz");
for (i = 0; (i < pdba->nr); i++)
{
if (!is_hydrogen(*pdba->atomname[i]) && !is_dummymass(*pdba->atomname[i]))
atomnm = *pdba->atomname[i];
const PreprocessResidue* localPpResidue = &restp_chain[pdba->atom[i].resind];
auto found =
- std::find_if(localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
+ std::find_if(localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
[&atomnm](char** it) { return gmx::equalCaseInsensitive(atomnm, *it); });
if (found == localPpResidue->atomname.end())
{
std::string buf = gmx::formatString(
"Atom %s in residue %s %d was not found in rtp entry %s with %d atoms\n"
"while sorting atoms.\n%s",
- atomnm, *pdba->resinfo[pdba->atom[i].resind].name,
- pdba->resinfo[pdba->atom[i].resind].nr, localPpResidue->resname.c_str(),
+ atomnm,
+ *pdba->resinfo[pdba->atom[i].resind].name,
+ pdba->resinfo[pdba->atom[i].resind].nr,
+ localPpResidue->resname.c_str(),
localPpResidue->natom(),
is_hydrogen(atomnm)
? "\nFor a hydrogen, this can be a different protonation state, or it\n"
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("deleting duplicate atom %4s %s%4d%c",
- *pdba->atomname[i], *ri->name, ri->nr, ri->ic);
+ *pdba->atomname[i],
+ *ri->name,
+ ri->nr,
+ ri->ic);
if (ri->chainid && (ri->chainid != ' '))
{
printf(" ch %c", ri->chainid);
gmx_fatal(FARGS,
"The chain covering the range %s--%s does not have a consistent chain ID. "
"The first residue has ID '%c', while residue %s has ID '%c'.",
- startResidueString.c_str(), endResidueString.c_str(), chainID0,
- residueString.c_str(), chainID);
+ startResidueString.c_str(),
+ endResidueString.c_str(),
+ chainID0,
+ residueString.c_str(),
+ chainID);
}
// At this point all residues have the same ID. If they are also non-blank
"file in the GROMACS library directory. If there are other molecules "
"such as ligands, they should not have the same chain ID as the "
"adjacent protein chain since it's a separate molecule.",
- startResidueString.c_str(), endResidueString.c_str(), restype0.c_str(),
- residueString.c_str(), restype.c_str());
+ startResidueString.c_str(),
+ endResidueString.c_str(),
+ restype0.c_str(),
+ residueString.c_str(),
+ restype.c_str());
}
}
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Identified residue %s%d as a starting terminus.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
*r_start = i;
}
else if (gmx::equalCaseInsensitive(*startrestype, "Ion"))
.appendTextFormatted(
"Residue %s%d has type 'Ion', assuming it is not linked into a "
"chain.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
}
if (ionNotes == 4)
{
"be catastrophic if they should in fact be linked. Please "
"check your structure, "
"and add %s to residuetypes.dat if this was not correct.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr, *pdba->resinfo[i].name);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr,
+ *pdba->resinfo[i].name);
}
else
{
"and add all "
"necessary residue names to residuetypes.dat if this was not "
"correct.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
}
}
if (startWarnings == 4)
.appendTextFormatted(
"Residue %s%d has type 'Ion', assuming it is not linked into a "
"chain.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr);
}
if (ionNotes == 4)
{
"linked. Please check your structure, and add %s to "
"residuetypes.dat "
"if this was not correct.",
- *pdba->resinfo[i].name, pdba->resinfo[i].nr, restype->c_str(),
- *pdba->resinfo[*r_start].name, pdba->resinfo[*r_start].nr,
- startrestype->c_str(), *pdba->resinfo[i].name);
+ *pdba->resinfo[i].name,
+ pdba->resinfo[i].nr,
+ restype->c_str(),
+ *pdba->resinfo[*r_start].name,
+ pdba->resinfo[*r_start].nr,
+ startrestype->c_str(),
+ *pdba->resinfo[i].name);
}
if (endWarnings == 4)
{
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Identified residue %s%d as a ending terminus.",
- *pdba->resinfo[*r_end].name, pdba->resinfo[*r_end].nr);
+ *pdba->resinfo[*r_end].name,
+ pdba->resinfo[*r_end].nr);
}
}
"Split the chain (and introduce termini) between residue %s%d (chain id '%c', atom %d %s)\
"
"and residue %s%d (chain id '%c', atom %d %s) ? [n/y]",
- prev_resname, prev_resnum, prev_chainid, prev_atomnum,
- prev_atomname, this_resname, this_resnum, this_chainid,
- this_atomnum, this_atomname);
+ prev_resname,
+ prev_resnum,
+ prev_chainid,
+ prev_atomnum,
+ prev_atomname,
+ this_resname,
+ this_resnum,
+ this_chainid,
+ this_atomnum,
+ this_atomname);
if (nullptr == fgets(select, STRLEN - 1, stdin))
{
Aromatics,
Count
};
-const gmx::EnumerationArray<VSitesType, const char*> c_vsitesTypeNames = { { "none", "hydrogens",
- "aromatics" } };
+const gmx::EnumerationArray<VSitesType, const char*> c_vsitesTypeNames = {
+ { "none", "hydrogens", "aromatics" }
+};
enum class WaterType : int
{
Interactive,
Count
};
-const gmx::EnumerationArray<MergeType, const char*> c_mergeTypeNames = { { "no", "all",
- "interactive" } };
+const gmx::EnumerationArray<MergeType, const char*> c_mergeTypeNames = {
+ { "no", "all", "interactive" }
+};
} // namespace
}
/* Force field selection, interactive or direct */
- choose_ff(strcmp(ff_.c_str(), "select") == 0 ? nullptr : ff_.c_str(), forcefield_,
- sizeof(forcefield_), ffdir_, sizeof(ffdir_), loggerOwner_->logger());
+ choose_ff(strcmp(ff_.c_str(), "select") == 0 ? nullptr : ff_.c_str(),
+ forcefield_,
+ sizeof(forcefield_),
+ ffdir_,
+ sizeof(ffdir_),
+ loggerOwner_->logger());
if (strlen(forcefield_) > 0)
{
PbcType pbcType;
t_atoms pdba_all;
rvec* pdbx;
- int natom = read_pdball(inputConfFile_.c_str(), bOutputSet_, outFile_.c_str(), &title, &pdba_all,
- &pdbx, &pbcType, box, bRemoveH_, &symtab, &rt, watres, &aps, bVerbose_);
+ int natom = read_pdball(inputConfFile_.c_str(),
+ bOutputSet_,
+ outFile_.c_str(),
+ &title,
+ &pdba_all,
+ &pdbx,
+ &pbcType,
+ box,
+ bRemoveH_,
+ &symtab,
+ &rt,
+ watres,
+ &aps,
+ bVerbose_);
if (natom == 0)
{
"%s) and chain starting with "
"residue %s%d (chain id '%c', atom %d %s) into a single "
"moleculetype (keeping termini)? [n/y]",
- prev_resname, prev_resnum, prev_chainid, prev_atomnum,
- prev_atomname, this_resname, this_resnum, this_chainid,
- this_atomnum, this_atomname);
+ prev_resname,
+ prev_resnum,
+ prev_chainid,
+ prev_atomnum,
+ prev_atomname,
+ this_resname,
+ this_resnum,
+ this_chainid,
+ this_atomnum,
+ this_atomname);
if (nullptr == fgets(select, STRLEN - 1, stdin))
{
.appendTextFormatted(
"There are %d chains and %d blocks of water and "
"%d residues with %d atoms",
- numChains - nwaterchain, nwaterchain, pdba_all.nres, natom);
+ numChains - nwaterchain,
+ nwaterchain,
+ pdba_all.nres,
+ natom);
GMX_LOG(logger.info)
.asParagraph()
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted(" %d '%c' %5d %6d %s\n", i + 1,
- chains[i].chainid ? chains[i].chainid : '-', chains[i].pdba->nres,
- chains[i].pdba->nr, chains[i].bAllWat ? "(only water)" : "");
+ .appendTextFormatted(" %d '%c' %5d %6d %s\n",
+ i + 1,
+ chains[i].chainid ? chains[i].chainid : '-',
+ chains[i].pdba->nres,
+ chains[i].pdba->nr,
+ chains[i].bAllWat ? "(only water)" : "");
}
check_occupancy(&pdba_all, inputConfFile_.c_str(), bVerbose_, logger);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Processing chain %d '%c' (%d atoms, %d residues)",
- chain + 1, cc->chainid, natom, nres);
+ chain + 1,
+ cc->chainid,
+ natom,
+ nres);
}
else
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Processing chain %d (%d atoms, %d residues)", chain + 1,
- natom, nres);
- }
-
- process_chain(logger, pdba, x, bUnA_, bUnA_, bUnA_, bLysMan_, bAspMan_, bGluMan_, bHisMan_,
- bArgMan_, bGlnMan_, angle_, distance_, &symtab, rtprename);
+ .appendTextFormatted(
+ "Processing chain %d (%d atoms, %d residues)", chain + 1, natom, nres);
+ }
+
+ process_chain(logger,
+ pdba,
+ x,
+ bUnA_,
+ bUnA_,
+ bUnA_,
+ bLysMan_,
+ bAspMan_,
+ bGluMan_,
+ bHisMan_,
+ bArgMan_,
+ bGlnMan_,
+ angle_,
+ distance_,
+ &symtab,
+ rtprename);
cc->chainstart[cc->nterpairs] = pdba->nres;
j = 0;
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, logger);
+ find_nc_ter(
+ pdba, cc->chainstart[i], cc->chainstart[i + 1], &(cc->r_start[j]), &(cc->r_end[j]), &rt, logger);
if (cc->r_start[j] >= 0 && cc->r_end[j] >= 0)
{
- if (checkChainCyclicity(pdba, pdbx, cc->r_start[j], cc->r_end[j], rtpFFDB,
- rtprename, long_bond_dist_, short_bond_dist_))
+ if (checkChainCyclicity(
+ pdba, pdbx, cc->r_start[j], cc->r_end[j], rtpFFDB, rtprename, long_bond_dist_, short_bond_dist_))
{
cc->cyclicBondsIndex.push_back(cc->r_start[j]);
cc->cyclicBondsIndex.push_back(cc->r_end[j]);
{
if (bTerMan_ && !tdblist.empty())
{
- sprintf(select, "Select start terminus type for %s-%d",
- *pdba->resinfo[cc->r_start[i]].name, pdba->resinfo[cc->r_start[i]].nr);
+ sprintf(select,
+ "Select start terminus type for %s-%d",
+ *pdba->resinfo[cc->r_start[i]].name,
+ pdba->resinfo[cc->r_start[i]].nr);
cc->ntdb.push_back(choose_ter(tdblist, select));
}
else
cc->ntdb.push_back(tdblist[0]);
}
- printf("Start terminus %s-%d: %s\n", *pdba->resinfo[cc->r_start[i]].name,
- pdba->resinfo[cc->r_start[i]].nr, (cc->ntdb[i])->name.c_str());
+ printf("Start terminus %s-%d: %s\n",
+ *pdba->resinfo[cc->r_start[i]].name,
+ pdba->resinfo[cc->r_start[i]].nr,
+ (cc->ntdb[i])->name.c_str());
tdblist.clear();
}
}
{
if (bTerMan_ && !tdblist.empty())
{
- sprintf(select, "Select end terminus type for %s-%d",
- *pdba->resinfo[cc->r_end[i]].name, pdba->resinfo[cc->r_end[i]].nr);
+ sprintf(select,
+ "Select end terminus type for %s-%d",
+ *pdba->resinfo[cc->r_end[i]].name,
+ pdba->resinfo[cc->r_end[i]].nr);
cc->ctdb.push_back(choose_ter(tdblist, select));
}
else
{
cc->ctdb.push_back(tdblist[0]);
}
- printf("End terminus %s-%d: %s\n", *pdba->resinfo[cc->r_end[i]].name,
- pdba->resinfo[cc->r_end[i]].nr, (cc->ctdb[i])->name.c_str());
+ printf("End terminus %s-%d: %s\n",
+ *pdba->resinfo[cc->r_end[i]].name,
+ pdba->resinfo[cc->r_end[i]].nr,
+ (cc->ctdb[i])->name.c_str());
tdblist.clear();
}
}
std::vector<MoleculePatchDatabase> hb_chain;
/* lookup hackblocks and rtp for all residues */
std::vector<PreprocessResidue> restp_chain;
- get_hackblocks_rtp(&hb_chain, &restp_chain, rtpFFDB, pdba->nres, pdba->resinfo, cc->nterpairs,
- &symtab, cc->ntdb, cc->ctdb, cc->r_start, cc->r_end, bAllowMissing_, logger);
+ get_hackblocks_rtp(&hb_chain,
+ &restp_chain,
+ rtpFFDB,
+ pdba->nres,
+ pdba->resinfo,
+ cc->nterpairs,
+ &symtab,
+ cc->ntdb,
+ cc->ctdb,
+ cc->r_start,
+ cc->r_end,
+ bAllowMissing_,
+ logger);
/* ideally, now we would not need the rtp itself anymore, but do
everything using the hb and restp arrays. Unfortunately, that
requires some re-thinking of code in gen_vsite.c, which I won't
.asParagraph()
.appendTextFormatted(
"Generating any missing hydrogen atoms and/or adding termini.");
- add_h(&pdba, &localAtoms[chain], &x, ah, &symtab, cc->nterpairs, cc->ntdb, cc->ctdb,
- cc->r_start, cc->r_end, bAllowMissing_, cc->cyclicBondsIndex);
+ add_h(&pdba,
+ &localAtoms[chain],
+ &x,
+ ah,
+ &symtab,
+ cc->nterpairs,
+ cc->ntdb,
+ cc->ctdb,
+ cc->r_start,
+ cc->r_end,
+ bAllowMissing_,
+ cc->cyclicBondsIndex);
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Now there are %d residues with %d atoms", pdba->nres, pdba->nr);
top_file2 = top_file;
}
- pdb2top(top_file2, posre_fn.c_str(), molname.c_str(), pdba, &x, &atype, &symtab, rtpFFDB,
- restp_chain, hb_chain, bAllowMissing_, bVsites_, bVsiteAromatics_, ffdir_, mHmult_,
- ssbonds, long_bond_dist_, short_bond_dist_, bDeuterate_, bChargeGroups_, bCmap_,
- bRenumRes_, bRTPresname_, cc->cyclicBondsIndex, logger);
+ pdb2top(top_file2,
+ posre_fn.c_str(),
+ molname.c_str(),
+ pdba,
+ &x,
+ &atype,
+ &symtab,
+ rtpFFDB,
+ restp_chain,
+ hb_chain,
+ bAllowMissing_,
+ bVsites_,
+ bVsiteAromatics_,
+ ffdir_,
+ mHmult_,
+ ssbonds,
+ long_bond_dist_,
+ short_bond_dist_,
+ bDeuterate_,
+ bChargeGroups_,
+ bCmap_,
+ bRenumRes_,
+ bRTPresname_,
+ cc->cyclicBondsIndex,
+ logger);
if (!cc->bAllWat)
{
"The topology file '%s' for the selected water "
"model '%s' can not be found in the force field "
"directory. Select a different water model.",
- waterFile.c_str(), watermodel_);
+ waterFile.c_str(),
+ watermodel_);
GMX_THROW(InconsistentInputError(message));
}
}
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted("Including chain %d in system: %d atoms %d residues",
- i + 1, chains[i].pdba->nr, chains[i].pdba->nres);
+ i + 1,
+ chains[i].pdba->nr,
+ chains[i].pdba->nres);
}
for (int j = 0; (j < chains[i].pdba->nr); j++)
{
{
make_new_box(atoms->nr, gmx::as_rvec_array(x.data()), box, box_space, false);
}
- write_sto_conf(outputConfFile_.c_str(), title, atoms, gmx::as_rvec_array(x.data()), nullptr,
- pbcType, box);
+ write_sto_conf(
+ outputConfFile_.c_str(), title, atoms, gmx::as_rvec_array(x.data()), nullptr, pbcType, box);
done_symtab(&symtab);
done_atom(&pdba_all);
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("The %s force field and the %s water model are used.", ffname_,
- watermodel_);
+ .appendTextFormatted(
+ "The %s force field and the %s water model are used.", ffname_, watermodel_);
sfree(watermodel_);
}
else
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff