GMX_LOG(logger.warning)
.asParagraph()
.appendTextFormatted("atom %s is missing in residue %s %d in the pdb file",
- name, *(at->resinfo[resind].name), at->resinfo[resind].nr);
+ name,
+ *(at->resinfo[resind].name),
+ at->resinfo[resind].nr);
if (name[0] == 'H' || name[0] == 'h')
{
GMX_LOG(logger.warning)
"You might need to add atom %s to the hydrogen database of "
"building block %s "
"in the file %s.hdb (see the manual)",
- name, *(at->resinfo[resind].rtp), rp->filebase.c_str());
+ name,
+ *(at->resinfo[resind].rtp),
+ rp->filebase.c_str());
}
}
}
"Force field '%s' occurs in %d places. pdb2gmx is using the one in "
"the current directory. Use interactive selection "
"(not the -ff option) if you would prefer a different one.",
- ffsel, nfound);
+ ffsel,
+ nfound);
}
else
{
"the current directory.\n"
"Run without the -ff switch and select the force "
"field interactively.",
- ffsel, nfound);
+ ffsel,
+ nfound);
GMX_THROW(gmx::InconsistentInputError(message));
}
}
"to point to the desired force field first, and/or "
"rename or move the force field directory present "
"in the current working directory.",
- ffs[sel].c_str(), fflib_forcefield_dir_ext());
+ ffs[sel].c_str(),
+ fflib_forcefield_dir_ext());
GMX_THROW(gmx::NotImplementedError(message));
}
}
if (ffs[sel].length() >= static_cast<size_t>(ff_maxlen))
{
std::string message = gmx::formatString("Length of force field name (%d) >= maxlen (%d)",
- static_cast<int>(ffs[sel].length()), ff_maxlen);
+ static_cast<int>(ffs[sel].length()),
+ ff_maxlen);
GMX_THROW(gmx::InvalidInputError(message));
}
strcpy(forcefield, ffs[sel].c_str());
if (ffpath.length() >= static_cast<size_t>(ffdir_maxlen))
{
std::string message = gmx::formatString("Length of force field dir (%d) >= maxlen (%d)",
- static_cast<int>(ffpath.length()), ffdir_maxlen);
+ static_cast<int>(ffpath.length()),
+ ffdir_maxlen);
GMX_THROW(gmx::InvalidInputError(message));
}
strcpy(ffdir, ffpath.c_str());
int aj = search_res_atom(bond.secondAtom.c_str(), rj, atoms, "special bond", bAllowMissing);
if ((ai == -1) || (aj == -1))
{
- gmx_fatal(FARGS, "Trying to make impossible special bond (%s-%s)!",
- bond.firstAtom.c_str(), bond.secondAtom.c_str());
+ gmx_fatal(FARGS,
+ "Trying to make impossible special bond (%s-%s)!",
+ bond.firstAtom.c_str(),
+ bond.secondAtom.c_str());
}
add_param(ps, ai, aj, {}, nullptr);
}
{
GMX_LOG(logger.warning)
.asParagraph()
- .appendTextFormatted("Long Bond (%d-%d = %g nm)", ai + 1, aj + 1,
- std::sqrt(dist2));
+ .appendTextFormatted(
+ "Long Bond (%d-%d = %g nm)", ai + 1, aj + 1, std::sqrt(dist2));
}
else if (dist2 < short_bond_dist2)
{
GMX_LOG(logger.warning)
.asParagraph()
- .appendTextFormatted("Short Bond (%d-%d = %g nm)", ai + 1, aj + 1,
- std::sqrt(dist2));
+ .appendTextFormatted(
+ "Short Bond (%d-%d = %g nm)", ai + 1, aj + 1, std::sqrt(dist2));
}
add_param(psb, ai, aj, {}, patch.s.c_str());
}
static void check_restp_types(const PreprocessResidue& r0, const PreprocessResidue& r1)
{
- check_restp_type("all dihedrals", static_cast<int>(r0.bKeepAllGeneratedDihedrals),
+ check_restp_type("all dihedrals",
+ static_cast<int>(r0.bKeepAllGeneratedDihedrals),
static_cast<int>(r1.bKeepAllGeneratedDihedrals));
check_restp_type("nrexcl", r0.nrexcl, r1.nrexcl);
- check_restp_type("HH14", static_cast<int>(r0.bGenerateHH14Interactions),
+ check_restp_type("HH14",
+ static_cast<int>(r0.bGenerateHH14Interactions),
static_cast<int>(r1.bGenerateHH14Interactions));
- check_restp_type("remove dihedrals", static_cast<int>(r0.bRemoveDihedralIfWithImproper),
+ check_restp_type("remove dihedrals",
+ static_cast<int>(r0.bRemoveDihedralIfWithImproper),
static_cast<int>(r1.bRemoveDihedralIfWithImproper));
for (int i = 0; i < ebtsNR; i++)
if (patch->nr != 0)
{
/* find atom in restp */
- auto found = std::find_if(posres->atomname.begin(), posres->atomname.end(),
- [&patch](char** name) {
- return (patch->oname.empty() && patch->a[0] == *name)
- || (patch->oname == *name);
- });
+ auto found = std::find_if(
+ posres->atomname.begin(), posres->atomname.end(), [&patch](char** name) {
+ return (patch->oname.empty() && patch->a[0] == *name)
+ || (patch->oname == *name);
+ });
if (found == posres->atomname.end())
{
"atom %s not found in buiding block %d%s "
"while combining tdb and rtp",
patch->oname.empty() ? patch->a[0].c_str() : patch->oname.c_str(),
- pos + 1, *resinfo[pos].rtp);
+ pos + 1,
+ *resinfo[pos].rtp);
}
}
else
/* This atom still has the old name, rename it */
std::string newnm = patch->nname;
auto found = std::find_if(
- localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
+ localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
[&newnm](char** name) { return gmx::equalCaseInsensitive(newnm, *name); });
if (found == localPpResidue->atomname.end())
{
*/
bool bFoundInAdd = false;
for (auto rtpModification = singlePatch.hack.begin();
- rtpModification != singlePatch.hack.end(); rtpModification++)
+ rtpModification != singlePatch.hack.end();
+ rtpModification++)
{
int k = std::distance(localPpResidue->atomname.begin(), found);
std::string start_at;
}
else
{
- start_at = gmx::formatString("%s%d", singlePatch.hack[k].nname.c_str(),
- anmnr - 1);
+ start_at = gmx::formatString(
+ "%s%d", singlePatch.hack[k].nname.c_str(), anmnr - 1);
}
- auto found2 =
- std::find_if(localPpResidue->atomname.begin(),
- localPpResidue->atomname.end(), [&start_at](char** name) {
- return gmx::equalCaseInsensitive(start_at, *name);
- });
+ auto found2 = std::find_if(localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
+ [&start_at](char** name) {
+ return gmx::equalCaseInsensitive(start_at, *name);
+ });
if (found2 == localPpResidue->atomname.end())
{
gmx_fatal(FARGS,
"Could not find atom '%s' in residue building block '%s' to "
"add atom '%s' to",
- start_at.c_str(), localPpResidue->resname.c_str(), newnm.c_str());
+ start_at.c_str(),
+ localPpResidue->resname.c_str(),
+ newnm.c_str());
}
/* We can add the atom after atom start_nr */
- add_atom_to_restp(localPpResidue, symtab,
+ add_atom_to_restp(localPpResidue,
+ symtab,
std::distance(localPpResidue->atomname.begin(), found2),
&(*patch));
"Could not find an 'add' entry for atom named '%s' corresponding to "
"the 'replace' entry from atom name '%s' to '%s' for tdb or hdb "
"database of residue type '%s'",
- newnm.c_str(), patch->oname.c_str(), patch->nname.c_str(),
+ newnm.c_str(),
+ patch->oname.c_str(),
+ patch->nname.c_str(),
localPpResidue->resname.c_str());
}
}
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Renaming atom '%s' in residue '%s' %d to '%s'", oldnm,
- localPpResidue->resname.c_str(), resnr, newnm.c_str());
+ .appendTextFormatted("Renaming atom '%s' in residue '%s' %d to '%s'",
+ oldnm,
+ localPpResidue->resname.c_str(),
+ resnr,
+ newnm.c_str());
}
/* Rename the atom in pdba */
pdba->atomname[atind] = put_symtab(symtab, newnm.c_str());
* in the rtp entry of this residue.
*/
auto found3 = std::find_if(
- localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
+ localPpResidue->atomname.begin(),
+ localPpResidue->atomname.end(),
[&oldnm](char** name) { return gmx::equalCaseInsensitive(oldnm, *name); });
if (found3 == localPpResidue->atomname.end())
{
{
GMX_LOG(logger.info)
.asParagraph()
- .appendTextFormatted("Deleting atom '%s' in residue '%s' %d", oldnm,
- localPpResidue->resname.c_str(), resnr);
+ .appendTextFormatted("Deleting atom '%s' in residue '%s' %d",
+ oldnm,
+ localPpResidue->resname.c_str(),
+ resnr);
}
/* We should free the atom name,
* but it might be used multiple times in the symtab.
const char* oldnm = *pdba->atomname[i];
PreprocessResidue* localPpResidue = &usedPpResidues[pdba->atom[i].resind];
auto found = std::find_if(
- localPpResidue->atomname.begin(), localPpResidue->atomname.end(),
- [&oldnm](char** name) { return gmx::equalCaseInsensitive(oldnm, *name); });
+ localPpResidue->atomname.begin(), localPpResidue->atomname.end(), [&oldnm](char** name) {
+ return gmx::equalCaseInsensitive(oldnm, *name);
+ });
if (found == localPpResidue->atomname.end())
{
/* Not found yet, check if we have to rename this atom */
- if (match_atomnames_with_rtp_atom(pdba, x, symtab, i, localPpResidue,
- globalPatches[pdba->atom[i].resind], bVerbose, logger))
+ if (match_atomnames_with_rtp_atom(
+ pdba, x, symtab, i, localPpResidue, globalPatches[pdba->atom[i].resind], bVerbose, logger))
{
/* We deleted this atom, decrease the atom counter by 1. */
i--;
if (bAddCMAP)
{
- add_cmap_param(psb, cmap_atomid[0], cmap_atomid[1], cmap_atomid[2], cmap_atomid[3],
- cmap_atomid[4], b.s.c_str());
+ add_cmap_param(psb,
+ cmap_atomid[0],
+ cmap_atomid[1],
+ cmap_atomid[2],
+ cmap_atomid[3],
+ cmap_atomid[4],
+ b.s.c_str());
}
}
ResidueType rt;
/* Make bonds */
- at2bonds(&(plist[F_BONDS]), globalPatches, atoms, *x, long_bond_dist, short_bond_dist,
- cyclicBondsIndex, logger);
+ at2bonds(&(plist[F_BONDS]), globalPatches, atoms, *x, long_bond_dist, short_bond_dist, cyclicBondsIndex, logger);
/* specbonds: disulphide bonds & heme-his */
do_ssbonds(&(plist[F_BONDS]), atoms, ssbonds, bAllowMissing);
gmx_fatal(FARGS,
"There were %d missing atoms in molecule %s, if you want to use this "
"incomplete topology anyhow, use the option -missing",
- nmissat, molname);
+ nmissat,
+ molname);
}
}
.appendTextFormatted(
"There are %4zu dihedrals, %4zu impropers, %4zu angles\n"
" %4zu pairs, %4zu bonds and %4zu virtual sites",
- plist[F_PDIHS].size(), plist[F_IDIHS].size(), plist[F_ANGLES].size(),
- plist[F_LJ14].size(), plist[F_BONDS].size(),
+ plist[F_PDIHS].size(),
+ plist[F_IDIHS].size(),
+ plist[F_ANGLES].size(),
+ plist[F_LJ14].size(),
+ plist[F_BONDS].size(),
plist[F_VSITE2].size() + plist[F_VSITE3].size() + plist[F_VSITE3FD].size()
+ plist[F_VSITE3FAD].size() + plist[F_VSITE3OUT].size()
+ plist[F_VSITE4FD].size() + plist[F_VSITE4FDN].size());
{
bts[i] = usedPpResidues[0].rb[i].type;
}
- write_top(top_file, posre_fn, molname, atoms, bRTPresname, bts, plist, excls, atype, cgnr,
+ write_top(top_file,
+ posre_fn,
+ molname,
+ atoms,
+ bRTPresname,
+ bts,
+ plist,
+ excls,
+ atype,
+ cgnr,
usedPpResidues[0].nrexcl);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff