#include "hackblock.h"
-PreprocessingAtomTypes read_atype(const char *ffdir, t_symtab *tab)
+PreprocessingAtomTypes read_atype(const char* ffdir, t_symtab* tab)
{
- FILE *in;
- char buf[STRLEN], name[STRLEN];
- double m;
- int nratt = 0;
- t_atom *a;
+ FILE* in;
+ char buf[STRLEN], name[STRLEN];
+ double m;
+ int nratt = 0;
+ t_atom* a;
std::vector<std::string> files = fflib_search_file_end(ffdir, ".atp", TRUE);
snew(a, 1);
- PreprocessingAtomTypes at;
+ PreprocessingAtomTypes at;
- for (const auto &filename : files)
+ for (const auto& filename : files)
{
in = fflib_open(filename);
while (!feof(in))
strip_comment(buf);
trim(buf);
}
- }
- while ((feof(in) == 0) && strlen(buf) == 0);
+ } while ((feof(in) == 0) && strlen(buf) == 0);
if (sscanf(buf, "%s%lf", name, &m) == 2)
{
return at;
}
-static void print_resatoms(FILE *out, const PreprocessingAtomTypes &atype, const PreprocessResidue &rtpDBEntry)
+static void print_resatoms(FILE* out, const PreprocessingAtomTypes& atype, const PreprocessResidue& rtpDBEntry)
{
fprintf(out, "[ %s ]\n", rtpDBEntry.resname.c_str());
fprintf(out, " [ atoms ]\n");
for (int j = 0; (j < rtpDBEntry.natom()); j++)
{
int tp = rtpDBEntry.atom[j].type;
- const char *tpnm = atype.atomNameFromAtomType(tp);
+ const char* tpnm = atype.atomNameFromAtomType(tp);
if (tpnm == nullptr)
{
gmx_fatal(FARGS, "Incorrect atomtype (%d)", tp);
}
- fprintf(out, "%6s %6s %8.3f %6d\n",
- *(rtpDBEntry.atomname[j]), tpnm, rtpDBEntry.atom[j].q, rtpDBEntry.cgnr[j]);
+ fprintf(out, "%6s %6s %8.3f %6d\n", *(rtpDBEntry.atomname[j]), tpnm,
+ rtpDBEntry.atom[j].q, rtpDBEntry.cgnr[j]);
}
}
-static bool read_atoms(FILE *in, char *line,
- PreprocessResidue *r0, t_symtab *tab, PreprocessingAtomTypes *atype)
+static bool read_atoms(FILE* in, char* line, PreprocessResidue* r0, t_symtab* tab, PreprocessingAtomTypes* atype)
{
int cg;
char buf[256], buf1[256];
r0->atom.emplace_back();
r0->atom.back().q = q;
r0->cgnr.push_back(cg);
- int j = atype->atomTypeFromName(buf1);
+ int j = atype->atomTypeFromName(buf1);
if (j == NOTSET)
{
- gmx_fatal(FARGS, "Atom type %s (residue %s) not found in atomtype "
- "database", buf1, r0->resname.c_str());
+ gmx_fatal(FARGS,
+ "Atom type %s (residue %s) not found in atomtype "
+ "database",
+ buf1, r0->resname.c_str());
}
r0->atom.back().type = j;
r0->atom.back().m = atype->atomMassFromAtomType(j);
return TRUE;
}
-static bool read_bondeds(int bt, FILE *in, char *line, PreprocessResidue *rtpDBEntry)
+static bool read_bondeds(int bt, FILE* in, char* line, PreprocessResidue* rtpDBEntry)
{
char str[STRLEN];
while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == nullptr))
{
- int n = 0;
- int ni;
+ int n = 0;
+ int ni;
rtpDBEntry->rb[bt].b.emplace_back();
- BondedInteraction *newBond = &rtpDBEntry->rb[bt].b.back();
+ BondedInteraction* newBond = &rtpDBEntry->rb[bt].b.back();
for (int j = 0; j < btsNiatoms[bt]; j++)
{
- if (sscanf(line+n, "%s%n", str, &ni) == 1)
+ if (sscanf(line + n, "%s%n", str, &ni) == 1)
{
- newBond->a[j] = str;
+ newBond->a[j] = str;
}
else
{
{
n++;
}
- rtrim(line+n);
- newBond->s = line+n;
+ rtrim(line + n);
+ newBond->s = line + n;
}
return TRUE;
}
-static void print_resbondeds(FILE *out, int bt, const PreprocessResidue &rtpDBEntry)
+static void print_resbondeds(FILE* out, int bt, const PreprocessResidue& rtpDBEntry)
{
if (!rtpDBEntry.rb[bt].b.empty())
{
fprintf(out, " [ %s ]\n", btsNames[bt]);
- for (const auto &b : rtpDBEntry.rb[bt].b)
+ for (const auto& b : rtpDBEntry.rb[bt].b)
{
for (int j = 0; j < btsNiatoms[bt]; j++)
{
}
}
-static void check_rtp(gmx::ArrayRef<const PreprocessResidue> rtpDBEntry, const std::string &libfn)
+static void check_rtp(gmx::ArrayRef<const PreprocessResidue> rtpDBEntry, const std::string& libfn)
{
/* check for double entries, assuming list is already sorted */
for (auto it = rtpDBEntry.begin() + 1; it != rtpDBEntry.end(); it++)
{
- auto prev = it-1;
+ auto prev = it - 1;
if (gmx::equalCaseInsensitive(prev->resname, it->resname))
{
- fprintf(stderr, "WARNING double entry %s in file %s\n",
- it->resname.c_str(), libfn.c_str());
+ fprintf(stderr, "WARNING double entry %s in file %s\n", it->resname.c_str(), libfn.c_str());
}
}
}
}
/* print all the ebtsNR type numbers */
-static void print_resall_header(FILE *out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
+static void print_resall_header(FILE* out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
fprintf(out, "[ bondedtypes ]\n");
- fprintf(out, "; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih\n");
- fprintf(out, " %5d %6d %9d %9d %14d %14d %14d %14d\n\n",
- rtpDBEntry[0].rb[0].type,
- rtpDBEntry[0].rb[1].type,
- rtpDBEntry[0].rb[2].type,
- rtpDBEntry[0].rb[3].type,
- static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals),
- rtpDBEntry[0].nrexcl,
+ fprintf(out,
+ "; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 "
+ "remove_dih\n");
+ fprintf(out, " %5d %6d %9d %9d %14d %14d %14d %14d\n\n", rtpDBEntry[0].rb[0].type,
+ rtpDBEntry[0].rb[1].type, rtpDBEntry[0].rb[2].type, rtpDBEntry[0].rb[3].type,
+ static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals), rtpDBEntry[0].nrexcl,
static_cast<int>(rtpDBEntry[0].bGenerateHH14Interactions),
static_cast<int>(rtpDBEntry[0].bRemoveDihedralIfWithImproper));
}
-void print_resall(FILE *out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
- const PreprocessingAtomTypes &atype)
+void print_resall(FILE* out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry, const PreprocessingAtomTypes& atype)
{
if (rtpDBEntry.empty())
{
print_resall_header(out, rtpDBEntry);
- for (const auto &r : rtpDBEntry)
+ for (const auto& r : rtpDBEntry)
{
if (r.natom() > 0)
{
}
}
-void readResidueDatabase(const std::string &rrdb, std::vector<PreprocessResidue> *rtpDBEntry,
- PreprocessingAtomTypes *atype, t_symtab *tab,
- bool bAllowOverrideRTP)
+void readResidueDatabase(const std::string& rrdb,
+ std::vector<PreprocessResidue>* rtpDBEntry,
+ PreprocessingAtomTypes* atype,
+ t_symtab* tab,
+ bool bAllowOverrideRTP)
{
- FILE *in;
- char filebase[STRLEN], line[STRLEN], header[STRLEN];
- int bt, nparam;
- int dum1, dum2, dum3;
- bool bNextResidue, bError;
+ FILE* in;
+ char filebase[STRLEN], line[STRLEN], header[STRLEN];
+ int bt, nparam;
+ int dum1, dum2, dum3;
+ bool bNextResidue, bError;
fflib_filename_base(rrdb.c_str(), filebase, STRLEN);
if (gmx::equalCaseInsensitive("bondedtypes", header, 5))
{
get_a_line(in, line, STRLEN);
- if ((nparam = sscanf(line, "%d %d %d %d %d %d %d %d",
- &header_settings.rb[ebtsBONDS].type, &header_settings.rb[ebtsANGLES].type,
+ if ((nparam = sscanf(line, "%d %d %d %d %d %d %d %d", &header_settings.rb[ebtsBONDS].type,
+ &header_settings.rb[ebtsANGLES].type,
&header_settings.rb[ebtsPDIHS].type, &header_settings.rb[ebtsIDIHS].type,
- &dum1, &header_settings.nrexcl, &dum2, &dum3)) < 4)
+ &dum1, &header_settings.nrexcl, &dum2, &dum3))
+ < 4)
{
- gmx_fatal(FARGS, "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n", rrdb.c_str(), line);
+ gmx_fatal(FARGS, "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n",
+ rrdb.c_str(), line);
}
header_settings.bKeepAllGeneratedDihedrals = (dum1 != 0);
header_settings.bGenerateHH14Interactions = (dum2 != 0);
}
if (nparam < 8)
{
- fprintf(stderr, "Using default: removing proper dihedrals found on the same bond as a proper dihedral\n");
+ fprintf(stderr,
+ "Using default: removing proper dihedrals found on the same bond as a proper "
+ "dihedral\n");
header_settings.bRemoveDihedralIfWithImproper = TRUE;
}
}
{
/* Initialise rtp entry structure */
rtpDBEntry->push_back(header_settings);
- PreprocessResidue *res = &rtpDBEntry->back();
+ PreprocessResidue* res = &rtpDBEntry->back();
if (!get_header(line, header))
{
gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
}
if (bError)
{
- gmx_fatal(FARGS, "in .rtp file in residue %s at line:\n%s\n",
- res->resname.c_str(), line);
+ gmx_fatal(FARGS, "in .rtp file in residue %s at line:\n%s\n", res->resname.c_str(), line);
}
- }
- while ((feof(in) == 0) && !bNextResidue);
+ } while ((feof(in) == 0) && !bNextResidue);
if (res->natom() == 0)
{
- gmx_fatal(FARGS, "No atoms found in .rtp file in residue %s\n",
- res->resname.c_str());
+ gmx_fatal(FARGS, "No atoms found in .rtp file in residue %s\n", res->resname.c_str());
}
- auto found = std::find_if(rtpDBEntry->begin(), rtpDBEntry->end()-1,
- [&res](const PreprocessResidue &entry)
- { return gmx::equalCaseInsensitive(entry.resname, res->resname); });
+ auto found = std::find_if(rtpDBEntry->begin(), rtpDBEntry->end() - 1,
+ [&res](const PreprocessResidue& entry) {
+ return gmx::equalCaseInsensitive(entry.resname, res->resname);
+ });
if (found == rtpDBEntry->end() - 1)
{
{
if (found >= oldArrayEnd)
{
- gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'",
- res->resname.c_str(), rrdb.c_str());
+ gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'", res->resname.c_str(),
+ rrdb.c_str());
}
if (bAllowOverrideRTP)
{
fprintf(stderr, "\n");
- fprintf(stderr, "Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
+ fprintf(stderr,
+ "Found another rtp entry for '%s' in '%s', ignoring this entry and keeping "
+ "the one from '%s.rtp'\n",
res->resname.c_str(), rrdb.c_str(), found->filebase.c_str());
/* We should free all the data for this entry.
* The current code gives a lot of dangling pointers.
}
else
{
- gmx_fatal(FARGS, "Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.", res->resname.c_str(), found->filebase.c_str(), rrdb.c_str());
+ gmx_fatal(FARGS,
+ "Found rtp entries for '%s' in both '%s' and '%s'. If you want the first "
+ "definition to override the second one, set the -rtpo option of pdb2gmx.",
+ res->resname.c_str(), found->filebase.c_str(), rrdb.c_str());
}
}
}
gmx_ffclose(in);
fprintf(stderr, "\nSorting it all out...\n");
- std::sort(rtpDBEntry->begin(), rtpDBEntry->end(), []
- (const PreprocessResidue &a,
- const PreprocessResidue &b)
- {return std::lexicographical_compare(
- a.resname.begin(), a.resname.end(),
- b.resname.begin(), b.resname.end(),
- [](const char &c1, const char &c2)
- { return std::toupper(c1) < std::toupper(c2); }); });
+ std::sort(rtpDBEntry->begin(), rtpDBEntry->end(), [](const PreprocessResidue& a, const PreprocessResidue& b) {
+ return std::lexicographical_compare(
+ a.resname.begin(), a.resname.end(), b.resname.begin(), b.resname.end(),
+ [](const char& c1, const char& c2) { return std::toupper(c1) < std::toupper(c2); });
+ });
check_rtp(*rtpDBEntry, rrdb);
}
/* Compares if the strins match except for a sign at the end
* of (only) one of the two.
*/
-static int neq_str_sign(const char *a1, const char *a2)
+static int neq_str_sign(const char* a1, const char* a2)
{
int l1, l2, lm;
l2 = static_cast<int>(strlen(a2));
lm = std::min(l1, l2);
- if (lm >= 1 &&
- ((l1 == l2+1 && is_sign(a1[l1-1])) ||
- (l2 == l1+1 && is_sign(a2[l2-1]))) &&
- gmx::equalCaseInsensitive(a1, a2, lm))
+ if (lm >= 1 && ((l1 == l2 + 1 && is_sign(a1[l1 - 1])) || (l2 == l1 + 1 && is_sign(a2[l2 - 1])))
+ && gmx::equalCaseInsensitive(a1, a2, lm))
{
return lm;
}
}
}
-std::string searchResidueDatabase(const std::string &key, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
+std::string searchResidueDatabase(const std::string& key, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
int nbest, best, besti;
std::string bestbuf;
- nbest = 0;
+ nbest = 0;
besti = -1;
/* We want to match at least one character */
- best = 1;
+ best = 1;
for (auto it = rtpDBEntry.begin(); it != rtpDBEntry.end(); it++)
{
if (gmx::equalCaseInsensitive(key, it->resname))
{
/* Allow a mismatch of at most a sign character (with warning) */
int n = neq_str_sign(key.c_str(), it->resname.c_str());
- if (n >= best &&
- n+1 >= gmx::index(key.length()) &&
- n+1 >= gmx::index(it->resname.length()))
+ if (n >= best && n + 1 >= gmx::index(key.length()) && n + 1 >= gmx::index(it->resname.length()))
{
if (n == best)
{
}
if (nbest > 1)
{
- gmx_fatal(FARGS, "Residue '%s' not found in residue topology database, looks a bit like %s", key.c_str(), bestbuf.c_str());
+ gmx_fatal(FARGS, "Residue '%s' not found in residue topology database, looks a bit like %s",
+ key.c_str(), bestbuf.c_str());
}
else if (besti == -1)
{
{
fprintf(stderr,
"\nWARNING: '%s' not found in residue topology database, "
- "trying to use '%s'\n\n", key.c_str(), rtpDBEntry[besti].resname.c_str());
+ "trying to use '%s'\n\n",
+ key.c_str(), rtpDBEntry[besti].resname.c_str());
}
return rtpDBEntry[besti].resname;
}
gmx::ArrayRef<const PreprocessResidue>::const_iterator
-getDatabaseEntry(const std::string &rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
+getDatabaseEntry(const std::string& rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
auto found = std::find_if(rtpDBEntry.begin(), rtpDBEntry.end(),
- [&rtpname](const PreprocessResidue &entry)
- { return gmx::equalCaseInsensitive(rtpname, entry.resname); });
+ [&rtpname](const PreprocessResidue& entry) {
+ return gmx::equalCaseInsensitive(rtpname, entry.resname);
+ });
if (found == rtpDBEntry.end())
{
/* This should never happen, since searchResidueDatabase should have been called
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff