do
{
c = toupper(fgetc(stdin));
- }
- while ((c != 'Y') && (c != 'N'));
+ } while ((c != 'Y') && (c != 'N'));
return (c == 'Y');
}
std::vector<SpecialBond> generateSpecialBonds()
{
- const char *sbfile = "specbond.dat";
+ const char* sbfile = "specbond.dat";
std::vector<SpecialBond> specialBonds;
char r1buf[32], r2buf[32], a1buf[32], a2buf[32], nr1buf[32], nr2buf[32];
double length;
int nb1, nb2;
- char **lines;
+ char** lines;
int nlines = get_lines(sbfile, &lines);
for (int i = 0; (i < nlines); i++)
{
- if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s",
- r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length, nr1buf, nr2buf) != 9)
+ if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s", r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length,
+ nr1buf, nr2buf)
+ != 9)
{
fprintf(stderr, "Invalid line '%s' in %s\n", lines[i], sbfile);
}
{
sfree(lines);
}
- fprintf(stderr, "%zu out of %d lines of %s converted successfully\n",
- specialBonds.size(), nlines, sbfile);
+ fprintf(stderr, "%zu out of %d lines of %s converted successfully\n", specialBonds.size(),
+ nlines, sbfile);
return specialBonds;
}
-static bool is_special(gmx::ArrayRef<const SpecialBond> sb, const char *res, const char *atom)
+static bool is_special(gmx::ArrayRef<const SpecialBond> sb, const char* res, const char* atom)
{
- for (const auto &bond : sb)
+ for (const auto& bond : sb)
{
- if (((strncmp(bond.firstResidue.c_str(), res, 3) == 0) &&
- (gmx::equalCaseInsensitive(bond.firstAtomName, atom))) ||
- ((strncmp(bond.secondResidue.c_str(), res, 3) == 0) &&
- (gmx::equalCaseInsensitive(bond.secondAtomName, atom))))
+ if (((strncmp(bond.firstResidue.c_str(), res, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.firstAtomName, atom)))
+ || ((strncmp(bond.secondResidue.c_str(), res, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.secondAtomName, atom))))
{
return TRUE;
}
return FALSE;
}
-static bool is_bond(gmx::ArrayRef<const SpecialBond> sb, t_atoms *pdba, int a1, int a2,
- real d, int *index_sb, bool *bSwap)
+static bool is_bond(gmx::ArrayRef<const SpecialBond> sb, t_atoms* pdba, int a1, int a2, real d, int* index_sb, bool* bSwap)
{
- const char *at1 = *pdba->atomname[a1];
- const char *at2 = *pdba->atomname[a2];
- const char *res1 = *pdba->resinfo[pdba->atom[a1].resind].name;
- const char *res2 = *pdba->resinfo[pdba->atom[a2].resind].name;
+ const char* at1 = *pdba->atomname[a1];
+ const char* at2 = *pdba->atomname[a2];
+ const char* res1 = *pdba->resinfo[pdba->atom[a1].resind].name;
+ const char* res2 = *pdba->resinfo[pdba->atom[a2].resind].name;
- int i = 0;
- for (const auto &bond : sb)
+ int i = 0;
+ for (const auto& bond : sb)
{
*index_sb = i;
- if (((strncmp(bond.firstResidue.c_str(), res1, 3) == 0) &&
- (gmx::equalCaseInsensitive(bond.firstAtomName, at1)) &&
- (strncmp(bond.secondResidue.c_str(), res2, 3) == 0) &&
- (gmx::equalCaseInsensitive(bond.secondAtomName, at2))))
+ if (((strncmp(bond.firstResidue.c_str(), res1, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.firstAtomName, at1))
+ && (strncmp(bond.secondResidue.c_str(), res2, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.secondAtomName, at2))))
{
*bSwap = FALSE;
- if ((0.9*bond.length < d) && (1.1*bond.length > d))
+ if ((0.9 * bond.length < d) && (1.1 * bond.length > d))
{
return TRUE;
}
}
- if (((strncmp(bond.firstResidue.c_str(), res2, 3) == 0) &&
- (gmx::equalCaseInsensitive(bond.firstAtomName, at2)) &&
- (strncmp(bond.secondResidue.c_str(), res1, 3) == 0) &&
- (gmx::equalCaseInsensitive(bond.secondAtomName, at1))))
+ if (((strncmp(bond.firstResidue.c_str(), res2, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.firstAtomName, at2))
+ && (strncmp(bond.secondResidue.c_str(), res1, 3) == 0)
+ && (gmx::equalCaseInsensitive(bond.secondAtomName, at1))))
{
*bSwap = TRUE;
- if ((0.9*bond.length < d) && (1.1*bond.length > d))
+ if ((0.9 * bond.length < d) && (1.1 * bond.length > d))
{
return TRUE;
}
return FALSE;
}
-static void rename_1res(t_atoms *pdba, int resind, const char *newres, bool bVerbose)
+static void rename_1res(t_atoms* pdba, int resind, const char* newres, bool bVerbose)
{
if (bVerbose)
{
- printf("Using rtp entry %s for %s %d\n",
- newres,
- *pdba->resinfo[resind].name,
+ printf("Using rtp entry %s for %s %d\n", newres, *pdba->resinfo[resind].name,
pdba->resinfo[resind].nr);
}
/* this used to free *resname, which messes up the symtab! */
*pdba->resinfo[resind].rtp = gmx_strdup(newres);
}
-std::vector<DisulfideBond> makeDisulfideBonds(t_atoms *pdba,
- rvec x[],
- bool bInteractive,
- bool bVerbose)
+std::vector<DisulfideBond> makeDisulfideBonds(t_atoms* pdba, rvec x[], bool bInteractive, bool bVerbose)
{
std::vector<SpecialBond> specialBonds = generateSpecialBonds();
std::vector<DisulfideBond> bonds;
{
prevAtom = specialBondAtomIdxs.back();
}
- if (is_special(specialBonds, *pdba->resinfo[pdba->atom[i].resind].name,
- *pdba->atomname[i]) &&
- !(!specialBondAtomIdxs.empty() &&
- pdba->atom[prevAtom].resind == pdba->atom[i].resind &&
- gmx_strcasecmp(*pdba->atomname[prevAtom],
- *pdba->atomname[i]) == 0))
+ if (is_special(specialBonds, *pdba->resinfo[pdba->atom[i].resind].name, *pdba->atomname[i])
+ && !(!specialBondAtomIdxs.empty() && pdba->atom[prevAtom].resind == pdba->atom[i].resind
+ && gmx_strcasecmp(*pdba->atomname[prevAtom], *pdba->atomname[i]) == 0))
{
specialBondResIdxs.push_back(pdba->atom[i].resind);
specialBondAtomIdxs.push_back(i);
}
}
/* distance matrix d[nspec][nspec] */
- int nspec = specialBondAtomIdxs.size();
- std::vector < std::vector < real>> d(nspec);
+ int nspec = specialBondAtomIdxs.size();
+ std::vector<std::vector<real>> d(nspec);
for (int i = 0; (i < nspec); i++)
{
d[i].resize(nspec);
int ai = specialBondAtomIdxs[i];
for (int j = 0; (j < nspec); j++)
{
- int aj = specialBondAtomIdxs[j];
+ int aj = specialBondAtomIdxs[j];
d[i][j] = std::sqrt(distance2(x[ai], x[aj]));
}
}
{
/* print resname/number column headings */
fprintf(stderr, "%8s%8s", "", "");
- int e = std::min(b+MAXCOL, nspec-1);
+ int e = std::min(b + MAXCOL, nspec - 1);
for (int i = b; (i < e); i++)
{
sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
fprintf(stderr, "\n");
/* print atomname/number column headings */
fprintf(stderr, "%8s%8s", "", "");
- e = std::min(b+MAXCOL, nspec-1);
+ e = std::min(b + MAXCOL, nspec - 1);
for (int i = b; (i < e); i++)
{
- std::string buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]], specialBondAtomIdxs[i]+1);
+ std::string buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
+ specialBondAtomIdxs[i] + 1);
fprintf(stderr, "%8s", buf.c_str());
}
fprintf(stderr, "\n");
/* print matrix */
- e = std::min(b+MAXCOL, nspec);
- for (int i = b+1; (i < nspec); i++)
+ e = std::min(b + MAXCOL, nspec);
+ for (int i = b + 1; (i < nspec); i++)
{
- std::string buf = gmx::formatString("%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
- pdba->resinfo[specialBondResIdxs[i]].nr);
+ std::string buf = gmx::formatString(
+ "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
+ pdba->resinfo[specialBondResIdxs[i]].nr);
fprintf(stderr, "%8s", buf.c_str());
- buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]], specialBondAtomIdxs[i]+1);
+ buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
+ specialBondAtomIdxs[i] + 1);
fprintf(stderr, "%8s", buf.c_str());
int e2 = std::min(i, e);
for (int j = b; (j < e2); j++)
for (int i = 0; (i < nspec); i++)
{
int ai = specialBondAtomIdxs[i];
- for (int j = i+1; (j < nspec); j++)
+ for (int j = i + 1; (j < nspec); j++)
{
int aj = specialBondAtomIdxs[j];
/* Ensure creation of at most nspec special bonds to avoid overflowing bonds[] */
- if (bonds.size() < specialBondAtomIdxs.size() &&
- is_bond(specialBonds, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
+ if (bonds.size() < specialBondAtomIdxs.size()
+ && is_bond(specialBonds, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
{
- fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s",
- bInteractive ? "Link" : "Linking",
+ fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s", bInteractive ? "Link" : "Linking",
*pdba->resinfo[pdba->atom[ai].resind].name,
- pdba->resinfo[specialBondResIdxs[i]].nr,
- *pdba->atomname[ai], ai+1,
+ pdba->resinfo[specialBondResIdxs[i]].nr, *pdba->atomname[ai], ai + 1,
*pdba->resinfo[pdba->atom[aj].resind].name,
- pdba->resinfo[specialBondResIdxs[j]].nr,
- *pdba->atomname[aj], aj+1,
+ pdba->resinfo[specialBondResIdxs[j]].nr, *pdba->atomname[aj], aj + 1,
bInteractive ? " (y/n) ?" : "...\n");
bool bDoit = bInteractive ? yesno() : true;
}
}
}
-
}
return bonds;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff