src/gromacs/gmxpreprocess/specbond.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "specbond.h"
  40
  41 #include <cctype>
  42 #include <cmath>
  43 #include <cstring>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/fileio/pdbio.h"
  48 #include "gromacs/gmxpreprocess/pdb2top.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/utility/cstringutil.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/smalloc.h"
  53 #include "gromacs/utility/strdb.h"
  54
  55 struct SpecialBond
  56 {
  57     std::string firstResidue, secondResidue;
  58     std::string firstAtomName, secondAtomName;
  59     std::string newFirstResidue, newSecondResidue;
  60     int         firstBondNumber, secondBondNumber;
  61     real        length;
  62 };
  63
  64 static bool yesno()
  65 {
  66     char c;
  67
  68     do
  69     {
  70         c = toupper(fgetc(stdin));
  71     } while ((c != 'Y') && (c != 'N'));
  72
  73     return (c == 'Y');
  74 }
  75
  76 std::vector<SpecialBond> generateSpecialBonds()
  77 {
  78     const char* sbfile = "specbond.dat";
  79
  80     std::vector<SpecialBond> specialBonds;
  81     char                     r1buf[32], r2buf[32], a1buf[32], a2buf[32], nr1buf[32], nr2buf[32];
  82     double                   length;
  83     int                      nb1, nb2;
  84     char**                   lines;
  85
  86     int nlines = get_lines(sbfile, &lines);
  87     for (int i = 0; (i < nlines); i++)
  88     {
  89         if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s", r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length,
  90                    nr1buf, nr2buf)
  91             != 9)
  92         {
  93             fprintf(stderr, "Invalid line '%s' in %s\n", lines[i], sbfile);
  94         }
  95         else
  96         {
  97             SpecialBond newBond;
  98
  99             newBond.firstResidue     = r1buf;
 100             newBond.secondResidue    = r2buf;
 101             newBond.newFirstResidue  = nr1buf;
 102             newBond.newSecondResidue = nr2buf;
 103             newBond.firstAtomName    = a1buf;
 104             newBond.secondAtomName   = a2buf;
 105             newBond.firstBondNumber  = nb1;
 106             newBond.secondBondNumber = nb2;
 107             newBond.length           = length;
 108             specialBonds.push_back(newBond);
 109         }
 110         sfree(lines[i]);
 111     }
 112     if (nlines > 0)
 113     {
 114         sfree(lines);
 115     }
 116     fprintf(stderr, "%zu out of %d lines of %s converted successfully\n", specialBonds.size(),
 117             nlines, sbfile);
 118
 119     return specialBonds;
 120 }
 121
 122 static bool is_special(gmx::ArrayRef<const SpecialBond> sb, const char* res, const char* atom)
 123 {
 124     for (const auto& bond : sb)
 125     {
 126         if (((strncmp(bond.firstResidue.c_str(), res, 3) == 0)
 127              && (gmx::equalCaseInsensitive(bond.firstAtomName, atom)))
 128             || ((strncmp(bond.secondResidue.c_str(), res, 3) == 0)
 129                 && (gmx::equalCaseInsensitive(bond.secondAtomName, atom))))
 130         {
 131             return TRUE;
 132         }
 133     }
 134     return FALSE;
 135 }
 136
 137 static bool is_bond(gmx::ArrayRef<const SpecialBond> sb, t_atoms* pdba, int a1, int a2, real d, int* index_sb, bool* bSwap)
 138 {
 139     const char* at1  = *pdba->atomname[a1];
 140     const char* at2  = *pdba->atomname[a2];
 141     const char* res1 = *pdba->resinfo[pdba->atom[a1].resind].name;
 142     const char* res2 = *pdba->resinfo[pdba->atom[a2].resind].name;
 143
 144     int i = 0;
 145     for (const auto& bond : sb)
 146     {
 147         *index_sb = i;
 148         if (((strncmp(bond.firstResidue.c_str(), res1, 3) == 0)
 149              && (gmx::equalCaseInsensitive(bond.firstAtomName, at1))
 150              && (strncmp(bond.secondResidue.c_str(), res2, 3) == 0)
 151              && (gmx::equalCaseInsensitive(bond.secondAtomName, at2))))
 152         {
 153             *bSwap = FALSE;
 154             if ((0.9 * bond.length < d) && (1.1 * bond.length > d))
 155             {
 156                 return TRUE;
 157             }
 158         }
 159         if (((strncmp(bond.firstResidue.c_str(), res2, 3) == 0)
 160              && (gmx::equalCaseInsensitive(bond.firstAtomName, at2))
 161              && (strncmp(bond.secondResidue.c_str(), res1, 3) == 0)
 162              && (gmx::equalCaseInsensitive(bond.secondAtomName, at1))))
 163         {
 164             *bSwap = TRUE;
 165             if ((0.9 * bond.length < d) && (1.1 * bond.length > d))
 166             {
 167                 return TRUE;
 168             }
 169         }
 170         i++;
 171     }
 172     return FALSE;
 173 }
 174
 175 static void rename_1res(t_atoms* pdba, int resind, const char* newres, bool bVerbose)
 176 {
 177     if (bVerbose)
 178     {
 179         printf("Using rtp entry %s for %s %d\n", newres, *pdba->resinfo[resind].name,
 180                pdba->resinfo[resind].nr);
 181     }
 182     /* this used to free *resname, which messes up the symtab! */
 183     snew(pdba->resinfo[resind].rtp, 1);
 184     *pdba->resinfo[resind].rtp = gmx_strdup(newres);
 185 }
 186
 187 std::vector<DisulfideBond> makeDisulfideBonds(t_atoms* pdba, rvec x[], bool bInteractive, bool bVerbose)
 188 {
 189     std::vector<SpecialBond>   specialBonds = generateSpecialBonds();
 190     std::vector<DisulfideBond> bonds;
 191     bool                       bSwap;
 192     int                        index_sb;
 193     char                       buf[10];
 194
 195
 196     if (!specialBonds.empty())
 197     {
 198         std::vector<int> specialBondResIdxs;
 199         std::vector<int> specialBondAtomIdxs;
 200
 201         for (int i = 0; (i < pdba->nr); i++)
 202         {
 203             /* Check if this atom is special and if it is not a double atom
 204              * in the input that still needs to be removed.
 205              */
 206             int prevAtom = -1;
 207             if (!specialBondAtomIdxs.empty())
 208             {
 209                 prevAtom = specialBondAtomIdxs.back();
 210             }
 211             if (is_special(specialBonds, *pdba->resinfo[pdba->atom[i].resind].name, *pdba->atomname[i])
 212                 && !(!specialBondAtomIdxs.empty() && pdba->atom[prevAtom].resind == pdba->atom[i].resind
 213                      && gmx_strcasecmp(*pdba->atomname[prevAtom], *pdba->atomname[i]) == 0))
 214             {
 215                 specialBondResIdxs.push_back(pdba->atom[i].resind);
 216                 specialBondAtomIdxs.push_back(i);
 217             }
 218         }
 219         /* distance matrix d[nspec][nspec] */
 220         int                            nspec = specialBondAtomIdxs.size();
 221         std::vector<std::vector<real>> d(nspec);
 222         for (int i = 0; (i < nspec); i++)
 223         {
 224             d[i].resize(nspec);
 225             int ai = specialBondAtomIdxs[i];
 226             for (int j = 0; (j < nspec); j++)
 227             {
 228                 int aj  = specialBondAtomIdxs[j];
 229                 d[i][j] = std::sqrt(distance2(x[ai], x[aj]));
 230             }
 231         }
 232         if (nspec > 1)
 233         {
 234 #define MAXCOL 7
 235             fprintf(stderr, "Special Atom Distance matrix:\n");
 236             for (int b = 0; (b < nspec); b += MAXCOL)
 237             {
 238                 /* print resname/number column headings */
 239                 fprintf(stderr, "%8s%8s", "", "");
 240                 int e = std::min(b + MAXCOL, nspec - 1);
 241                 for (int i = b; (i < e); i++)
 242                 {
 243                     sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
 244                             pdba->resinfo[specialBondResIdxs[i]].nr);
 245                     fprintf(stderr, "%8s", buf);
 246                 }
 247                 fprintf(stderr, "\n");
 248                 /* print atomname/number column headings */
 249                 fprintf(stderr, "%8s%8s", "", "");
 250                 e = std::min(b + MAXCOL, nspec - 1);
 251                 for (int i = b; (i < e); i++)
 252                 {
 253                     std::string buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
 254                                                         specialBondAtomIdxs[i] + 1);
 255                     fprintf(stderr, "%8s", buf.c_str());
 256                 }
 257                 fprintf(stderr, "\n");
 258                 /* print matrix */
 259                 e = std::min(b + MAXCOL, nspec);
 260                 for (int i = b + 1; (i < nspec); i++)
 261                 {
 262                     std::string buf = gmx::formatString(
 263                             "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
 264                             pdba->resinfo[specialBondResIdxs[i]].nr);
 265                     fprintf(stderr, "%8s", buf.c_str());
 266                     buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
 267                                             specialBondAtomIdxs[i] + 1);
 268                     fprintf(stderr, "%8s", buf.c_str());
 269                     int e2 = std::min(i, e);
 270                     for (int j = b; (j < e2); j++)
 271                     {
 272                         fprintf(stderr, " %7.3f", d[i][j]);
 273                     }
 274                     fprintf(stderr, "\n");
 275                 }
 276             }
 277         }
 278
 279         for (int i = 0; (i < nspec); i++)
 280         {
 281             int ai = specialBondAtomIdxs[i];
 282             for (int j = i + 1; (j < nspec); j++)
 283             {
 284                 int aj = specialBondAtomIdxs[j];
 285                 /* Ensure creation of at most nspec special bonds to avoid overflowing bonds[] */
 286                 if (bonds.size() < specialBondAtomIdxs.size()
 287                     && is_bond(specialBonds, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
 288                 {
 289                     fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s", bInteractive ? "Link" : "Linking",
 290                             *pdba->resinfo[pdba->atom[ai].resind].name,
 291                             pdba->resinfo[specialBondResIdxs[i]].nr, *pdba->atomname[ai], ai + 1,
 292                             *pdba->resinfo[pdba->atom[aj].resind].name,
 293                             pdba->resinfo[specialBondResIdxs[j]].nr, *pdba->atomname[aj], aj + 1,
 294                             bInteractive ? " (y/n) ?" : "...\n");
 295                     bool bDoit = bInteractive ? yesno() : true;
 296
 297                     if (bDoit)
 298                     {
 299                         DisulfideBond newBond;
 300                         /* Store the residue numbers in the bonds array */
 301                         newBond.firstResidue  = specialBondResIdxs[i];
 302                         newBond.secondResidue = specialBondResIdxs[j];
 303                         newBond.firstAtom     = *pdba->atomname[ai];
 304                         newBond.secondAtom    = *pdba->atomname[aj];
 305                         bonds.push_back(newBond);
 306                         /* rename residues */
 307                         if (bSwap)
 308                         {
 309                             rename_1res(pdba, specialBondResIdxs[i],
 310                                         specialBonds[index_sb].newSecondResidue.c_str(), bVerbose);
 311                             rename_1res(pdba, specialBondResIdxs[j],
 312                                         specialBonds[index_sb].newFirstResidue.c_str(), bVerbose);
 313                         }
 314                         else
 315                         {
 316                             rename_1res(pdba, specialBondResIdxs[i],
 317                                         specialBonds[index_sb].newFirstResidue.c_str(), bVerbose);
 318                             rename_1res(pdba, specialBondResIdxs[j],
 319                                         specialBonds[index_sb].newSecondResidue.c_str(), bVerbose);
 320                         }
 321                     }
 322                 }
 323             }
 324         }
 325     }
 326
 327     return bonds;
 328 }