src/gromacs/gmxpreprocess/specbond.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "specbond.h"
  41
  42 #include <cctype>
  43 #include <cmath>
  44 #include <cstring>
  45
  46 #include <algorithm>
  47
  48 #include "gromacs/fileio/pdbio.h"
  49 #include "gromacs/gmxpreprocess/pdb2top.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/utility/arrayref.h"
  52 #include "gromacs/utility/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/smalloc.h"
  55 #include "gromacs/utility/strdb.h"
  56
  57 struct SpecialBond
  58 {
  59     std::string firstResidue, secondResidue;
  60     std::string firstAtomName, secondAtomName;
  61     std::string newFirstResidue, newSecondResidue;
  62     int         firstBondNumber, secondBondNumber;
  63     real        length;
  64 };
  65
  66 static bool yesno()
  67 {
  68     char c;
  69
  70     do
  71     {
  72         c = toupper(fgetc(stdin));
  73     } while ((c != 'Y') && (c != 'N'));
  74
  75     return (c == 'Y');
  76 }
  77
  78 std::vector<SpecialBond> generateSpecialBonds()
  79 {
  80     const char* sbfile = "specbond.dat";
  81
  82     std::vector<SpecialBond> specialBonds;
  83     char                     r1buf[32], r2buf[32], a1buf[32], a2buf[32], nr1buf[32], nr2buf[32];
  84     double                   length;
  85     int                      nb1, nb2;
  86     char**                   lines;
  87
  88     int nlines = get_lines(sbfile, &lines);
  89     for (int i = 0; (i < nlines); i++)
  90     {
  91         if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s", r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length,
  92                    nr1buf, nr2buf)
  93             != 9)
  94         {
  95             fprintf(stderr, "Invalid line '%s' in %s\n", lines[i], sbfile);
  96         }
  97         else
  98         {
  99             SpecialBond newBond;
 100
 101             newBond.firstResidue     = r1buf;
 102             newBond.secondResidue    = r2buf;
 103             newBond.newFirstResidue  = nr1buf;
 104             newBond.newSecondResidue = nr2buf;
 105             newBond.firstAtomName    = a1buf;
 106             newBond.secondAtomName   = a2buf;
 107             newBond.firstBondNumber  = nb1;
 108             newBond.secondBondNumber = nb2;
 109             newBond.length           = length;
 110             specialBonds.push_back(newBond);
 111         }
 112         sfree(lines[i]);
 113     }
 114     if (nlines > 0)
 115     {
 116         sfree(lines);
 117     }
 118     fprintf(stderr, "%zu out of %d lines of %s converted successfully\n", specialBonds.size(),
 119             nlines, sbfile);
 120
 121     return specialBonds;
 122 }
 123
 124 static bool is_special(gmx::ArrayRef<const SpecialBond> sb, const char* res, const char* atom)
 125 {
 126     for (const auto& bond : sb)
 127     {
 128         if (((strncmp(bond.firstResidue.c_str(), res, 3) == 0)
 129              && (gmx::equalCaseInsensitive(bond.firstAtomName, atom)))
 130             || ((strncmp(bond.secondResidue.c_str(), res, 3) == 0)
 131                 && (gmx::equalCaseInsensitive(bond.secondAtomName, atom))))
 132         {
 133             return TRUE;
 134         }
 135     }
 136     return FALSE;
 137 }
 138
 139 static bool is_bond(gmx::ArrayRef<const SpecialBond> sb, t_atoms* pdba, int a1, int a2, real d, int* index_sb, bool* bSwap)
 140 {
 141     const char* at1  = *pdba->atomname[a1];
 142     const char* at2  = *pdba->atomname[a2];
 143     const char* res1 = *pdba->resinfo[pdba->atom[a1].resind].name;
 144     const char* res2 = *pdba->resinfo[pdba->atom[a2].resind].name;
 145
 146     int i = 0;
 147     for (const auto& bond : sb)
 148     {
 149         *index_sb = i;
 150         if (((strncmp(bond.firstResidue.c_str(), res1, 3) == 0)
 151              && (gmx::equalCaseInsensitive(bond.firstAtomName, at1))
 152              && (strncmp(bond.secondResidue.c_str(), res2, 3) == 0)
 153              && (gmx::equalCaseInsensitive(bond.secondAtomName, at2))))
 154         {
 155             *bSwap = FALSE;
 156             if ((0.9 * bond.length < d) && (1.1 * bond.length > d))
 157             {
 158                 return TRUE;
 159             }
 160         }
 161         if (((strncmp(bond.firstResidue.c_str(), res2, 3) == 0)
 162              && (gmx::equalCaseInsensitive(bond.firstAtomName, at2))
 163              && (strncmp(bond.secondResidue.c_str(), res1, 3) == 0)
 164              && (gmx::equalCaseInsensitive(bond.secondAtomName, at1))))
 165         {
 166             *bSwap = TRUE;
 167             if ((0.9 * bond.length < d) && (1.1 * bond.length > d))
 168             {
 169                 return TRUE;
 170             }
 171         }
 172         i++;
 173     }
 174     return FALSE;
 175 }
 176
 177 static void rename_1res(t_atoms* pdba, int resind, const char* newres, bool bVerbose)
 178 {
 179     if (bVerbose)
 180     {
 181         printf("Using rtp entry %s for %s %d\n", newres, *pdba->resinfo[resind].name,
 182                pdba->resinfo[resind].nr);
 183     }
 184     /* this used to free *resname, which messes up the symtab! */
 185     snew(pdba->resinfo[resind].rtp, 1);
 186     *pdba->resinfo[resind].rtp = gmx_strdup(newres);
 187 }
 188
 189 std::vector<DisulfideBond> makeDisulfideBonds(t_atoms* pdba, rvec x[], bool bInteractive, bool bVerbose)
 190 {
 191     std::vector<SpecialBond>   specialBonds = generateSpecialBonds();
 192     std::vector<DisulfideBond> bonds;
 193     bool                       bSwap;
 194     int                        index_sb;
 195     char                       buf[10];
 196
 197
 198     if (!specialBonds.empty())
 199     {
 200         std::vector<int> specialBondResIdxs;
 201         std::vector<int> specialBondAtomIdxs;
 202
 203         for (int i = 0; (i < pdba->nr); i++)
 204         {
 205             /* Check if this atom is special and if it is not a double atom
 206              * in the input that still needs to be removed.
 207              */
 208             int prevAtom = -1;
 209             if (!specialBondAtomIdxs.empty())
 210             {
 211                 prevAtom = specialBondAtomIdxs.back();
 212             }
 213             if (is_special(specialBonds, *pdba->resinfo[pdba->atom[i].resind].name, *pdba->atomname[i])
 214                 && !(!specialBondAtomIdxs.empty() && pdba->atom[prevAtom].resind == pdba->atom[i].resind
 215                      && gmx_strcasecmp(*pdba->atomname[prevAtom], *pdba->atomname[i]) == 0))
 216             {
 217                 specialBondResIdxs.push_back(pdba->atom[i].resind);
 218                 specialBondAtomIdxs.push_back(i);
 219             }
 220         }
 221         /* distance matrix d[nspec][nspec] */
 222         int                            nspec = specialBondAtomIdxs.size();
 223         std::vector<std::vector<real>> d(nspec);
 224         for (int i = 0; (i < nspec); i++)
 225         {
 226             d[i].resize(nspec);
 227             int ai = specialBondAtomIdxs[i];
 228             for (int j = 0; (j < nspec); j++)
 229             {
 230                 int aj  = specialBondAtomIdxs[j];
 231                 d[i][j] = std::sqrt(distance2(x[ai], x[aj]));
 232             }
 233         }
 234         if (nspec > 1)
 235         {
 236 #define MAXCOL 7
 237             fprintf(stderr, "Special Atom Distance matrix:\n");
 238             for (int b = 0; (b < nspec); b += MAXCOL)
 239             {
 240                 /* print resname/number column headings */
 241                 fprintf(stderr, "%8s%8s", "", "");
 242                 int e = std::min(b + MAXCOL, nspec - 1);
 243                 for (int i = b; (i < e); i++)
 244                 {
 245                     sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
 246                             pdba->resinfo[specialBondResIdxs[i]].nr);
 247                     fprintf(stderr, "%8s", buf);
 248                 }
 249                 fprintf(stderr, "\n");
 250                 /* print atomname/number column headings */
 251                 fprintf(stderr, "%8s%8s", "", "");
 252                 e = std::min(b + MAXCOL, nspec - 1);
 253                 for (int i = b; (i < e); i++)
 254                 {
 255                     std::string buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
 256                                                         specialBondAtomIdxs[i] + 1);
 257                     fprintf(stderr, "%8s", buf.c_str());
 258                 }
 259                 fprintf(stderr, "\n");
 260                 /* print matrix */
 261                 e = std::min(b + MAXCOL, nspec);
 262                 for (int i = b + 1; (i < nspec); i++)
 263                 {
 264                     std::string buf = gmx::formatString(
 265                             "%s%d", *pdba->resinfo[pdba->atom[specialBondAtomIdxs[i]].resind].name,
 266                             pdba->resinfo[specialBondResIdxs[i]].nr);
 267                     fprintf(stderr, "%8s", buf.c_str());
 268                     buf = gmx::formatString("%s%d", *pdba->atomname[specialBondAtomIdxs[i]],
 269                                             specialBondAtomIdxs[i] + 1);
 270                     fprintf(stderr, "%8s", buf.c_str());
 271                     int e2 = std::min(i, e);
 272                     for (int j = b; (j < e2); j++)
 273                     {
 274                         fprintf(stderr, " %7.3f", d[i][j]);
 275                     }
 276                     fprintf(stderr, "\n");
 277                 }
 278             }
 279         }
 280
 281         for (int i = 0; (i < nspec); i++)
 282         {
 283             int ai = specialBondAtomIdxs[i];
 284             for (int j = i + 1; (j < nspec); j++)
 285             {
 286                 int aj = specialBondAtomIdxs[j];
 287                 /* Ensure creation of at most nspec special bonds to avoid overflowing bonds[] */
 288                 if (bonds.size() < specialBondAtomIdxs.size()
 289                     && is_bond(specialBonds, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
 290                 {
 291                     fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s", bInteractive ? "Link" : "Linking",
 292                             *pdba->resinfo[pdba->atom[ai].resind].name,
 293                             pdba->resinfo[specialBondResIdxs[i]].nr, *pdba->atomname[ai], ai + 1,
 294                             *pdba->resinfo[pdba->atom[aj].resind].name,
 295                             pdba->resinfo[specialBondResIdxs[j]].nr, *pdba->atomname[aj], aj + 1,
 296                             bInteractive ? " (y/n) ?" : "...\n");
 297                     bool bDoit = bInteractive ? yesno() : true;
 298
 299                     if (bDoit)
 300                     {
 301                         DisulfideBond newBond;
 302                         /* Store the residue numbers in the bonds array */
 303                         newBond.firstResidue  = specialBondResIdxs[i];
 304                         newBond.secondResidue = specialBondResIdxs[j];
 305                         newBond.firstAtom     = *pdba->atomname[ai];
 306                         newBond.secondAtom    = *pdba->atomname[aj];
 307                         bonds.push_back(newBond);
 308                         /* rename residues */
 309                         if (bSwap)
 310                         {
 311                             rename_1res(pdba, specialBondResIdxs[i],
 312                                         specialBonds[index_sb].newSecondResidue.c_str(), bVerbose);
 313                             rename_1res(pdba, specialBondResIdxs[j],
 314                                         specialBonds[index_sb].newFirstResidue.c_str(), bVerbose);
 315                         }
 316                         else
 317                         {
 318                             rename_1res(pdba, specialBondResIdxs[i],
 319                                         specialBonds[index_sb].newFirstResidue.c_str(), bVerbose);
 320                             rename_1res(pdba, specialBondResIdxs[j],
 321                                         specialBonds[index_sb].newSecondResidue.c_str(), bVerbose);
 322                         }
 323                     }
 324                 }
 325             }
 326         }
 327     }
 328
 329     return bonds;
 330 }