src/gromacs/gmxpreprocess/genhydro.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
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  37 #include "gmxpre.h"
  38
  39 #include "genhydro.h"
  40
  41 #include <cstring>
  42 #include <ctime>
  43
  44 #include "gromacs/fileio/confio.h"
  45 #include "gromacs/gmxlib/network.h"
  46 #include "gromacs/gmxpreprocess/calch.h"
  47 #include "gromacs/gmxpreprocess/h_db.h"
  48 #include "gromacs/gmxpreprocess/notset.h"
  49 #include "gromacs/gmxpreprocess/pgutil.h"
  50 #include "gromacs/gmxpreprocess/ter_db.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/topology/atoms.h"
  53 #include "gromacs/topology/symtab.h"
  54 #include "gromacs/utility/cstringutil.h"
  55 #include "gromacs/utility/exceptions.h"
  56 #include "gromacs/utility/fatalerror.h"
  57 #include "gromacs/utility/futil.h"
  58 #include "gromacs/utility/smalloc.h"
  59
  60 #include "hackblock.h"
  61 #include "resall.h"
  62
  63 static void copy_atom(const t_atoms* atoms1, int a1, t_atoms* atoms2, int a2, t_symtab* symtab)
  64 {
  65     atoms2->atom[a2]     = atoms1->atom[a1];
  66     atoms2->atomname[a2] = put_symtab(symtab, *atoms1->atomname[a1]);
  67 }
  68
  69 static int pdbasearch_atom(const char*              name,
  70                            int                      resind,
  71                            const t_atoms*           pdba,
  72                            const char*              searchtype,
  73                            bool                     bAllowMissing,
  74                            gmx::ArrayRef<const int> cyclicBondsIndex)
  75 {
  76     int i;
  77
  78     for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++) {}
  79
  80     return search_atom(name, i, pdba, searchtype, bAllowMissing, cyclicBondsIndex);
  81 }
  82
  83 static void hacksearch_atom(int*                                            ii,
  84                             int*                                            jj,
  85                             const char*                                     name,
  86                             gmx::ArrayRef<const std::vector<MoleculePatch>> patches,
  87                             int                                             resind,
  88                             const t_atoms*                                  pdba)
  89 {
  90     int i;
  91
  92     *ii = -1;
  93     if (name[0] == '-')
  94     {
  95         name++;
  96         resind--;
  97     }
  98     for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++) {}
  99     for (; (i < pdba->nr) && (pdba->atom[i].resind == resind) && (*ii < 0); i++)
 100     {
 101         int j = 0;
 102         for (const auto& patch : patches[i])
 103         {
 104             if (patch.nname == name)
 105             {
 106                 *ii = i;
 107                 *jj = j;
 108             }
 109             j++;
 110         }
 111     }
 112 }
 113
 114 static std::vector<MoleculePatchDatabase>
 115 getMoleculePatchDatabases(const t_atoms*                              pdba,
 116                           gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
 117                           int                                         nterpairs,
 118                           gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
 119                           gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
 120                           gmx::ArrayRef<const int>                    rN,
 121                           gmx::ArrayRef<const int>                    rC)
 122 {
 123     std::vector<MoleculePatchDatabase> modBlock(pdba->nres);
 124     /* make space */
 125     /* first the termini */
 126     for (int i = 0; i < nterpairs; i++)
 127     {
 128         if (ntdb[i] != nullptr)
 129         {
 130             copyModificationBlocks(*ntdb[i], &modBlock[rN[i]]);
 131         }
 132         if (ctdb[i] != nullptr)
 133         {
 134             mergeAtomAndBondModifications(*ctdb[i], &modBlock[rC[i]]);
 135         }
 136     }
 137     /* then the whole hdb */
 138     for (int rnr = 0; rnr < pdba->nres; rnr++)
 139     {
 140         auto ahptr = search_h_db(globalPatches, *pdba->resinfo[rnr].rtp);
 141         if (ahptr != globalPatches.end())
 142         {
 143             if (modBlock[rnr].name.empty())
 144             {
 145                 modBlock[rnr].name = ahptr->name;
 146             }
 147             mergeAtomModifications(*ahptr, &modBlock[rnr]);
 148         }
 149     }
 150     return modBlock;
 151 }
 152
 153 static void expand_hackblocks_one(const MoleculePatchDatabase& newPatch,
 154                                   const std::string localAtomName, //NOLINT(performance-unnecessary-value-param)
 155                                   std::vector<MoleculePatch>* globalPatches,
 156                                   bool                        bN,
 157                                   bool                        bC)
 158 {
 159     /* we'll recursively add atoms to atoms */
 160     int pos = 0;
 161     for (auto& singlePatch : newPatch.hack)
 162     {
 163         /* first check if we're in the N- or C-terminus, then we should ignore
 164            all hacks involving atoms from resp. previous or next residue
 165            (i.e. which name begins with '-' (N) or '+' (C) */
 166         bool bIgnore = false;
 167         if (bN) /* N-terminus: ignore '-' */
 168         {
 169             for (int k = 0; k < 4 && !singlePatch.a[k].empty() && !bIgnore; k++)
 170             {
 171                 bIgnore = singlePatch.a[k][0] == '-';
 172             }
 173         }
 174         if (bC) /* C-terminus: ignore '+' */
 175         {
 176             for (int k = 0; k < 4 && !singlePatch.a[k].empty() && !bIgnore; k++)
 177             {
 178                 bIgnore = singlePatch.a[k][0] == '+';
 179             }
 180         }
 181         /* must be either hdb entry (tp>0) or add from tdb (oname==NULL)
 182            and first control aton (AI) matches this atom or
 183            delete/replace from tdb (oname!=NULL) and oname matches this atom */
 184
 185         if (!bIgnore
 186             && (((singlePatch.tp > 0 || singlePatch.oname.empty()) && singlePatch.a[0] == localAtomName)
 187                 || (singlePatch.oname == localAtomName)))
 188         {
 189             /* now expand all hacks for this atom */
 190             for (int k = 0; k < singlePatch.nr; k++)
 191             {
 192                 globalPatches->push_back(singlePatch);
 193                 MoleculePatch* patch = &globalPatches->back();
 194                 patch->bXSet         = false;
 195                 /* if we're adding (oname==NULL) and don't have a new name (nname)
 196                    yet, build it from localAtomName */
 197                 if (patch->nname.empty())
 198                 {
 199                     if (patch->oname.empty())
 200                     {
 201                         patch->nname    = localAtomName;
 202                         patch->nname[0] = 'H';
 203                     }
 204                 }
 205                 else
 206                 {
 207                     if (gmx_debug_at)
 208                     {
 209                         fprintf(debug,
 210                                 "Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n",
 211                                 localAtomName.c_str(),
 212                                 pos,
 213                                 patch->nname.c_str(),
 214                                 singlePatch.nname.c_str(),
 215                                 patch->oname.empty() ? "" : patch->oname.c_str());
 216                     }
 217                     patch->nname = singlePatch.nname;
 218                 }
 219
 220                 if (singlePatch.tp == 10 && k == 2)
 221                 {
 222                     /* This is a water virtual site, not a hydrogen */
 223                     /* Ugly hardcoded name hack */
 224                     patch->nname.assign("M");
 225                 }
 226                 else if (singlePatch.tp == 11 && k >= 2)
 227                 {
 228                     /* This is a water lone pair, not a hydrogen */
 229                     /* Ugly hardcoded name hack */
 230                     patch->nname.assign(gmx::formatString("LP%d", 1 + k - 2));
 231                 }
 232                 else if (singlePatch.nr > 1)
 233                 {
 234                     /* adding more than one atom, number them */
 235                     patch->nname.append(gmx::formatString("%d", 1 + k));
 236                 }
 237             }
 238
 239             /* add hacks to atoms we've just added */
 240             if (singlePatch.tp > 0 || singlePatch.oname.empty())
 241             {
 242                 for (int k = 0; k < singlePatch.nr; k++)
 243                 {
 244                     expand_hackblocks_one(
 245                             newPatch,
 246                             globalPatches->at(globalPatches->size() - singlePatch.nr + k).nname,
 247                             globalPatches,
 248                             bN,
 249                             bC);
 250                 }
 251             }
 252         }
 253         pos++;
 254     }
 255 }
 256
 257 static void expand_hackblocks(const t_atoms*                             pdba,
 258                               gmx::ArrayRef<const MoleculePatchDatabase> hb,
 259                               gmx::ArrayRef<std::vector<MoleculePatch>>  patches,
 260                               int                                        nterpairs,
 261                               gmx::ArrayRef<const int>                   rN,
 262                               gmx::ArrayRef<const int>                   rC)
 263 {
 264     for (int i = 0; i < pdba->nr; i++)
 265     {
 266         bool bN = false;
 267         for (int j = 0; j < nterpairs && !bN; j++)
 268         {
 269             bN = pdba->atom[i].resind == rN[j];
 270         }
 271         bool bC = false;
 272         for (int j = 0; j < nterpairs && !bC; j++)
 273         {
 274             bC = pdba->atom[i].resind == rC[j];
 275         }
 276
 277         /* add hacks to this atom */
 278         expand_hackblocks_one(hb[pdba->atom[i].resind], *pdba->atomname[i], &patches[i], bN, bC);
 279     }
 280 }
 281
 282 static int check_atoms_present(const t_atoms*                            pdba,
 283                                gmx::ArrayRef<std::vector<MoleculePatch>> patches,
 284                                gmx::ArrayRef<const int>                  cyclicBondsIndex)
 285 {
 286     int nadd = 0;
 287     for (int i = 0; i < pdba->nr; i++)
 288     {
 289         int rnr = pdba->atom[i].resind;
 290         for (auto patch = patches[i].begin(); patch != patches[i].end(); patch++)
 291         {
 292             switch (patch->type())
 293             {
 294                 case MoleculePatchType::Add:
 295                 {
 296                     /* we're adding */
 297                     /* check if the atom is already present */
 298                     int k = pdbasearch_atom(patch->nname.c_str(), rnr, pdba, "check", TRUE, cyclicBondsIndex);
 299                     if (k != -1)
 300                     {
 301                         /* We found the added atom. */
 302                         patch->bAlreadyPresent = true;
 303                     }
 304                     else
 305                     {
 306                         patch->bAlreadyPresent = false;
 307                         /* count how many atoms we'll add */
 308                         nadd++;
 309                     }
 310                     break;
 311                 }
 312                 case MoleculePatchType::Delete:
 313                 {
 314                     /* we're deleting */
 315                     nadd--;
 316                     break;
 317                 }
 318                 case MoleculePatchType::Replace: { break;
 319                 }
 320                 default: { GMX_THROW(gmx::InternalError("Case not handled"));
 321                 }
 322             }
 323         }
 324     }
 325     return nadd;
 326 }
 327
 328 static void calc_all_pos(const t_atoms*                            pdba,
 329                          gmx::ArrayRef<const gmx::RVec>            x,
 330                          gmx::ArrayRef<std::vector<MoleculePatch>> patches,
 331                          bool                                      bCheckMissing,
 332                          gmx::ArrayRef<const int>                  cyclicBondsIndex)
 333 {
 334     int ii, l = 0;
 335 #define MAXH 4
 336     rvec xa[4];    /* control atoms for calc_h_pos */
 337     rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
 338
 339     int jj = 0;
 340
 341     for (int i = 0; i < pdba->nr; i++)
 342     {
 343         int rnr = pdba->atom[i].resind;
 344         for (auto patch = patches[i].begin(); patch != patches[i].end(); patch += patch->nr)
 345         {
 346             GMX_RELEASE_ASSERT(patch < patches[i].end(),
 347                                "The number of patches in the last patch can not exceed the total "
 348                                "number of patches");
 349             /* check if we're adding: */
 350             if (patch->type() == MoleculePatchType::Add && patch->tp > 0)
 351             {
 352                 bool bFoundAll = true;
 353                 for (int m = 0; (m < patch->nctl && bFoundAll); m++)
 354                 {
 355                     int ia = pdbasearch_atom(patch->a[m].c_str(),
 356                                              rnr,
 357                                              pdba,
 358                                              bCheckMissing ? "atom" : "check",
 359                                              !bCheckMissing,
 360                                              cyclicBondsIndex);
 361                     if (ia < 0)
 362                     {
 363                         /* not found in original atoms, might still be in
 364                          * the patch Instructions (patches) */
 365                         hacksearch_atom(&ii, &jj, patch->a[m].c_str(), patches, rnr, pdba);
 366                         if (ii >= 0)
 367                         {
 368                             copy_rvec(patches[ii][jj].newx, xa[m]);
 369                         }
 370                         else
 371                         {
 372                             bFoundAll = false;
 373                             if (bCheckMissing)
 374                             {
 375                                 gmx_fatal(FARGS,
 376                                           "Atom %s not found in residue %s %d"
 377                                           ", rtp entry %s"
 378                                           " while adding hydrogens",
 379                                           patch->a[m].c_str(),
 380                                           *pdba->resinfo[rnr].name,
 381                                           pdba->resinfo[rnr].nr,
 382                                           *pdba->resinfo[rnr].rtp);
 383                             }
 384                         }
 385                     }
 386                     else
 387                     {
 388                         copy_rvec(x[ia], xa[m]);
 389                     }
 390                 }
 391                 if (bFoundAll)
 392                 {
 393                     for (int m = 0; (m < MAXH); m++)
 394                     {
 395                         for (int d = 0; d < DIM; d++)
 396                         {
 397                             if (m < patch->nr)
 398                             {
 399                                 xh[m][d] = 0;
 400                             }
 401                             else
 402                             {
 403                                 xh[m][d] = NOTSET;
 404                             }
 405                         }
 406                     }
 407                     calc_h_pos(patch->tp, xa, xh, &l);
 408                     for (int m = 0; m < patch->nr; m++)
 409                     {
 410                         auto next = patch + m;
 411                         copy_rvec(xh[m], next->newx);
 412                         next->bXSet = true;
 413                     }
 414                 }
 415             }
 416         }
 417     }
 418 }
 419
 420 static int add_h_low(t_atoms**                                   initialAtoms,
 421                      t_atoms**                                   modifiedAtoms,
 422                      std::vector<gmx::RVec>*                     xptr,
 423                      gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
 424                      t_symtab*                                   symtab,
 425                      const int                                   nterpairs,
 426                      gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
 427                      gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
 428                      gmx::ArrayRef<const int>                    rN,
 429                      gmx::ArrayRef<const int>                    rC,
 430                      const bool                                  bCheckMissing,
 431                      gmx::ArrayRef<const int>                    cyclicBondsIndex)
 432 {
 433     int                                     nadd;
 434     int                                     newi, natoms, nalreadypresent;
 435     std::vector<std::vector<MoleculePatch>> patches;
 436     std::vector<gmx::RVec>                  xn;
 437
 438     t_atoms* pdba = *initialAtoms;
 439
 440     /* set flags for adding hydrogens (according to hdb) */
 441     natoms = pdba->nr;
 442
 443     {
 444         /* We'll have to do all the hard work */
 445         /* first get all the hackblocks for each residue: */
 446         std::vector<MoleculePatchDatabase> hb =
 447                 getMoleculePatchDatabases(pdba, globalPatches, nterpairs, ntdb, ctdb, rN, rC);
 448
 449         /* expand the hackblocks to atom level */
 450         patches.resize(natoms);
 451         expand_hackblocks(pdba, hb, patches, nterpairs, rN, rC);
 452     }
 453
 454     /* Now calc the positions */
 455     calc_all_pos(pdba, *xptr, patches, bCheckMissing, cyclicBondsIndex);
 456
 457     /* we don't have to add atoms that are already present in initialAtoms,
 458        so we will remove them from the patches (MoleculePatch) */
 459     nadd = check_atoms_present(pdba, patches, cyclicBondsIndex);
 460
 461     /* Copy old atoms, making space for new ones */
 462     if (nadd > 0)
 463     {
 464         srenew(*modifiedAtoms, 1);
 465         init_t_atoms(*modifiedAtoms, natoms + nadd, FALSE);
 466         (*modifiedAtoms)->nres = pdba->nres;
 467         srenew((*modifiedAtoms)->resinfo, pdba->nres);
 468         std::copy(pdba->resinfo, pdba->resinfo + pdba->nres, (*modifiedAtoms)->resinfo);
 469     }
 470     if (nadd == 0)
 471     {
 472         return natoms;
 473     }
 474
 475     xn.resize(natoms + nadd);
 476     newi = 0;
 477     for (int i = 0; (i < natoms); i++)
 478     {
 479         /* check if this atom wasn't scheduled for deletion */
 480         if (patches[i].empty() || (!patches[i][0].nname.empty()))
 481         {
 482             if (newi >= natoms + nadd)
 483             {
 484                 /*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
 485                 nadd += 10;
 486                 xn.resize(natoms + nadd);
 487                 srenew((*modifiedAtoms)->atom, natoms + nadd);
 488                 srenew((*modifiedAtoms)->atomname, natoms + nadd);
 489             }
 490             copy_atom(pdba, i, (*modifiedAtoms), newi, symtab);
 491             copy_rvec((*xptr)[i], xn[newi]);
 492             /* process the hacks for this atom */
 493             nalreadypresent = 0;
 494             for (auto patch = patches[i].begin(); patch != patches[i].end(); patch++)
 495             {
 496                 if (patch->type() == MoleculePatchType::Add) /* add */
 497                 {
 498                     newi++;
 499                     if (newi >= natoms + nadd)
 500                     {
 501                         /* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
 502                         nadd += 10;
 503                         xn.resize(natoms + nadd);
 504                         srenew((*modifiedAtoms)->atom, natoms + nadd);
 505                         srenew((*modifiedAtoms)->atomname, natoms + nadd);
 506                     }
 507                     (*modifiedAtoms)->atom[newi].resind = pdba->atom[i].resind;
 508                 }
 509                 if (!patch->nname.empty()
 510                     && (patch->oname.empty() || patch->oname == *(*modifiedAtoms)->atomname[newi]))
 511                 {
 512                     /* add or replace */
 513                     if (patch->type() == MoleculePatchType::Add && patch->bAlreadyPresent)
 514                     {
 515                         /* This atom is already present, copy it from the input. */
 516                         nalreadypresent++;
 517                         copy_atom(pdba, i + nalreadypresent, (*modifiedAtoms), newi, symtab);
 518                         copy_rvec((*xptr)[i + nalreadypresent], xn[newi]);
 519                     }
 520                     else
 521                     {
 522                         if (gmx_debug_at)
 523                         {
 524                             fprintf(debug,
 525                                     "Replacing %d '%s' with (old name '%s') %s\n",
 526                                     newi,
 527                                     ((*modifiedAtoms)->atomname[newi] && *(*modifiedAtoms)->atomname[newi])
 528                                             ? *(*modifiedAtoms)->atomname[newi]
 529                                             : "",
 530                                     patch->oname.empty() ? "" : patch->oname.c_str(),
 531                                     patch->nname.c_str());
 532                         }
 533                         (*modifiedAtoms)->atomname[newi] = put_symtab(symtab, patch->nname.c_str());
 534                         if (patch->bXSet)
 535                         {
 536                             copy_rvec(patch->newx, xn[newi]);
 537                         }
 538                     }
 539                     if (debug)
 540                     {
 541                         fprintf(debug,
 542                                 " %s %g %g",
 543                                 *(*modifiedAtoms)->atomname[newi],
 544                                 (*modifiedAtoms)->atom[newi].m,
 545                                 (*modifiedAtoms)->atom[newi].q);
 546                     }
 547                 }
 548             }
 549             newi++;
 550             i += nalreadypresent;
 551         }
 552     }
 553     (*modifiedAtoms)->nr = newi;
 554
 555     done_atom(pdba);
 556     *initialAtoms = *modifiedAtoms;
 557
 558     *xptr = xn;
 559
 560     return newi;
 561 }
 562
 563 int add_h(t_atoms**                                   initialAtoms,
 564           t_atoms**                                   localAtoms,
 565           std::vector<gmx::RVec>*                     xptr,
 566           gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
 567           t_symtab*                                   symtab,
 568           const int                                   nterpairs,
 569           gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
 570           gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
 571           gmx::ArrayRef<const int>                    rN,
 572           gmx::ArrayRef<const int>                    rC,
 573           const bool                                  bAllowMissing,
 574           gmx::ArrayRef<const int>                    cyclicBondsIndex)
 575 {
 576     int nold, nnew, niter;
 577
 578     /* Here we loop to be able to add atoms to added atoms.
 579      * We should not check for missing atoms here.
 580      */
 581     niter = 0;
 582     nnew  = 0;
 583     do
 584     {
 585         nold = nnew;
 586         nnew = add_h_low(
 587                 initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb, ctdb, rN, rC, FALSE, cyclicBondsIndex);
 588         niter++;
 589         if (niter > 100)
 590         {
 591             gmx_fatal(FARGS,
 592                       "More than 100 iterations of add_h. Maybe you are trying to replace an added "
 593                       "atom (this is not supported)?");
 594         }
 595     } while (nnew > nold);
 596
 597     if (!bAllowMissing)
 598     {
 599         /* Call add_h_low once more, now only for the missing atoms check */
 600         add_h_low(initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb, ctdb, rN, rC, TRUE, cyclicBondsIndex);
 601     }
 602
 603     return nnew;
 604 }