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, 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
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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, int resind, const t_atoms* pdba, const char* searchtype, bool bAllowMissing)
  70 {
  71     int i;
  72
  73     for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++) {}
  74
  75     return search_atom(name, i, pdba, searchtype, bAllowMissing);
  76 }
  77
  78 static void hacksearch_atom(int*                                            ii,
  79                             int*                                            jj,
  80                             const char*                                     name,
  81                             gmx::ArrayRef<const std::vector<MoleculePatch>> patches,
  82                             int                                             resind,
  83                             const t_atoms*                                  pdba)
  84 {
  85     int i;
  86
  87     *ii = -1;
  88     if (name[0] == '-')
  89     {
  90         name++;
  91         resind--;
  92     }
  93     for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++) {}
  94     for (; (i < pdba->nr) && (pdba->atom[i].resind == resind) && (*ii < 0); i++)
  95     {
  96         int j = 0;
  97         for (const auto& patch : patches[i])
  98         {
  99             if (patch.nname == name)
 100             {
 101                 *ii = i;
 102                 *jj = j;
 103             }
 104             j++;
 105         }
 106     }
 107 }
 108
 109 static std::vector<MoleculePatchDatabase>
 110 getMoleculePatchDatabases(const t_atoms*                              pdba,
 111                           gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
 112                           int                                         nterpairs,
 113                           gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
 114                           gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
 115                           gmx::ArrayRef<const int>                    rN,
 116                           gmx::ArrayRef<const int>                    rC)
 117 {
 118     std::vector<MoleculePatchDatabase> modBlock(pdba->nres);
 119     /* make space */
 120     /* first the termini */
 121     for (int i = 0; i < nterpairs; i++)
 122     {
 123         if (ntdb[i] != nullptr)
 124         {
 125             copyModificationBlocks(*ntdb[i], &modBlock[rN[i]]);
 126         }
 127         if (ctdb[i] != nullptr)
 128         {
 129             mergeAtomAndBondModifications(*ctdb[i], &modBlock[rC[i]]);
 130         }
 131     }
 132     /* then the whole hdb */
 133     for (int rnr = 0; rnr < pdba->nres; rnr++)
 134     {
 135         auto ahptr = search_h_db(globalPatches, *pdba->resinfo[rnr].rtp);
 136         if (ahptr != globalPatches.end())
 137         {
 138             if (modBlock[rnr].name.empty())
 139             {
 140                 modBlock[rnr].name = ahptr->name;
 141             }
 142             mergeAtomModifications(*ahptr, &modBlock[rnr]);
 143         }
 144     }
 145     return modBlock;
 146 }
 147
 148 static void expand_hackblocks_one(const MoleculePatchDatabase& newPatch,
 149                                   const std::string localAtomName, //NOLINT(performance-unnecessary-value-param)
 150                                   std::vector<MoleculePatch>* globalPatches,
 151                                   bool                        bN,
 152                                   bool                        bC)
 153 {
 154     /* we'll recursively add atoms to atoms */
 155     int pos = 0;
 156     for (auto& singlePatch : newPatch.hack)
 157     {
 158         /* first check if we're in the N- or C-terminus, then we should ignore
 159            all hacks involving atoms from resp. previous or next residue
 160            (i.e. which name begins with '-' (N) or '+' (C) */
 161         bool bIgnore = false;
 162         if (bN) /* N-terminus: ignore '-' */
 163         {
 164             for (int k = 0; k < 4 && !singlePatch.a[k].empty() && !bIgnore; k++)
 165             {
 166                 bIgnore = singlePatch.a[k][0] == '-';
 167             }
 168         }
 169         if (bC) /* C-terminus: ignore '+' */
 170         {
 171             for (int k = 0; k < 4 && !singlePatch.a[k].empty() && !bIgnore; k++)
 172             {
 173                 bIgnore = singlePatch.a[k][0] == '+';
 174             }
 175         }
 176         /* must be either hdb entry (tp>0) or add from tdb (oname==NULL)
 177            and first control aton (AI) matches this atom or
 178            delete/replace from tdb (oname!=NULL) and oname matches this atom */
 179
 180         if (!bIgnore
 181             && (((singlePatch.tp > 0 || singlePatch.oname.empty()) && singlePatch.a[0] == localAtomName)
 182                 || (singlePatch.oname == localAtomName)))
 183         {
 184             /* now expand all hacks for this atom */
 185             for (int k = 0; k < singlePatch.nr; k++)
 186             {
 187                 globalPatches->push_back(singlePatch);
 188                 MoleculePatch* patch = &globalPatches->back();
 189                 patch->bXSet         = false;
 190                 /* if we're adding (oname==NULL) and don't have a new name (nname)
 191                    yet, build it from localAtomName */
 192                 if (patch->nname.empty())
 193                 {
 194                     if (patch->oname.empty())
 195                     {
 196                         patch->nname    = localAtomName;
 197                         patch->nname[0] = 'H';
 198                     }
 199                 }
 200                 else
 201                 {
 202                     if (gmx_debug_at)
 203                     {
 204                         fprintf(debug,
 205                                 "Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n",
 206                                 localAtomName.c_str(), pos, patch->nname.c_str(),
 207                                 singlePatch.nname.c_str(),
 208                                 patch->oname.empty() ? "" : patch->oname.c_str());
 209                     }
 210                     patch->nname = singlePatch.nname;
 211                 }
 212
 213                 if (singlePatch.tp == 10 && k == 2)
 214                 {
 215                     /* This is a water virtual site, not a hydrogen */
 216                     /* Ugly hardcoded name hack */
 217                     patch->nname.assign("M");
 218                 }
 219                 else if (singlePatch.tp == 11 && k >= 2)
 220                 {
 221                     /* This is a water lone pair, not a hydrogen */
 222                     /* Ugly hardcoded name hack */
 223                     patch->nname.assign(gmx::formatString("LP%d", 1 + k - 2));
 224                 }
 225                 else if (singlePatch.nr > 1)
 226                 {
 227                     /* adding more than one atom, number them */
 228                     patch->nname.append(gmx::formatString("%d", 1 + k));
 229                 }
 230             }
 231
 232             /* add hacks to atoms we've just added */
 233             if (singlePatch.tp > 0 || singlePatch.oname.empty())
 234             {
 235                 for (int k = 0; k < singlePatch.nr; k++)
 236                 {
 237                     expand_hackblocks_one(
 238                             newPatch, globalPatches->at(globalPatches->size() - singlePatch.nr + k).nname,
 239                             globalPatches, bN, bC);
 240                 }
 241             }
 242         }
 243         pos++;
 244     }
 245 }
 246
 247 static void expand_hackblocks(const t_atoms*                             pdba,
 248                               gmx::ArrayRef<const MoleculePatchDatabase> hb,
 249                               gmx::ArrayRef<std::vector<MoleculePatch>>  patches,
 250                               int                                        nterpairs,
 251                               gmx::ArrayRef<const int>                   rN,
 252                               gmx::ArrayRef<const int>                   rC)
 253 {
 254     for (int i = 0; i < pdba->nr; i++)
 255     {
 256         bool bN = false;
 257         for (int j = 0; j < nterpairs && !bN; j++)
 258         {
 259             bN = pdba->atom[i].resind == rN[j];
 260         }
 261         bool bC = false;
 262         for (int j = 0; j < nterpairs && !bC; j++)
 263         {
 264             bC = pdba->atom[i].resind == rC[j];
 265         }
 266
 267         /* add hacks to this atom */
 268         expand_hackblocks_one(hb[pdba->atom[i].resind], *pdba->atomname[i], &patches[i], bN, bC);
 269     }
 270 }
 271
 272 static int check_atoms_present(const t_atoms* pdba, gmx::ArrayRef<std::vector<MoleculePatch>> patches)
 273 {
 274     int nadd = 0;
 275     for (int i = 0; i < pdba->nr; i++)
 276     {
 277         int rnr = pdba->atom[i].resind;
 278         for (auto patch = patches[i].begin(); patch != patches[i].end(); patch++)
 279         {
 280             switch (patch->type())
 281             {
 282                 case MoleculePatchType::Add:
 283                 {
 284                     /* we're adding */
 285                     /* check if the atom is already present */
 286                     int k = pdbasearch_atom(patch->nname.c_str(), rnr, pdba, "check", TRUE);
 287                     if (k != -1)
 288                     {
 289                         /* We found the added atom. */
 290                         patch->bAlreadyPresent = true;
 291                     }
 292                     else
 293                     {
 294                         patch->bAlreadyPresent = false;
 295                         /* count how many atoms we'll add */
 296                         nadd++;
 297                     }
 298                     break;
 299                 }
 300                 case MoleculePatchType::Delete:
 301                 {
 302                     /* we're deleting */
 303                     nadd--;
 304                     break;
 305                 }
 306                 case MoleculePatchType::Replace: { break;
 307                 }
 308                 default: { GMX_THROW(gmx::InternalError("Case not handled"));
 309                 }
 310             }
 311         }
 312     }
 313     return nadd;
 314 }
 315
 316 static void calc_all_pos(const t_atoms*                            pdba,
 317                          gmx::ArrayRef<const gmx::RVec>            x,
 318                          gmx::ArrayRef<std::vector<MoleculePatch>> patches,
 319                          bool                                      bCheckMissing)
 320 {
 321     int ii, l = 0;
 322 #define MAXH 4
 323     rvec xa[4];    /* control atoms for calc_h_pos */
 324     rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
 325
 326     int jj = 0;
 327
 328     for (int i = 0; i < pdba->nr; i++)
 329     {
 330         int rnr = pdba->atom[i].resind;
 331         for (auto patch = patches[i].begin(); patch != patches[i].end(); patch += patch->nr)
 332         {
 333             GMX_RELEASE_ASSERT(patch < patches[i].end(),
 334                                "The number of patches in the last patch can not exceed the total "
 335                                "number of patches");
 336             /* check if we're adding: */
 337             if (patch->type() == MoleculePatchType::Add && patch->tp > 0)
 338             {
 339                 bool bFoundAll = true;
 340                 for (int m = 0; (m < patch->nctl && bFoundAll); m++)
 341                 {
 342                     int ia = pdbasearch_atom(patch->a[m].c_str(), rnr, pdba,
 343                                              bCheckMissing ? "atom" : "check", !bCheckMissing);
 344                     if (ia < 0)
 345                     {
 346                         /* not found in original atoms, might still be in
 347                          * the patch Instructions (patches) */
 348                         hacksearch_atom(&ii, &jj, patch->a[m].c_str(), patches, rnr, pdba);
 349                         if (ii >= 0)
 350                         {
 351                             copy_rvec(patches[ii][jj].newx, xa[m]);
 352                         }
 353                         else
 354                         {
 355                             bFoundAll = false;
 356                             if (bCheckMissing)
 357                             {
 358                                 gmx_fatal(FARGS,
 359                                           "Atom %s not found in residue %s %d"
 360                                           ", rtp entry %s"
 361                                           " while adding hydrogens",
 362                                           patch->a[m].c_str(), *pdba->resinfo[rnr].name,
 363                                           pdba->resinfo[rnr].nr, *pdba->resinfo[rnr].rtp);
 364                             }
 365                         }
 366                     }
 367                     else
 368                     {
 369                         copy_rvec(x[ia], xa[m]);
 370                     }
 371                 }
 372                 if (bFoundAll)
 373                 {
 374                     for (int m = 0; (m < MAXH); m++)
 375                     {
 376                         for (int d = 0; d < DIM; d++)
 377                         {
 378                             if (m < patch->nr)
 379                             {
 380                                 xh[m][d] = 0;
 381                             }
 382                             else
 383                             {
 384                                 xh[m][d] = NOTSET;
 385                             }
 386                         }
 387                     }
 388                     calc_h_pos(patch->tp, xa, xh, &l);
 389                     for (int m = 0; m < patch->nr; m++)
 390                     {
 391                         auto next = patch + m;
 392                         copy_rvec(xh[m], next->newx);
 393                         next->bXSet = true;
 394                     }
 395                 }
 396             }
 397         }
 398     }
 399 }
 400
 401 static int add_h_low(t_atoms**                                   initialAtoms,
 402                      t_atoms**                                   modifiedAtoms,
 403                      std::vector<gmx::RVec>*                     xptr,
 404                      gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
 405                      t_symtab*                                   symtab,
 406                      const int                                   nterpairs,
 407                      gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
 408                      gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
 409                      gmx::ArrayRef<const int>                    rN,
 410                      gmx::ArrayRef<const int>                    rC,
 411                      const bool                                  bCheckMissing)
 412 {
 413     int                                     nadd;
 414     int                                     newi, natoms, nalreadypresent;
 415     std::vector<std::vector<MoleculePatch>> patches;
 416     std::vector<gmx::RVec>                  xn;
 417
 418     t_atoms* pdba = *initialAtoms;
 419
 420     /* set flags for adding hydrogens (according to hdb) */
 421     natoms = pdba->nr;
 422
 423     {
 424         /* We'll have to do all the hard work */
 425         /* first get all the hackblocks for each residue: */
 426         std::vector<MoleculePatchDatabase> hb =
 427                 getMoleculePatchDatabases(pdba, globalPatches, nterpairs, ntdb, ctdb, rN, rC);
 428
 429         /* expand the hackblocks to atom level */
 430         patches.resize(natoms);
 431         expand_hackblocks(pdba, hb, patches, nterpairs, rN, rC);
 432     }
 433
 434     /* Now calc the positions */
 435     calc_all_pos(pdba, *xptr, patches, bCheckMissing);
 436
 437     /* we don't have to add atoms that are already present in initialAtoms,
 438        so we will remove them from the patches (MoleculePatch) */
 439     nadd = check_atoms_present(pdba, patches);
 440
 441     /* Copy old atoms, making space for new ones */
 442     if (nadd > 0)
 443     {
 444         srenew(*modifiedAtoms, 1);
 445         init_t_atoms(*modifiedAtoms, natoms + nadd, FALSE);
 446         (*modifiedAtoms)->nres = pdba->nres;
 447         srenew((*modifiedAtoms)->resinfo, pdba->nres);
 448         std::copy(pdba->resinfo, pdba->resinfo + pdba->nres, (*modifiedAtoms)->resinfo);
 449     }
 450     if (nadd == 0)
 451     {
 452         return natoms;
 453     }
 454
 455     xn.resize(natoms + nadd);
 456     newi = 0;
 457     for (int i = 0; (i < natoms); i++)
 458     {
 459         /* check if this atom wasn't scheduled for deletion */
 460         if (patches[i].empty() || (!patches[i][0].nname.empty()))
 461         {
 462             if (newi >= natoms + nadd)
 463             {
 464                 /*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
 465                 nadd += 10;
 466                 xn.resize(natoms + nadd);
 467                 srenew((*modifiedAtoms)->atom, natoms + nadd);
 468                 srenew((*modifiedAtoms)->atomname, natoms + nadd);
 469             }
 470             copy_atom(pdba, i, (*modifiedAtoms), newi, symtab);
 471             copy_rvec((*xptr)[i], xn[newi]);
 472             /* process the hacks for this atom */
 473             nalreadypresent = 0;
 474             for (auto patch = patches[i].begin(); patch != patches[i].end(); patch++)
 475             {
 476                 if (patch->type() == MoleculePatchType::Add) /* add */
 477                 {
 478                     newi++;
 479                     if (newi >= natoms + nadd)
 480                     {
 481                         /* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
 482                         nadd += 10;
 483                         xn.resize(natoms + nadd);
 484                         srenew((*modifiedAtoms)->atom, natoms + nadd);
 485                         srenew((*modifiedAtoms)->atomname, natoms + nadd);
 486                     }
 487                     (*modifiedAtoms)->atom[newi].resind = pdba->atom[i].resind;
 488                 }
 489                 if (!patch->nname.empty()
 490                     && (patch->oname.empty() || patch->oname == *(*modifiedAtoms)->atomname[newi]))
 491                 {
 492                     /* add or replace */
 493                     if (patch->type() == MoleculePatchType::Add && patch->bAlreadyPresent)
 494                     {
 495                         /* This atom is already present, copy it from the input. */
 496                         nalreadypresent++;
 497                         copy_atom(pdba, i + nalreadypresent, (*modifiedAtoms), newi, symtab);
 498                         copy_rvec((*xptr)[i + nalreadypresent], xn[newi]);
 499                     }
 500                     else
 501                     {
 502                         if (gmx_debug_at)
 503                         {
 504                             fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n", newi,
 505                                     ((*modifiedAtoms)->atomname[newi] && *(*modifiedAtoms)->atomname[newi])
 506                                             ? *(*modifiedAtoms)->atomname[newi]
 507                                             : "",
 508                                     patch->oname.empty() ? "" : patch->oname.c_str(),
 509                                     patch->nname.c_str());
 510                         }
 511                         (*modifiedAtoms)->atomname[newi] = put_symtab(symtab, patch->nname.c_str());
 512                         if (patch->bXSet)
 513                         {
 514                             copy_rvec(patch->newx, xn[newi]);
 515                         }
 516                     }
 517                     if (debug)
 518                     {
 519                         fprintf(debug, " %s %g %g", *(*modifiedAtoms)->atomname[newi],
 520                                 (*modifiedAtoms)->atom[newi].m, (*modifiedAtoms)->atom[newi].q);
 521                     }
 522                 }
 523             }
 524             newi++;
 525             i += nalreadypresent;
 526         }
 527     }
 528     (*modifiedAtoms)->nr = newi;
 529
 530     done_atom(pdba);
 531     *initialAtoms = *modifiedAtoms;
 532
 533     *xptr = xn;
 534
 535     return newi;
 536 }
 537
 538 int add_h(t_atoms**                                   initialAtoms,
 539           t_atoms**                                   localAtoms,
 540           std::vector<gmx::RVec>*                     xptr,
 541           gmx::ArrayRef<const MoleculePatchDatabase>  globalPatches,
 542           t_symtab*                                   symtab,
 543           const int                                   nterpairs,
 544           gmx::ArrayRef<MoleculePatchDatabase* const> ntdb,
 545           gmx::ArrayRef<MoleculePatchDatabase* const> ctdb,
 546           gmx::ArrayRef<const int>                    rN,
 547           gmx::ArrayRef<const int>                    rC,
 548           const bool                                  bAllowMissing)
 549 {
 550     int nold, nnew, niter;
 551
 552     /* Here we loop to be able to add atoms to added atoms.
 553      * We should not check for missing atoms here.
 554      */
 555     niter = 0;
 556     nnew  = 0;
 557     do
 558     {
 559         nold = nnew;
 560         nnew = add_h_low(initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb,
 561                          ctdb, rN, rC, FALSE);
 562         niter++;
 563         if (niter > 100)
 564         {
 565             gmx_fatal(FARGS,
 566                       "More than 100 iterations of add_h. Maybe you are trying to replace an added "
 567                       "atom (this is not supported)?");
 568         }
 569     } while (nnew > nold);
 570
 571     if (!bAllowMissing)
 572     {
 573         /* Call add_h_low once more, now only for the missing atoms check */
 574         add_h_low(initialAtoms, localAtoms, xptr, globalPatches, symtab, nterpairs, ntdb, ctdb, rN,
 575                   rC, TRUE);
 576     }
 577
 578     return nnew;
 579 }