src/gromacs/topology/mtop_lookup.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \libinternal \file
  36  *
  37  * \brief This file contains inline functions to look up atom information
  38  * using the global atom index.
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \inlibraryapi
  42  * \ingroup module_mtop
  43  */
  44
  45 #ifndef GMX_TOPOLOGY_MTOP_LOOKUP_H
  46 #define GMX_TOPOLOGY_MTOP_LOOKUP_H
  47
  48 #include "gromacs/topology/topology.h"
  49 #include "gromacs/utility/basedefinitions.h"
  50 #include "gromacs/utility/gmxassert.h"
  51
  52 struct t_atom;
  53
  54 // TODO All of the functions taking a const gmx_mtop * are deprecated
  55 // and should be replaced by versions taking const gmx_mtop & when
  56 // their callers are refactored similarly.
  57
  58 /*! \brief Look up the molecule block and other indices of a global atom index
  59  *
  60  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
  61  * The input value of moleculeBlock should be in range. Use 0 as starting value.
  62  * For subsequent calls to this function, e.g. in a loop, pass in the previously
  63  * returned value for best performance. Atoms in a group tend to be in the same
  64  * molecule(block), so this minimizes the search time.
  65  *
  66  * \param[in]     mtop                 The molecule topology
  67  * \param[in]     globalAtomIndex      The global atom index to look up
  68  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
  69  * \param[out]    moleculeIndex        The index of the molecule in the block, can be NULL
  70  * \param[out]    atomIndexInMolecule  The atom index in the molecule, can be NULL
  71  */
  72 static inline void
  73 mtopGetMolblockIndex(const gmx_mtop_t *mtop,
  74                      int               globalAtomIndex,
  75                      int              *moleculeBlock,
  76                      int              *moleculeIndex,
  77                      int              *atomIndexInMolecule)
  78 {
  79     GMX_ASSERT(globalAtomIndex >= 0, "The atom index to look up should not be negative");
  80     GMX_ASSERT(globalAtomIndex < mtop->natoms, "The atom index to look up should be within range");
  81     GMX_ASSERT(moleculeBlock != nullptr, "molBlock can not be NULL");
  82     GMX_ASSERT(!mtop->moleculeBlockIndices.empty(),
  83                "The moleculeBlockIndices should not be empty");
  84     GMX_ASSERT(*moleculeBlock >= 0,
  85                "The starting molecule block index for the search should not be negative");
  86     GMX_ASSERT(*moleculeBlock < gmx::ssize(mtop->moleculeBlockIndices),
  87                "The starting molecule block index for the search should be within range");
  88
  89     /* Search the molecule block index using bisection */
  90     int molBlock0 = -1;
  91     int molBlock1 = mtop->molblock.size();
  92
  93     int globalAtomStart;
  94     while (TRUE)
  95     {
  96         globalAtomStart = mtop->moleculeBlockIndices[*moleculeBlock].globalAtomStart;
  97         if (globalAtomIndex < globalAtomStart)
  98         {
  99             molBlock1 = *moleculeBlock;
 100         }
 101         else if (globalAtomIndex >= mtop->moleculeBlockIndices[*moleculeBlock].globalAtomEnd)
 102         {
 103             molBlock0 = *moleculeBlock;
 104         }
 105         else
 106         {
 107             break;
 108         }
 109         *moleculeBlock = ((molBlock0 + molBlock1 + 1) >> 1);
 110     }
 111
 112     int molIndex = (globalAtomIndex - globalAtomStart) / mtop->moleculeBlockIndices[*moleculeBlock].numAtomsPerMolecule;
 113     if (moleculeIndex != nullptr)
 114     {
 115         *moleculeIndex = molIndex;
 116     }
 117     if (atomIndexInMolecule != nullptr)
 118     {
 119         *atomIndexInMolecule = globalAtomIndex - globalAtomStart - molIndex*mtop->moleculeBlockIndices[*moleculeBlock].numAtomsPerMolecule;
 120     }
 121 }
 122
 123 /*! \brief Returns the global molecule index of a global atom index
 124  *
 125  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 126  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 127  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 128  * returned value for best performance. Atoms in a group tend to be in the same
 129  * molecule(block), so this minimizes the search time.
 130  *
 131  * \param[in]     mtop                 The molecule topology
 132  * \param[in]     globalAtomIndex      The global atom index to look up
 133  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 134  */
 135 static inline int
 136 mtopGetMoleculeIndex(const gmx_mtop_t *mtop,
 137                      int               globalAtomIndex,
 138                      int              *moleculeBlock)
 139 {
 140     int localMoleculeIndex;
 141     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, &localMoleculeIndex, nullptr);
 142
 143     return mtop->moleculeBlockIndices[*moleculeBlock].moleculeIndexStart + localMoleculeIndex;
 144 }
 145
 146 /*! \brief Returns the atom data for an atom based on global atom index
 147  *
 148  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 149  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 150  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 151  * returned value for best performance. Atoms in a group tend to be in the same
 152  * molecule(block), so this minimizes the search time.
 153  *
 154  * \param[in]     mtop                 The molecule topology
 155  * \param[in]     globalAtomIndex      The global atom index to look up
 156  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 157  */
 158 static inline const t_atom &
 159 mtopGetAtomParameters(const gmx_mtop_t  *mtop,
 160                       int                globalAtomIndex,
 161                       int               *moleculeBlock)
 162 {
 163     int atomIndexInMolecule;
 164     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 165                          nullptr, &atomIndexInMolecule);
 166     const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
 167     return moltype.atoms.atom[atomIndexInMolecule];
 168 }
 169
 170 /*! \brief Returns the mass of an atom based on global atom index
 171  *
 172  * Returns that A-state mass of the atom with global index \p globalAtomIndex.
 173  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 174  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 175  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 176  * returned value for best performance. Atoms in a group tend to be in the same
 177  * molecule(block), so this minimizes the search time.
 178  *
 179  * \param[in]     mtop                 The molecule topology
 180  * \param[in]     globalAtomIndex      The global atom index to look up
 181  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 182  */
 183 static inline real
 184 mtopGetAtomMass(const gmx_mtop_t  *mtop,
 185                 int                globalAtomIndex,
 186                 int               *moleculeBlock)
 187 {
 188     const t_atom &atom = mtopGetAtomParameters(mtop, globalAtomIndex, moleculeBlock);
 189     return atom.m;
 190 }
 191
 192 /*! \brief Look up the atom and residue name and residue number and index of a global atom index
 193  *
 194  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 195  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 196  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 197  * returned value for best performance. Atoms in a group tend to be in the same
 198  * molecule(block), so this minimizes the search time.
 199  * Note that this function does a (somewhat expensive) lookup. If you want
 200  * to look up data sequentially for all atoms in a molecule or the system,
 201  * use one of the mtop loop functionalities.
 202  *
 203  * \param[in]     mtop                The molecule topology
 204  * \param[in]     globalAtomIndex     The global atom index to look up
 205  * \param[in,out] moleculeBlock       The molecule block index in \p mtop
 206  * \param[out]    atomName            The atom name, input can be NULL
 207  * \param[out]    residueNumber       The residue number, input can be NULL
 208  * \param[out]    residueName         The residue name, input can be NULL
 209  * \param[out]    globalResidueIndex  The gobal residue index, input can be NULL
 210  */
 211 static inline void
 212 mtopGetAtomAndResidueName(const gmx_mtop_t  *mtop,
 213                           int                globalAtomIndex,
 214                           int               *moleculeBlock,
 215                           const char       **atomName,
 216                           int               *residueNumber,
 217                           const char       **residueName,
 218                           int               *globalResidueIndex)
 219 {
 220     int moleculeIndex;
 221     int atomIndexInMolecule;
 222     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 223                          &moleculeIndex, &atomIndexInMolecule);
 224
 225     const gmx_molblock_t       &molb    = mtop->molblock[*moleculeBlock];
 226     const t_atoms              &atoms   = mtop->moltype[molb.type].atoms;
 227     const MoleculeBlockIndices &indices = mtop->moleculeBlockIndices[*moleculeBlock];
 228     if (atomName != nullptr)
 229     {
 230         *atomName = *(atoms.atomname[atomIndexInMolecule]);
 231     }
 232     if (residueNumber != nullptr)
 233     {
 234         if (atoms.nres > mtop->maxres_renum)
 235         {
 236             *residueNumber = atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].nr;
 237         }
 238         else
 239         {
 240             /* Single residue molecule, keep counting */
 241             *residueNumber = indices.residueNumberStart + moleculeIndex*atoms.nres + atoms.atom[atomIndexInMolecule].resind;
 242         }
 243     }
 244     if (residueName != nullptr)
 245     {
 246         *residueName = *(atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].name);
 247     }
 248     if (globalResidueIndex != nullptr)
 249     {
 250         *globalResidueIndex = indices.globalResidueStart + moleculeIndex*atoms.nres + atoms.atom[atomIndexInMolecule].resind;
 251     }
 252 }
 253
 254 //! \copydoc mtopGetAtomAndResidueName()
 255 static inline void
 256 mtopGetAtomAndResidueName(const gmx_mtop_t  &mtop,
 257                           int                globalAtomIndex,
 258                           int               *moleculeBlock,
 259                           const char       **atomName,
 260                           int               *residueNumber,
 261                           const char       **residueName,
 262                           int               *globalResidueIndex)
 263 {
 264     mtopGetAtomAndResidueName(&mtop, globalAtomIndex, moleculeBlock,
 265                               atomName, residueNumber, residueName, globalResidueIndex);
 266 }
 267
 268 /*! \brief Returns residue information for an atom based on global atom index
 269  *
 270  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 271  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 272  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 273  * returned value for best performance. Atoms in a group tend to be in the same
 274  * molecule(block), so this minimizes the search time.
 275  *
 276  * \param[in]     mtop                 The molecule topology
 277  * \param[in]     globalAtomIndex      The global atom index to look up
 278  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 279  */
 280 static inline const t_resinfo &
 281 mtopGetResidueInfo(const gmx_mtop_t  *mtop,
 282                    int                globalAtomIndex,
 283                    int               *moleculeBlock)
 284 {
 285     int atomIndexInMolecule;
 286     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 287                          nullptr, &atomIndexInMolecule);
 288     const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
 289     const int            resind  = moltype.atoms.atom[atomIndexInMolecule].resind;
 290     return moltype.atoms.resinfo[resind];
 291 }
 292
 293 /*! \brief Returns PDB information for an atom based on global atom index
 294  *
 295  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 296  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 297  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 298  * returned value for best performance. Atoms in a group tend to be in the same
 299  * molecule(block), so this minimizes the search time.
 300  *
 301  * \param[in]     mtop                 The molecule topology
 302  * \param[in]     globalAtomIndex      The global atom index to look up
 303  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 304  */
 305 static inline const t_pdbinfo &
 306 mtopGetAtomPdbInfo(const gmx_mtop_t  *mtop,
 307                    int                globalAtomIndex,
 308                    int               *moleculeBlock)
 309 {
 310     int atomIndexInMolecule;
 311     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 312                          nullptr, &atomIndexInMolecule);
 313     const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
 314     GMX_ASSERT(moltype.atoms.havePdbInfo, "PDB information not present when requested");
 315     return moltype.atoms.pdbinfo[atomIndexInMolecule];
 316 }
 317
 318 #endif