src/gromacs/topology/mtop_lookup.h

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  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 /*! \brief Look up the molecule block and other indices of a global atom index
  55  *
  56  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
  57  * The input value of moleculeBlock should be in range. Use 0 as starting value.
  58  * For subsequent calls to this function, e.g. in a loop, pass in the previously
  59  * returned value for best performance. Atoms in a group tend to be in the same
  60  * molecule(block), so this minimizes the search time.
  61  *
  62  * \param[in]     mtop                 The molecule topology
  63  * \param[in]     globalAtomIndex      The global atom index to look up
  64  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
  65  * \param[out]    moleculeIndex        The index of the molecule in the block, can be NULL
  66  * \param[out]    atomIndexInMolecule  The atom index in the molecule, can be NULL
  67  */
  68 static inline void
  69 mtopGetMolblockIndex(const gmx_mtop_t *mtop,
  70                      int               globalAtomIndex,
  71                      int              *moleculeBlock,
  72                      int              *moleculeIndex,
  73                      int              *atomIndexInMolecule)
  74 {
  75     GMX_ASSERT(globalAtomIndex >= 0 && globalAtomIndex < mtop->natoms, "The atom index to look up should be within range");
  76     GMX_ASSERT(moleculeBlock != nullptr, "molBlock can not be NULL");
  77     GMX_ASSERT(*moleculeBlock >= 0 && *moleculeBlock < static_cast<int>(mtop->molblock.size()), "The starting molecule block index for the search should be within range");
  78
  79     /* Search the molecue block index using bisection */
  80     int molBlock0 = -1;
  81     int molBlock1 = mtop->molblock.size();
  82
  83     int globalAtomStart;
  84     while (TRUE)
  85     {
  86         globalAtomStart = mtop->molblock[*moleculeBlock].globalAtomStart;
  87         if (globalAtomIndex < globalAtomStart)
  88         {
  89             molBlock1 = *moleculeBlock;
  90         }
  91         else if (globalAtomIndex >= mtop->molblock[*moleculeBlock].globalAtomEnd)
  92         {
  93             molBlock0 = *moleculeBlock;
  94         }
  95         else
  96         {
  97             break;
  98         }
  99         *moleculeBlock = ((molBlock0 + molBlock1 + 1) >> 1);
 100     }
 101
 102     int molIndex = (globalAtomIndex - globalAtomStart) / mtop->molblock[*moleculeBlock].natoms_mol;
 103     if (moleculeIndex != nullptr)
 104     {
 105         *moleculeIndex = molIndex;
 106     }
 107     if (atomIndexInMolecule != nullptr)
 108     {
 109         *atomIndexInMolecule = globalAtomIndex - globalAtomStart - molIndex*mtop->molblock[*moleculeBlock].natoms_mol;
 110     }
 111 }
 112
 113 /*! \brief Returns the global molecule index of a global atom index
 114  *
 115  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 116  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 117  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 118  * returned value for best performance. Atoms in a group tend to be in the same
 119  * molecule(block), so this minimizes the search time.
 120  *
 121  * \param[in]     mtop                 The molecule topology
 122  * \param[in]     globalAtomIndex      The global atom index to look up
 123  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 124  */
 125 static inline int
 126 mtopGetMoleculeIndex(const gmx_mtop_t *mtop,
 127                      int               globalAtomIndex,
 128                      int              *moleculeBlock)
 129 {
 130     int localMoleculeIndex;
 131     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock, &localMoleculeIndex, nullptr);
 132
 133     return mtop->molblock[*moleculeBlock].moleculeIndexStart + localMoleculeIndex;
 134 }
 135
 136 /*! \brief Returns the atom data for an atom based on global atom index
 137  *
 138  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 139  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 140  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 141  * returned value for best performance. Atoms in a group tend to be in the same
 142  * molecule(block), so this minimizes the search time.
 143  *
 144  * \param[in]     mtop                 The molecule topology
 145  * \param[in]     globalAtomIndex      The global atom index to look up
 146  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 147  */
 148 static inline const t_atom &
 149 mtopGetAtomParameters(const gmx_mtop_t  *mtop,
 150                       int                globalAtomIndex,
 151                       int               *moleculeBlock)
 152 {
 153     int atomIndexInMolecule;
 154     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 155                          nullptr, &atomIndexInMolecule);
 156     const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
 157     return moltype.atoms.atom[atomIndexInMolecule];
 158 }
 159
 160 /*! \brief Returns the mass of an atom based on global atom index
 161  *
 162  * Returns that A-state mass of the atom with global index \p globalAtomIndex.
 163  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 164  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 165  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 166  * returned value for best performance. Atoms in a group tend to be in the same
 167  * molecule(block), so this minimizes the search time.
 168  *
 169  * \param[in]     mtop                 The molecule topology
 170  * \param[in]     globalAtomIndex      The global atom index to look up
 171  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 172  */
 173 static inline real
 174 mtopGetAtomMass(const gmx_mtop_t  *mtop,
 175                 int                globalAtomIndex,
 176                 int               *moleculeBlock)
 177 {
 178     const t_atom &atom = mtopGetAtomParameters(mtop, globalAtomIndex, moleculeBlock);
 179     return atom.m;
 180 }
 181
 182 /*! \brief Look up the atom and residue name and residue number and index of a global atom index
 183  *
 184  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 185  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 186  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 187  * returned value for best performance. Atoms in a group tend to be in the same
 188  * molecule(block), so this minimizes the search time.
 189  * Note that this function does a (somewhat expensive) lookup. If you want
 190  * to look up data sequentially for all atoms in a molecule or the system,
 191  * use one of the mtop loop functionalities.
 192  *
 193  * \param[in]     mtop                The molecule topology
 194  * \param[in]     globalAtomIndex     The global atom index to look up
 195  * \param[in,out] moleculeBlock       The molecule block index in \p mtop
 196  * \param[out]    atomName            The atom name, input can be NULL
 197  * \param[out]    residueNumber       The residue number, input can be NULL
 198  * \param[out]    residueName         The residue name, input can be NULL
 199  * \param[out]    globalResidueIndex  The gobal residue index, input can be NULL
 200  */
 201 static inline void
 202 mtopGetAtomAndResidueName(const gmx_mtop_t  *mtop,
 203                           int                globalAtomIndex,
 204                           int               *moleculeBlock,
 205                           const char       **atomName,
 206                           int               *residueNumber,
 207                           const char       **residueName,
 208                           int               *globalResidueIndex)
 209 {
 210     int moleculeIndex;
 211     int atomIndexInMolecule;
 212     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 213                          &moleculeIndex, &atomIndexInMolecule);
 214
 215     const gmx_molblock_t &molb  = mtop->molblock[*moleculeBlock];
 216     const t_atoms        &atoms = mtop->moltype[molb.type].atoms;
 217     if (atomName != nullptr)
 218     {
 219         *atomName = *(atoms.atomname[atomIndexInMolecule]);
 220     }
 221     if (residueNumber != nullptr)
 222     {
 223         if (atoms.nres > mtop->maxres_renum)
 224         {
 225             *residueNumber = atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].nr;
 226         }
 227         else
 228         {
 229             /* Single residue molecule, keep counting */
 230             *residueNumber = molb.residueNumberStart + moleculeIndex*atoms.nres + atoms.atom[atomIndexInMolecule].resind;
 231         }
 232     }
 233     if (residueName != nullptr)
 234     {
 235         *residueName = *(atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].name);
 236     }
 237     if (globalResidueIndex != nullptr)
 238     {
 239         *globalResidueIndex = molb.globalResidueStart + moleculeIndex*atoms.nres + atoms.atom[atomIndexInMolecule].resind;
 240     }
 241 }
 242
 243 /*! \brief Returns residue information for an atom based on global atom index
 244  *
 245  * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
 246  * The input value of moleculeBlock should be in range. Use 0 as starting value.
 247  * For subsequent calls to this function, e.g. in a loop, pass in the previously
 248  * returned value for best performance. Atoms in a group tend to be in the same
 249  * molecule(block), so this minimizes the search time.
 250  *
 251  * \param[in]     mtop                 The molecule topology
 252  * \param[in]     globalAtomIndex      The global atom index to look up
 253  * \param[in,out] moleculeBlock        The molecule block index in \p mtop
 254  */
 255 static inline const t_resinfo &
 256 mtopGetResidueInfo(const gmx_mtop_t  *mtop,
 257                    int                globalAtomIndex,
 258                    int               *moleculeBlock)
 259 {
 260     int atomIndexInMolecule;
 261     mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
 262                          nullptr, &atomIndexInMolecule);
 263     const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
 264     const int            resind  = moltype.atoms.atom[atomIndexInMolecule].resind;
 265     return moltype.atoms.resinfo[resind];
 266 }
 267
 268 /*! \brief Returns PDB 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_pdbinfo &
 281 mtopGetAtomPdbInfo(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     GMX_ASSERT(moltype.atoms.havePdbInfo, "PDB information not present when requested");
 290     return moltype.atoms.pdbinfo[atomIndexInMolecule];
 291 }
 292
 293 #endif