src/gromacs/selection/selection.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in selection.h.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "selection.h"
  45
  46 #include <string>
  47
  48 #include "gromacs/selection/nbsearch.h"
  49 #include "gromacs/selection/position.h"
  50 #include "gromacs/topology/mtop_lookup.h"
  51 #include "gromacs/topology/topology.h"
  52 #include "gromacs/utility/exceptions.h"
  53 #include "gromacs/utility/gmxassert.h"
  54 #include "gromacs/utility/stringutil.h"
  55 #include "gromacs/utility/textwriter.h"
  56
  57 #include "selelem.h"
  58 #include "selvalue.h"
  59
  60 namespace gmx
  61 {
  62
  63 namespace internal
  64 {
  65
  66 /********************************************************************
  67  * SelectionData
  68  */
  69
  70 SelectionData::SelectionData(SelectionTreeElement *elem,
  71                              const char           *selstr)
  72     : name_(elem->name()), selectionText_(selstr),
  73       rootElement_(*elem), coveredFractionType_(CFRAC_NONE),
  74       coveredFraction_(1.0), averageCoveredFraction_(1.0),
  75       bDynamic_(false), bDynamicCoveredFraction_(false)
  76 {
  77     if (elem->child->type == SEL_CONST)
  78     {
  79         // TODO: This is not exception-safe if any called function throws.
  80         gmx_ana_pos_copy(&rawPositions_, elem->child->v.u.p, true);
  81     }
  82     else
  83     {
  84         SelectionTreeElementPointer child = elem->child;
  85         child->flags     &= ~SEL_ALLOCVAL;
  86         _gmx_selvalue_setstore(&child->v, &rawPositions_);
  87         /* We should also skip any modifiers to determine the dynamic
  88          * status. */
  89         while (child->type == SEL_MODIFIER)
  90         {
  91             child = child->child;
  92             if (!child)
  93             {
  94                 break;
  95             }
  96             if (child->type == SEL_SUBEXPRREF)
  97             {
  98                 child = child->child;
  99                 /* Because most subexpression elements are created
 100                  * during compilation, we need to check for them
 101                  * explicitly here.
 102                  */
 103                 if (child->type == SEL_SUBEXPR)
 104                 {
 105                     child = child->child;
 106                 }
 107             }
 108         }
 109         if (child)
 110         {
 111             /* For variable references, we should skip the
 112              * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
 113             if (child->type == SEL_SUBEXPRREF)
 114             {
 115                 child = child->child->child;
 116             }
 117             bDynamic_ = (child->child->flags & SEL_DYNAMIC);
 118         }
 119     }
 120     initCoveredFraction(CFRAC_NONE);
 121 }
 122
 123
 124 SelectionData::~SelectionData()
 125 {
 126 }
 127
 128
 129 bool
 130 SelectionData::initCoveredFraction(e_coverfrac_t type)
 131 {
 132     coveredFractionType_ = type;
 133     if (type == CFRAC_NONE)
 134     {
 135         bDynamicCoveredFraction_ = false;
 136     }
 137     else if (!_gmx_selelem_can_estimate_cover(rootElement()))
 138     {
 139         coveredFractionType_     = CFRAC_NONE;
 140         bDynamicCoveredFraction_ = false;
 141     }
 142     else
 143     {
 144         bDynamicCoveredFraction_ = true;
 145     }
 146     coveredFraction_        = bDynamicCoveredFraction_ ? 0.0 : 1.0;
 147     averageCoveredFraction_ = coveredFraction_;
 148     return type == CFRAC_NONE || coveredFractionType_ != CFRAC_NONE;
 149 }
 150
 151 namespace
 152 {
 153
 154 /*! \brief
 155  * Helper function to compute total masses and charges for positions.
 156  *
 157  * \param[in]  top     Topology to take atom masses from.
 158  * \param[in]  pos     Positions to compute masses and charges for.
 159  * \param[out] masses  Output masses.
 160  * \param[out] charges Output charges.
 161  *
 162  * Does not throw if enough space has been reserved for the output vectors.
 163  */
 164 void computeMassesAndCharges(const gmx_mtop_t *top, const gmx_ana_pos_t &pos,
 165                              std::vector<real> *masses,
 166                              std::vector<real> *charges)
 167 {
 168     GMX_ASSERT(top != NULL, "Should not have been called with NULL topology");
 169     masses->clear();
 170     charges->clear();
 171     int molb = 0;
 172     for (int b = 0; b < pos.count(); ++b)
 173     {
 174         real mass   = 0.0;
 175         real charge = 0.0;
 176         for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b+1]; ++i)
 177         {
 178             const int     index  = pos.m.mapb.a[i];
 179             const t_atom &atom   = mtopGetAtomParameters(top, index, &molb);
 180             mass                += atom.m;
 181             charge              += atom.q;
 182         }
 183         masses->push_back(mass);
 184         charges->push_back(charge);
 185     }
 186 }
 187
 188 }       // namespace
 189
 190 bool
 191 SelectionData::hasSortedAtomIndices() const
 192 {
 193     gmx_ana_index_t g;
 194     gmx_ana_index_set(&g, rawPositions_.m.mapb.nra, rawPositions_.m.mapb.a, -1);
 195     return gmx_ana_index_check_sorted(&g);
 196 }
 197
 198 void
 199 SelectionData::refreshName()
 200 {
 201     rootElement_.fillNameIfMissing(selectionText_.c_str());
 202     name_ = rootElement_.name();
 203 }
 204
 205 void
 206 SelectionData::initializeMassesAndCharges(const gmx_mtop_t *top)
 207 {
 208     GMX_ASSERT(posMass_.empty() && posCharge_.empty(),
 209                "Should not be called more than once");
 210     posMass_.reserve(posCount());
 211     posCharge_.reserve(posCount());
 212     if (top == NULL)
 213     {
 214         posMass_.resize(posCount(), 1.0);
 215         posCharge_.resize(posCount(), 0.0);
 216     }
 217     else
 218     {
 219         computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
 220     }
 221 }
 222
 223
 224 void
 225 SelectionData::refreshMassesAndCharges(const gmx_mtop_t *top)
 226 {
 227     if (top != NULL && isDynamic() && !hasFlag(efSelection_DynamicMask))
 228     {
 229         computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
 230     }
 231 }
 232
 233
 234 void
 235 SelectionData::updateCoveredFractionForFrame()
 236 {
 237     if (isCoveredFractionDynamic())
 238     {
 239         real cfrac = _gmx_selelem_estimate_coverfrac(rootElement());
 240         coveredFraction_         = cfrac;
 241         averageCoveredFraction_ += cfrac;
 242     }
 243 }
 244
 245
 246 void
 247 SelectionData::computeAverageCoveredFraction(int nframes)
 248 {
 249     if (isCoveredFractionDynamic() && nframes > 0)
 250     {
 251         averageCoveredFraction_ /= nframes;
 252     }
 253 }
 254
 255
 256 void
 257 SelectionData::restoreOriginalPositions(const gmx_mtop_t *top)
 258 {
 259     if (isDynamic())
 260     {
 261         gmx_ana_pos_t &p = rawPositions_;
 262         gmx_ana_indexmap_update(&p.m, rootElement().v.u.g,
 263                                 hasFlag(gmx::efSelection_DynamicMask));
 264         refreshMassesAndCharges(top);
 265     }
 266 }
 267
 268 }   // namespace internal
 269
 270 /********************************************************************
 271  * Selection
 272  */
 273
 274 Selection::operator AnalysisNeighborhoodPositions() const
 275 {
 276     AnalysisNeighborhoodPositions pos(data().rawPositions_.x,
 277                                       data().rawPositions_.count());
 278     if (hasOnlyAtoms())
 279     {
 280         pos.exclusionIds(atomIndices());
 281     }
 282     return pos;
 283 }
 284
 285
 286 void
 287 Selection::setOriginalId(int i, int id)
 288 {
 289     data().rawPositions_.m.mapid[i] = id;
 290     data().rawPositions_.m.orgid[i] = id;
 291 }
 292
 293
 294 int
 295 Selection::initOriginalIdsToGroup(const gmx_mtop_t *top, e_index_t type)
 296 {
 297     try
 298     {
 299         return gmx_ana_indexmap_init_orgid_group(&data().rawPositions_.m, top, type);
 300     }
 301     catch (const InconsistentInputError &)
 302     {
 303         GMX_ASSERT(type == INDEX_RES || type == INDEX_MOL,
 304                    "Expected that only grouping by residue/molecule would fail");
 305         std::string message =
 306             formatString("Cannot group selection '%s' into %s, because some "
 307                          "positions have atoms from more than one such group.",
 308                          name(), type == INDEX_MOL ? "molecules" : "residues");
 309         GMX_THROW(InconsistentInputError(message));
 310     }
 311 }
 312
 313
 314 void
 315 Selection::printInfo(FILE *fp) const
 316 {
 317     fprintf(fp, "\"%s\" (%d position%s, %d atom%s%s)", name(),
 318             posCount(),  posCount()  == 1 ? "" : "s",
 319             atomCount(), atomCount() == 1 ? "" : "s",
 320             isDynamic() ? ", dynamic" : "");
 321     fprintf(fp, "\n");
 322 }
 323
 324
 325 void
 326 Selection::printDebugInfo(FILE *fp, int nmaxind) const
 327 {
 328     const gmx_ana_pos_t &p = data().rawPositions_;
 329
 330     fprintf(fp, "  ");
 331     printInfo(fp);
 332     fprintf(fp, "    Group ");
 333     gmx_ana_index_t g;
 334     gmx_ana_index_set(&g, p.m.mapb.nra, p.m.mapb.a, 0);
 335     TextWriter      writer(fp);
 336     gmx_ana_index_dump(&writer, &g, nmaxind);
 337
 338     fprintf(fp, "    Block (size=%d):", p.m.mapb.nr);
 339     if (!p.m.mapb.index)
 340     {
 341         fprintf(fp, " (null)");
 342     }
 343     else
 344     {
 345         int n = p.m.mapb.nr;
 346         if (nmaxind >= 0 && n > nmaxind)
 347         {
 348             n = nmaxind;
 349         }
 350         for (int i = 0; i <= n; ++i)
 351         {
 352             fprintf(fp, " %d", p.m.mapb.index[i]);
 353         }
 354         if (n < p.m.mapb.nr)
 355         {
 356             fprintf(fp, " ...");
 357         }
 358     }
 359     fprintf(fp, "\n");
 360
 361     int n = posCount();
 362     if (nmaxind >= 0 && n > nmaxind)
 363     {
 364         n = nmaxind;
 365     }
 366     fprintf(fp, "    RefId:");
 367     if (!p.m.refid)
 368     {
 369         fprintf(fp, " (null)");
 370     }
 371     else
 372     {
 373         for (int i = 0; i < n; ++i)
 374         {
 375             fprintf(fp, " %d", p.m.refid[i]);
 376         }
 377         if (n < posCount())
 378         {
 379             fprintf(fp, " ...");
 380         }
 381     }
 382     fprintf(fp, "\n");
 383
 384     fprintf(fp, "    MapId:");
 385     if (!p.m.mapid)
 386     {
 387         fprintf(fp, " (null)");
 388     }
 389     else
 390     {
 391         for (int i = 0; i < n; ++i)
 392         {
 393             fprintf(fp, " %d", p.m.mapid[i]);
 394         }
 395         if (n < posCount())
 396         {
 397             fprintf(fp, " ...");
 398         }
 399     }
 400     fprintf(fp, "\n");
 401 }
 402
 403
 404 /********************************************************************
 405  * SelectionPosition
 406  */
 407
 408 SelectionPosition::operator AnalysisNeighborhoodPositions() const
 409 {
 410     AnalysisNeighborhoodPositions pos(sel_->rawPositions_.x,
 411                                       sel_->rawPositions_.count());
 412     if (sel_->hasOnlyAtoms())
 413     {
 414         // TODO: Move atomIndices() such that it can be reused here as well.
 415         pos.exclusionIds(constArrayRefFromArray<int>(sel_->rawPositions_.m.mapb.a,
 416                                                      sel_->rawPositions_.m.mapb.nra));
 417     }
 418     return pos.selectSingleFromArray(i_);
 419 }
 420
 421 } // namespace gmx