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