src/gromacs/selection/symrec.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2017, 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 /*! \internal \file
  36  * \brief
  37  * Implements classes in symrec.h.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "symrec.h"
  45
  46 #include <map>
  47 #include <memory>
  48 #include <string>
  49 #include <utility>
  50
  51 #include "gromacs/utility/arraysize.h"
  52 #include "gromacs/utility/exceptions.h"
  53 #include "gromacs/utility/gmxassert.h"
  54 #include "gromacs/utility/stringutil.h"
  55
  56 #include "poscalc.h"
  57 #include "selelem.h"
  58
  59 namespace gmx
  60 {
  61
  62 /********************************************************************
  63  * SelectionParserSymbol
  64  */
  65
  66 /*! \internal \brief
  67  * Private implementation class for SelectionParserSymbol.
  68  *
  69  * \ingroup module_selection
  70  */
  71 class SelectionParserSymbol::Impl
  72 {
  73     public:
  74         /*! \brief
  75          * Initializes a symbol.
  76          *
  77          * \param[in] type  Type for the symbol.
  78          * \param[in] name  Name for the symbol.
  79          *
  80          * The symbol table is responsible for initializing the \a meth_ and
  81          * \a var_ members as appropriate.
  82          */
  83         Impl(SymbolType type, const char *name)
  84             : name_(name), type_(type), meth_(nullptr)
  85         {
  86         }
  87
  88         //! Name of the symbol.
  89         std::string                     name_;
  90         //! Type of the symbol.
  91         SymbolType                      type_;
  92         //! Pointer to the method structure (\ref MethodSymbol).
  93         gmx_ana_selmethod_t            *meth_;
  94         //! Pointer to the variable value (\ref VariableSymbol).
  95         SelectionTreeElementPointer     var_;
  96 };
  97
  98 SelectionParserSymbol::SelectionParserSymbol(Impl *impl)
  99     : impl_(impl)
 100 {
 101 }
 102
 103 SelectionParserSymbol::~SelectionParserSymbol()
 104 {
 105 }
 106
 107 const std::string &
 108 SelectionParserSymbol::name() const
 109 {
 110     return impl_->name_;
 111 }
 112
 113 SelectionParserSymbol::SymbolType
 114 SelectionParserSymbol::type() const
 115 {
 116     return impl_->type_;
 117 }
 118
 119 gmx_ana_selmethod_t *
 120 SelectionParserSymbol::methodValue() const
 121 {
 122     GMX_RELEASE_ASSERT(type() == MethodSymbol,
 123                        "Attempting to get method handle for a non-method symbol");
 124     return impl_->meth_;
 125 }
 126
 127 const gmx::SelectionTreeElementPointer &
 128 SelectionParserSymbol::variableValue() const
 129 {
 130     GMX_RELEASE_ASSERT(type() == VariableSymbol,
 131                        "Attempting to get variable value for a non-variable symbol");
 132     return impl_->var_;
 133 }
 134
 135 /********************************************************************
 136  * SelectionParserSymbolTable::Impl
 137  */
 138
 139 /*! \internal
 140  * \brief
 141  * Private implementation class for SelectionParserSymbolTable.
 142  *
 143  * All methods in this class may throw std::bad_alloc if out of memory.
 144  *
 145  * \ingroup module_selection
 146  */
 147 class SelectionParserSymbolTable::Impl
 148 {
 149     public:
 150         //! Smart pointer type for managing a SelectionParserSymbol.
 151         typedef std::unique_ptr<SelectionParserSymbol>
 152             SymbolPointer;
 153         //! Container type for the list of symbols.
 154         typedef std::map<std::string, SymbolPointer> SymbolMap;
 155
 156         /*! \brief
 157          * Adds a symbol to the symbol list.
 158          *
 159          * \param[in] symbol  Symbol to add.
 160          */
 161         void addSymbol(SymbolPointer symbol);
 162         //! Adds the reserved symbols to this symbol table.
 163         void addReservedSymbols();
 164         //! Adds the position symbols to this symbol table.
 165         void addPositionSymbols();
 166
 167         //! Symbols in this symbol table.
 168         SymbolMap               symbols_;
 169 };
 170
 171 void
 172 SelectionParserSymbolTable::Impl::addSymbol(SymbolPointer symbol)
 173 {
 174     symbols_.insert(std::make_pair(symbol->name(), std::move(symbol)));
 175 }
 176
 177 void
 178 SelectionParserSymbolTable::Impl::addReservedSymbols()
 179 {
 180     const char *const sym_reserved[] = {
 181         "group",
 182         "to",
 183         "not",
 184         "and",
 185         "or",
 186         "xor",
 187         "yes",
 188         "no",
 189         "on",
 190         "off"
 191     };
 192
 193     for (size_t i = 0; i < asize(sym_reserved); ++i)
 194     {
 195         SymbolPointer sym(new SelectionParserSymbol(
 196                                   new SelectionParserSymbol::Impl(
 197                                           SelectionParserSymbol::ReservedSymbol, sym_reserved[i])));
 198         addSymbol(std::move(sym));
 199     }
 200 }
 201
 202 void
 203 SelectionParserSymbolTable::Impl::addPositionSymbols()
 204 {
 205     const char *const *postypes
 206         = gmx::PositionCalculationCollection::typeEnumValues;
 207     for (int i = 0; postypes[i] != nullptr; ++i)
 208     {
 209         SymbolPointer sym(new SelectionParserSymbol(
 210                                   new SelectionParserSymbol::Impl(
 211                                           SelectionParserSymbol::PositionSymbol, postypes[i])));
 212         addSymbol(std::move(sym));
 213     }
 214 }
 215
 216 /********************************************************************
 217  * SelectionParserSymbolIterator
 218  */
 219
 220 /*! \internal \brief
 221  * Private implementation class for SelectionParserSymbolIterator.
 222  *
 223  * \ingroup module_selection
 224  */
 225 class SelectionParserSymbolIterator::Impl
 226 {
 227     public:
 228         //! Shorthand for the underlying iterator type.
 229         typedef SelectionParserSymbolTable::Impl::SymbolMap::const_iterator
 230             IteratorType;
 231
 232         /*! \brief
 233          * Constructs an end iterator.
 234          *
 235          * \param[in] end  Iterator to the end of the iterated container.
 236          */
 237         explicit Impl(IteratorType end)
 238             : iter_(end), end_(end)
 239         {
 240         }
 241         /*! \brief
 242          * Constructs an iterator.
 243          *
 244          * \param[in] iter Iterator to the current symbol.
 245          * \param[in] end  Iterator to the end of the iterated container.
 246          */
 247         Impl(IteratorType iter, IteratorType end)
 248             : iter_(iter), end_(end)
 249         {
 250         }
 251
 252         //! Underlying iterator to the symbol container.
 253         IteratorType            iter_;
 254         //! End of the symbol container being iterated.
 255         IteratorType            end_;
 256 };
 257
 258 SelectionParserSymbolIterator::SelectionParserSymbolIterator(Impl *impl)
 259     : impl_(impl)
 260 {
 261 }
 262
 263 SelectionParserSymbolIterator::SelectionParserSymbolIterator(
 264         const SelectionParserSymbolIterator &other)
 265     : impl_(new Impl(*other.impl_))
 266 {
 267 }
 268
 269 SelectionParserSymbolIterator::~SelectionParserSymbolIterator()
 270 {
 271 }
 272
 273 SelectionParserSymbolIterator &SelectionParserSymbolIterator::operator=(
 274         const SelectionParserSymbolIterator &other)
 275 {
 276     impl_.reset(new Impl(*other.impl_));
 277     return *this;
 278 }
 279
 280 bool SelectionParserSymbolIterator::operator==(
 281         const SelectionParserSymbolIterator &other) const
 282 {
 283     return impl_->iter_ == other.impl_->iter_;
 284 }
 285
 286 const SelectionParserSymbol &SelectionParserSymbolIterator::operator*() const
 287 {
 288     return *impl_->iter_->second;
 289 }
 290
 291 SelectionParserSymbolIterator &SelectionParserSymbolIterator::operator++()
 292 {
 293     SelectionParserSymbol::SymbolType type = impl_->iter_->second->type();
 294     do
 295     {
 296         ++impl_->iter_;
 297     }
 298     while (impl_->iter_ != impl_->end_ && impl_->iter_->second->type() != type);
 299     return *this;
 300 }
 301
 302 /********************************************************************
 303  * SelectionParserSymbolTable
 304  */
 305
 306 SelectionParserSymbolTable::SelectionParserSymbolTable()
 307     : impl_(new Impl)
 308 {
 309     impl_->addReservedSymbols();
 310     impl_->addPositionSymbols();
 311 }
 312
 313 SelectionParserSymbolTable::~SelectionParserSymbolTable()
 314 {
 315 }
 316
 317 const SelectionParserSymbol *
 318 SelectionParserSymbolTable::findSymbol(const std::string &name) const
 319 {
 320     Impl::SymbolMap::const_iterator sym = impl_->symbols_.lower_bound(name);
 321     if (sym == impl_->symbols_.end())
 322     {
 323         return nullptr;
 324     }
 325     if (sym->second->name() == name)
 326     {
 327         return sym->second.get();
 328     }
 329     return nullptr;
 330 }
 331
 332 SelectionParserSymbolIterator
 333 SelectionParserSymbolTable::beginIterator(SelectionParserSymbol::SymbolType type) const
 334 {
 335     Impl::SymbolMap::const_iterator sym;
 336     Impl::SymbolMap::const_iterator end = impl_->symbols_.end();
 337     for (sym = impl_->symbols_.begin(); sym != end; ++sym)
 338     {
 339         if (sym->second->type() == type)
 340         {
 341             return SelectionParserSymbolIterator(
 342                     new SelectionParserSymbolIterator::Impl(sym, end));
 343         }
 344     }
 345     return endIterator();
 346 }
 347
 348 SelectionParserSymbolIterator
 349 SelectionParserSymbolTable::endIterator() const
 350 {
 351     return SelectionParserSymbolIterator(
 352             new SelectionParserSymbolIterator::Impl(impl_->symbols_.end()));
 353 }
 354
 355 void
 356 SelectionParserSymbolTable::addVariable(const char                             *name,
 357                                         const gmx::SelectionTreeElementPointer &sel)
 358 {
 359     // In the current parser implementation, a syntax error is produced before
 360     // this point is reached, but the check is here for robustness.
 361     Impl::SymbolMap::const_iterator other = impl_->symbols_.find(name);
 362     if (other != impl_->symbols_.end())
 363     {
 364         if (other->second->type() == SelectionParserSymbol::VariableSymbol)
 365         {
 366             GMX_THROW(InvalidInputError(
 367                               formatString("Reassigning variable '%s' is not supported",
 368                                            name)));
 369         }
 370         else
 371         {
 372             GMX_THROW(InvalidInputError(
 373                               formatString("Variable name '%s' conflicts with a reserved keyword",
 374                                            name)));
 375         }
 376     }
 377     Impl::SymbolPointer sym(new SelectionParserSymbol(
 378                                     new SelectionParserSymbol::Impl(
 379                                             SelectionParserSymbol::VariableSymbol, name)));
 380     sym->impl_->var_ = sel;
 381     impl_->addSymbol(std::move(sym));
 382 }
 383
 384 void
 385 SelectionParserSymbolTable::addMethod(const char          *name,
 386                                       gmx_ana_selmethod_t *method)
 387 {
 388     if (impl_->symbols_.find(name) != impl_->symbols_.end())
 389     {
 390         GMX_THROW(APIError(
 391                           formatString("Method name '%s' conflicts with another symbol",
 392                                        name)));
 393     }
 394     Impl::SymbolPointer sym(new SelectionParserSymbol(
 395                                     new SelectionParserSymbol::Impl(
 396                                             SelectionParserSymbol::MethodSymbol, name)));
 397     sym->impl_->meth_ = method;
 398     impl_->addSymbol(std::move(sym));
 399 }
 400
 401 } // namespace gmx