AtomDictionary.hpp

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/* 
 * AtomDictionary.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_CHEM_ATOMDICTIONARY_HPP
#define CDPL_CHEM_ATOMDICTIONARY_HPP
 
#include <cstddef>
#include <string>
#include <utility>
#include <unordered_map>
#include <memory>
#include <functional>
 
#include <boost/iterator/transform_iterator.hpp>
#include <boost/functional/hash.hpp>
 
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Util/Array.hpp"
#include "CDPL/Util/Map.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class CDPL_CHEM_API AtomDictionary
        {
 
          public:
            class CDPL_CHEM_API Entry
            {
 
              public:
                typedef Util::Map<std::size_t, double> IsotopeMassMap;
 
                Entry();
 
                Entry(unsigned int atom_type, std::size_t iso, const std::string& sym,
                      const std::string& name, std::size_t most_abdt_iso, double avg_weight,
                      std::size_t iupac_grp, std::size_t period, bool metal, bool non_metal, const Util::STArray& val_states,
                      double vdw_rad, const double cov_radii[3], double ar_eneg, const IsotopeMassMap& iso_masses);
 
                unsigned int getType() const;
 
                std::size_t getIsotope() const;
 
                const std::string& getSymbol() const;
 
                const std::string& getName() const;
 
                std::size_t getMostAbundantIsotope() const;
 
                double getAverageWeight() const;
 
                std::size_t getIUPACGroup() const;
 
                std::size_t getPeriod() const;
 
                bool isMetal() const;
 
                bool isNonMetal() const;
 
                const Util::STArray& getValenceStates() const;
 
                double getVdWRadius() const;
 
                double getCovalentRadius(std::size_t order) const;
 
                double getAllredRochowElectronegativity() const;
 
                const IsotopeMassMap& getIsotopeMasses() const;
 
              private:
                unsigned int   atomType;
                std::size_t    isotope;
                std::string    symbol;
                std::string    name;
                std::size_t    mostAbundantIso;
                double         avgWeight;
                std::size_t    iupacGroup;
                std::size_t    period;
                bool           isMet;
                bool           isNonMet;
                Util::STArray  valenceStates;
                double         vdwRadius;
                double         covalentRadii[3];
                double         allredRochowEneg;
                IsotopeMassMap isoMassMap;
            };
 
          private:
            typedef std::unordered_map<std::pair<unsigned int, std::size_t>, Entry, boost::hash<std::pair<unsigned int, std::size_t> > > EntryLookupTable;
            typedef std::unordered_map<std::string, unsigned int>                                                                        SymbolToTypeLookupTable;
 
          public:
            typedef std::shared_ptr<AtomDictionary> SharedPointer;
 
            typedef boost::transform_iterator<std::function<const Entry&(const EntryLookupTable::value_type&)>,
                                              EntryLookupTable::const_iterator>
                ConstEntryIterator;
 
            void addEntry(const Entry& entry);
 
            bool containsEntry(unsigned int type, std::size_t isotope) const;
 
            void removeEntry(unsigned int type, std::size_t isotope);
 
            const Entry& getEntry(unsigned int type, std::size_t isotope) const;
 
            void clear();
 
            std::size_t getNumEntries() const;
 
            ConstEntryIterator getEntriesBegin() const;
 
            ConstEntryIterator getEntriesEnd() const;
 
            ConstEntryIterator begin() const;
 
            ConstEntryIterator end() const;
 
            void loadDefaults();
 
            static void set(const SharedPointer& dict);
 
            static const SharedPointer& get();
 
            static const std::string& getSymbol(unsigned int type, std::size_t isotope = 0);
 
            static const std::string& getName(unsigned int type, std::size_t isotope = 0);
 
            static unsigned int getType(const std::string& symbol, bool strict = false);
 
            static std::size_t getMostAbundantIsotope(unsigned int type);
 
            static std::size_t getIUPACGroup(unsigned int type);
 
            static std::size_t getPeriod(unsigned int type);
 
            static std::size_t getNumValenceElectrons(unsigned int type);
 
            static double getAtomicWeight(unsigned int type, std::size_t isotope = 0);
 
            static double getVdWRadius(unsigned int type);
 
            static double getCovalentRadius(unsigned int type, std::size_t order = 1);
 
            static double getAllredRochowElectronegativity(unsigned int type);
 
            static const Util::STArray& getValenceStates(unsigned int type);
 
            static bool isChemicalElement(unsigned int type);
 
            static bool isMainGroupElement(unsigned int type);
 
            static bool isTransitionMetal(unsigned int type);
 
            static bool isMetal(unsigned int type);
 
            static bool isSemiMetal(unsigned int type);
 
            static bool isNonMetal(unsigned int type);
 
            static bool isHalogen(unsigned int type);
 
            static bool isNobleGas(unsigned int type);
 
          private:
            static SharedPointer    defaultDict;
            EntryLookupTable        entries;
            SymbolToTypeLookupTable strictSymToTypeTable;
            SymbolToTypeLookupTable nonstrictSymToTypeTable;
        };
    }; // namespace Chem
} // namespace CDPL
 
#endif // CDPL_CHEM_ATOMDICTIONARY_HPP