ResidueDictionary.hpp

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/* 
 * ResidueDictionary.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_BIOMOL_RESIDUEDICTIONARY_HPP
#define CDPL_BIOMOL_RESIDUEDICTIONARY_HPP
 
#include <string>
#include <unordered_map>
#include <memory>
#include <functional>
 
#include <boost/iterator/transform_iterator.hpp>
 
#include "CDPL/Biomol/APIPrefix.hpp"
#include "CDPL/Chem/MolecularGraph.hpp"
 
 
namespace CDPL
{
 
    namespace Biomol
    {
 
        class CDPL_BIOMOL_API ResidueDictionary
        {
 
          public:
            class CDPL_BIOMOL_API Entry
            {
 
              public:
                typedef std::function<Chem::MolecularGraph::SharedPointer(const std::string&)> StructureRetrievalFunction;
 
                Entry(const std::string& code, const std::string& rep_code, const std::string& rep_by_code, const std::string& parent_code,
                      const std::string& one_letter_code,bool obsolete, const std::string& name, unsigned int type,
                      const StructureRetrievalFunction& struc_ret_func);
                
                Entry();
                
                const std::string& getCode() const;
 
                const std::string& getReplacedCode() const;
 
                const std::string& getReplacedByCode() const;
 
                const std::string& getParentCode() const;
 
                const std::string& getOneLetterCode() const;
 
                bool isObsolete() const;
 
                const std::string& getName() const;
 
                unsigned int getType() const;
 
                Chem::MolecularGraph::SharedPointer getStructure() const;
 
              private:
                std::string                code;
                std::string                replacesCode;
                std::string                replacedByCode;
                std::string                parentCode;
                std::string                oneLetterCode;
                bool                       obsolete;
                std::string                name;
                unsigned int               type;
                StructureRetrievalFunction structRetrievalFunc;
            };
 
          private:
            struct CIStringHashFunc
            {
 
                std::size_t operator()(const std::string& str) const;
            };
 
            struct CIStringCmpFunc
            {
 
                bool operator()(const std::string& str1, const std::string& str2) const;
            };
              
            typedef std::unordered_map<std::string, Entry, CIStringHashFunc, CIStringCmpFunc> EntryLookupTable;
 
          public:
            typedef std::shared_ptr<ResidueDictionary> SharedPointer;
 
            typedef boost::transform_iterator<std::function<const Entry&(const EntryLookupTable::value_type&)>,
                                              EntryLookupTable::const_iterator>   ConstEntryIterator;
 
            static bool isStdResidue(const std::string& code);
            
            void addEntry(const Entry& entry);
 
            void addEntry(Entry&& entry);
 
            bool containsEntry(const std::string& code) const;
 
            void removeEntry(const std::string& code);
 
            const Entry& getEntry(const std::string& code) const;
 
            void clear();
 
            std::size_t getNumEntries() const;
 
            ConstEntryIterator getEntriesBegin() const;
 
            ConstEntryIterator getEntriesEnd() const;
 
            ConstEntryIterator begin() const;
 
            ConstEntryIterator end() const;
 
            const std::string& getReplacedCode(const std::string& code) const;
 
            const std::string& getReplacedByCode(const std::string& code) const;
 
            const std::string& getParentCode(const std::string& code) const;
 
            const std::string& getOneLetterCode(const std::string& code) const;
           
            bool isObsolete(const std::string& code) const;
 
            const std::string& getName(const std::string& code) const;
 
            unsigned int getType(const std::string& code) const;
 
            Chem::MolecularGraph::SharedPointer getStructure(const std::string& code) const;
            
            void loadDefaults();
 
            static void set(const SharedPointer& dict);
 
            static const SharedPointer& get();
 
          private:
            static SharedPointer defaultDict;
            EntryLookupTable     entries;
        };
    } // namespace Biomol
} // namespace CDPL
 
#endif // CDPL_BIOMOL_RESIDUEDICTIONARY_HPP