MMFF94AtomTyper.hpp

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/* 
 * MMFF94AtomTyper.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_FORCEFIELD_MMFF94ATOMTYPER_HPP
#define CDPL_FORCEFIELD_MMFF94ATOMTYPER_HPP
 
#include <vector>
#include <string>
#include <cstddef>
#include <memory>
 
#include "CDPL/ForceField/APIPrefix.hpp"
#include "CDPL/ForceField/MMFF94SymbolicAtomTypePatternTable.hpp"
#include "CDPL/ForceField/MMFF94AromaticAtomTypeDefinitionTable.hpp"
#include "CDPL/ForceField/MMFF94HeavyToHydrogenAtomTypeMap.hpp"
#include "CDPL/ForceField/MMFF94SymbolicToNumericAtomTypeMap.hpp"
#include "CDPL/ForceField/MMFF94AtomTypePropertyTable.hpp"
#include "CDPL/ForceField/MMFF94PropertyFunctions.hpp"
#include "CDPL/Chem/PatternAtomTyper.hpp"
#include "CDPL/Util/Array.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class Fragment;
    }
 
    namespace ForceField
    {
 
        class CDPL_FORCEFIELD_API MMFF94AtomTyper
        {
 
          public:
            typedef std::shared_ptr<MMFF94AtomTyper> SharedPointer;
 
            MMFF94AtomTyper();
 
            MMFF94AtomTyper(const Chem::MolecularGraph& molgraph, Util::SArray& sym_types, Util::UIArray& num_types, bool strict);
 
            void setSymbolicAtomTypePatternTable(const MMFF94SymbolicAtomTypePatternTable::SharedPointer& table);
 
            void setAromaticAtomTypeDefinitionTable(const MMFF94AromaticAtomTypeDefinitionTable::SharedPointer& table);
 
            void setHeavyToHydrogenAtomTypeMap(const MMFF94HeavyToHydrogenAtomTypeMap::SharedPointer& map);
 
            void setSymbolicToNumericAtomTypeMap(const MMFF94SymbolicToNumericAtomTypeMap::SharedPointer& map);
 
            void setAtomTypePropertyTable(const MMFF94AtomTypePropertyTable::SharedPointer& table);
 
            void setAromaticRingSetFunction(const MMFF94RingSetFunction& func);
 
            void perceiveTypes(const Chem::MolecularGraph& molgraph, Util::SArray& sym_types, Util::UIArray& num_types, bool strict);
 
          private:
            typedef MMFF94AromaticAtomTypeDefinitionTable::Entry AromTypeDefEntry;
 
            void init(const Chem::MolecularGraph& molgraph, Util::SArray& sym_types, Util::UIArray& num_types);
 
            void assignProvisionalSymbolicAtomTypes(bool strict);
            void assignAromaticAtomTypes();
            void assignHydrogenAtomTypes();
            void assignNumericAtomTypes(Util::UIArray& num_types);
 
            void assignAromaticAtomTypes(const Chem::Fragment* ring);
 
            std::size_t getUniqueHeteroAtomIndex(const Chem::Fragment& ring) const;
            std::size_t calcHeteroAtomDistance(std::size_t r_size, std::size_t het_atom_idx, std::size_t from_atom_idx) const;
 
            bool isN5Anion(const Chem::Fragment& ring) const;
            bool isImidazoliumCation(const Chem::Fragment& ring) const;
 
            bool matchesAromTypeDefEntry(bool wc_match, const std::string& sym_type, unsigned int atomic_no,
                                         std::size_t r_size, std::size_t het_dist, bool im_cat, bool n5_anion,
                                         const AromTypeDefEntry& entry) const;
 
            typedef std::vector<const Chem::Fragment*> RingList;
 
            MMFF94SymbolicAtomTypePatternTable::SharedPointer    symTypePatternTable;
            MMFF94AromaticAtomTypeDefinitionTable::SharedPointer aromTypeDefTable;
            MMFF94HeavyToHydrogenAtomTypeMap::SharedPointer      hydTypeMap;
            MMFF94SymbolicToNumericAtomTypeMap::SharedPointer    numTypeMap;
            MMFF94AtomTypePropertyTable::SharedPointer           atomTypePropTable;
            MMFF94RingSetFunction                                aromRingSetFunc;
            const Chem::MolecularGraph*                          molGraph;
            Util::SArray*                                        symTypes;
            RingList                                             aromRings;
            Chem::PatternAtomTyper                               atomTyper;
        };
    } // namespace ForceField
} // namespace CDPL
 
#endif // CDPL_FORCEFIELD_MMFF94ATOMTYPER_HPP