Atom.h

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/*
 * This file is a part of the Biology project by eons LLC.
 * Biology (aka Develop Biology) is a framework for approaching software
 * development from a natural sciences perspective.
 *
 * Copyright (C) 2021 Séon O'Shannon & eons LLC
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program 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 Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
#pragma once
 
#include "bio/common/Cast.h"
#include "bio/common/macros/Macros.h"
#include "bio/common/IsPrimitive.h"
#include "bio/common/macros/OSMacros.h"
#include "bio/physical/Quantum.h"
#include "bio/physical/common/Class.h"
#include "bio/chemical/common/BondTypes.h"
#include "PeriodicTable.h"
#include "Bond.h"
 
namespace bio {
namespace chemical {
 
class Symmetry;
 
class Atom :
    public physical::Class< Atom >
{
public:
 
    BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical,
        Atom)
 
    
    explicit Atom();
 
    explicit Atom(const Atom& other);
 
    virtual ~Atom();
 
    virtual physical::Symmetry* Spin() const;
 
    virtual Code Reify(physical::Symmetry* symmetry);
 
    virtual Code Attenuate(const Wave* other);
 
    virtual Code Disattenuate(const Wave* other);
 
    Wave* GetBonded(Valence position);
 
    const Wave* GetBonded(Valence position) const;
 
    template < typename T >
    T AsBonded()
    {
        Valence position = GetBondPosition< T >();
        BIO_SANITIZE(position, ,
            return NULL);
        return ForceCast< T >(m_bonds.OptimizedAccess(position)->GetBonded());
    }
 
    template < typename T >
    const T AsBonded() const
    {
        Valence position = GetBondPosition< T >();
 
        BIO_SANITIZE(position, ,
            return NULL);
        return ForceCast< const T >(m_bonds.OptimizedAccess(position)->GetBonded());
    }
 
    template < typename T >
    T AsBondedQuantum()
    {
        return Cast< T >(AsBonded< physical::Quantum< T >* >());
    }
 
    template < typename T >
    const T AsBondedQuantum() const
    {
        return *AsBonded< physical::Quantum< T >* >();
    }
 
    template < typename T >
    T As()
    {
        #if BIO_CPP_VERSION < 11
        return AsBondedQuantum< T >();
        #else
        if (IsPrimitive< T >())
        {
            return AsBondedQuantum< T >();
        }
        else
        {
            return AsBonded< T >();
        }
        #endif
    }
 
    template < typename T >
    const T As() const
    {
        #if BIO_CPP_VERSION < 11
        return AsBondedQuantum< T >();
        #else
        if (IsPrimitive< T >())
        {
            return AsBondedQuantum< T >();
        }
        else
        {
            return AsBonded< T >();
        }
        #endif
    }
 
 
    template < typename T >
    operator T()
    {
        return As< T >();
    }
 
    template < typename T >
    bool FormBond(
        T toBond,
        BondType type = bond_type::Unknown())
    {
        #if BIO_CPP_VERSION < 11
        AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >();
        return FormBondImplementation((new physical::Quantum< T >(toBond))->AsWave(),
            bondedId,
            type
        );
        #else
        if (IsPrimitive< T >())
        {
            AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >();
            return FormBondImplementation(
                (new physical::Quantum< T >(toBond))->AsWave(),
                bondedId,
                type
            );
        }
        else
        {
            AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< T >();
            return FormBondImplementation(
                toBond->AsWave(),
                bondedId,
                type
            );
        }
        #endif
    }
 
    template < typename T >
    bool BreakBond(
        T toDisassociate,
        BondType type = bond_type::Unknown())
    {
        #if BIO_CPP_VERSION < 11
        return BreakBond< physical::Quantum< T >* >(
            NULL,
            type
        );
        #else
        if (IsPrimitive< T >())
        {
            return BreakBond< physical::Quantum< T >* >(NULL, type); //T matters, toDisassociate does not.
        }
 
        AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< T >();
        return BreakBondImplementation(
            toDisassociate,
            bondedId,
            type
        );
        #endif
    }
 
 
    Valence GetBondPosition(AtomicNumber bondedId) const;
 
    Valence GetBondPosition(Name typeName) const;
 
 
    template < typename T >
    Valence GetBondPosition() const
    {
        #if BIO_CPP_VERSION < 11
        return GetBondPosition(PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >());
        #else
        if (IsPrimitive< T >())
        {
            return GetBondPosition(PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >());
        }
        return GetBondPosition(PeriodicTable::Instance().GetIdFromType< T >());
        #endif
    }
 
    BondType GetBondType(Valence position) const;
 
    template < typename T >
    BondType GetBondType() const
    {
        #if BIO_CPP_VERSION < 11
        return GetBondType(GetBondPosition< physical::Quantum< T > >());
        #else
        if (IsPrimitive< T >())
        {
            return GetBondType(GetBondPosition< physical::Quantum< T > >());
        }
        return GetBondType(GetBondPosition< T >());
        #endif
    }
 
    Bonds* GetAllBonds();
 
    const Bonds* GetAllBonds() const;
 
protected:
    Bonds m_bonds;
 
    virtual bool FormBondImplementation(
        Wave* toBond,
        AtomicNumber id,
        BondType type
    );
 
    virtual bool BreakBondImplementation(
        Wave* toDisassociate,
        AtomicNumber id,
        BondType type
    );
};
 
} //chemical namespace
} //bio namespace