Atom.cpp

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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/>.
 */
 
#include "bio/chemical/Atom.h"
#include "bio/chemical/PeriodicTable.h"
#include "bio/chemical/Symmetry.h"
 
namespace bio {
namespace chemical {
 
Atom::Atom()
    :
    physical::Class< Atom >(this),
    m_bonds(4)
{
}
 
Atom::Atom(const Atom& other)
    :
    physical::Class< Atom >(this),
    m_bonds(other.m_bonds.GetCapacity())
{
 
}
 
Atom::~Atom()
{
 
}
 
Code Atom::Attenuate(const physical::Wave* other)
{
    BIO_SANITIZE(other, ,
        return code::BadArgument1())
 
    const physical::Wave* demodulated = other->Demodulate();
    Code ret = code::Success();
 
    Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->IsEmpty())
        {
            continue;
        }
        if (physical::Wave::GetResonanceBetween(
            bondBuffer->GetBonded(),
            other
        ).size())
        {
            if (bondBuffer->GetBonded()->Attenuate(demodulated) != code::Success())
            {
                ret = code::UnknownError(); //user can debug from logs for now.
            }
        }
    }
    return ret;
}
 
Code Atom::Disattenuate(const physical::Wave* other)
{
    BIO_SANITIZE(other, ,
        return code::BadArgument1())
 
    const physical::Wave* demodulated = other->Demodulate();
    Code ret = code::Success();
 
    Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->IsEmpty())
        {
            continue;
        }
        if (physical::Wave::GetResonanceBetween(
            bondBuffer->GetBonded(),
            other
        ).size())
        {
            if (bondBuffer->GetBonded()->Disattenuate(demodulated) != code::Success())
            {
                ret = code::UnknownError(); //user can debug from logs for now.
            }
        }
    }
    return ret;
}
 
bool Atom::FormBondImplementation(
    Wave* toBond,
    AtomicNumber id,
    BondType type
)
{
    BIO_SANITIZE(!toBond || !id, ,
        return false);
 
    Valence position = GetBondPosition(id);
    Bond* bondBuffer;
    if (m_bonds.IsAllocated(position))
    {
        bondBuffer = m_bonds.OptimizedAccess(position);
        BIO_SANITIZE(!bondBuffer->IsEmpty(), ,
            return false)
        return bondBuffer->Form(
            id,
            toBond,
            type
        );
    }
    //implicitly cast the addition index to a bool.
    return m_bonds.Add(
        Bond(
            id,
            toBond,
            type
        ));
}
 
bool Atom::BreakBondImplementation(
    Wave* toBreak,
    AtomicNumber id,
    BondType type
)
{
    Valence position = GetBondPosition(id);
 
    BIO_SANITIZE(id && position, ,
        return false);
    BIO_SANITIZE(m_bonds.IsAllocated(position), ,
        return false);
 
    m_bonds.OptimizedAccess(position)->Break();
    //Let dtor cleanup.
 
    return true;
}
 
 
Valence Atom::GetBondPosition(AtomicNumber bondedId) const
{
    BIO_SANITIZE(bondedId, ,
        return 0);
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        if ((*bnd).template As< Bond >() == bondedId)
        {
            return bnd.GetIndex();
        }
    }
    return 0;
}
 
Valence Atom::GetBondPosition(Name typeName) const
{
    return GetBondPosition(PeriodicTable::Instance().GetIdWithoutCreation(typeName));
}
 
BondType Atom::GetBondType(Valence position) const
{
    BIO_SANITIZE(m_bonds.IsAllocated(position), ,
        return BondTypePerspective::InvalidId());
    return m_bonds.OptimizedAccess(position)->GetId();
}
 
physical::Symmetry* Atom::Spin() const
{
    //TODO...
    return Wave::Spin();
}
 
Code Atom::Reify(physical::Symmetry* symmetry)
{
    //TODO...
    return Wave::Reify(symmetry);
}
 
physical::Wave* Atom::GetBonded(Valence position)
{
    BIO_SANITIZE(m_bonds.IsAllocated(position), ,
        return NULL)
    return m_bonds.OptimizedAccess(position)->GetBonded();
}
 
const physical::Wave* Atom::GetBonded(Valence position) const
{
    BIO_SANITIZE(m_bonds.IsAllocated(position), ,
        return NULL)
    return m_bonds.OptimizedAccess(position)->GetBonded();
}
 
Bonds* Atom::GetAllBonds()
{
    return &m_bonds;
}
 
const Bonds* Atom::GetAllBonds() const
{
    return &m_bonds;
}
 
 
} //chemical namespace
} //bio namespace