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