Surface.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/molecular/Surface.h"
#include "bio/molecular/Molecule.h"
#include "bio/molecular/common/Filters.h"
#include "bio/molecular/common/SymmetryTypes.h"
 
namespace bio {
namespace molecular {
 
Surface::Surface(
 Name name,
 Molecule* environment
)
 :
 molecular::Class< Surface >(
 this,
 name,
 environment,
 filter::Molecular(),
 symmetry_type::Variable()),
 EnvironmentDependent< Molecule >(environment)
{
 
}
 
Surface::Surface(const Surface& toCopy)
 :
 molecular::Class< Surface >(
 this,
 toCopy.GetName(),
 toCopy.GetPerspective(),
 toCopy.GetFilter(),
 symmetry_type::Variable()),
 chemical::LinearMotif< Molecule* >(toCopy),
 EnvironmentDependent< Molecule >(toCopy)
{
 chemical::Bond* bondBuffer;
 for (
 SmartIterator bnd = toCopy.m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->GetType() == bond_type::Manage())
 {
 //Calling FormBondImplementation directly saves us some work and should be safer than trying to do auto-template type determination from Clone().
 FormBondImplementation(
 bondBuffer->GetBonded()->Clone(),
 bondBuffer->GetId(),
 bondBuffer->GetType());
 }
 }
}
 
Surface::~Surface()
{
 chemical::Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->GetType() == bond_type::Manage())
 {
 //bypass BreakBondImplementation and just do it.
 delete bondBuffer->GetBonded();
 bondBuffer->Break();
 }
 }
}
 
void Surface::SetEnvironment(Molecule* environment)
{
 m_environment = environment;
 SetId(0); //0 should always be invalid.
 Identifiable< StandardDimension >::SetPerspective(environment);
}
 
void Surface::SetPerspective(Molecule* perspective)
{
 SetEnvironment(perspective);
}
 
Code Surface::Reify(physical::Symmetry* symmetry)
{
 //TODO...
 return code::NotImplemented();
}
 
physical::Symmetry* Surface::Spin() const
{
 //TODO...
 return NULL;
}
 
physical::Wave* Surface::Release(
 physical::Wave* toRelease,
 BondType bondType
)
{
 physical::Wave* ret = NULL;
 chemical::Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->GetType() == bondType)
 {
 ret = ChemicalCast< physical::Wave* >(bondBuffer->GetBonded());
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(!ret || ret != toRelease,
 continue,);
 bondBuffer->Break();
 break;
 }
 }
 return ret;
}
 
chemical::Substance* Surface::Release(
 Name toRelease,
 physical::Perspective<StandardDimension>* perspective,
 BondType bondType
)
{
 chemical::Substance* ret = NULL;
 chemical::Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->GetType() == bondType)
 {
 ret = ChemicalCast< chemical::Substance* >(bondBuffer->GetBonded());
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
 continue);
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret->IsName(toRelease), ,
 continue);
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(perspective && ret->GetPerspective() != perspective,
 continue,);
 bondBuffer->Break();
 break;
 }
 }
 return ret;
}
 
chemical::Substance* Surface::Release(
 StandardDimension toRelease,
 physical::Perspective<StandardDimension>* perspective,
 BondType bondType
)
{
 chemical::Substance* ret = NULL;
 chemical::Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->GetType() == bondType)
 {
 ret = ChemicalCast< chemical::Substance* >(bondBuffer->GetBonded());
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
 continue);
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret->IsId(toRelease), ,
 continue);
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(perspective && ret->GetPerspective() != perspective,
 continue,);
 bondBuffer->Break();
 break;
 }
 }
 return ret;
}
 
physical::Waves Surface::ReleaseAll(BondType bondType)
{
 physical::Waves ret;
 chemical::Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->GetType() == bondType)
 {
 ret.push_back(ChemicalCast< physical::Wave* >(bondBuffer->GetBonded()));
 bondBuffer->Break();
 }
 }
 return ret;
}
 
physical::Wave* Surface::operator-=(physical::Wave* toRelease)
{
 return Release(toRelease);
}
 
chemical::Substance* Surface::operator-=(Name toRelease)
{
 return Release(toRelease);
}
 
chemical::Substance* Surface::operator-=(StandardDimension toRelease)
{
 return Release(toRelease);
}
 
physical::Waves Surface::operator--()
{
 return ReleaseAll();
}
 
 
} //molecular namespace
} //bio namespace