Reaction.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) 2022 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/chemical/common/Types.h"
#include "Reactants.h"
#include "Products.h"
#include "bio/chemical/common/Class.h"
#include "bio/chemical/common/Filters.h"
#include "bio/chemical/common/States.h"
#include "bio/chemical/structure/motif/LinearMotif.h"
#include "bio/physical/Identifiable.h"
#include "bio/common/TypeName.h"
 
namespace bio {
namespace chemical {
 
class Reaction :
 public chemical::Class< Reaction >,
 virtual public Structure //for use in LinearMotifs downstream, we must have interface methods available, even though Reaction does not directly contain anything.
{
public:
 
 BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical,
 Reaction)
 
 BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical,
 Reaction,
 &ReactionPerspective::Instance(),
 filter::Chemical(),
 symmetry_type::Operation())
 
 
 explicit Reaction(
 Name name,
 const Reactants* reactants
 );
 
 virtual void Require(Reactant* reactant);
 
 void Require(
 Name typeName,
 const Substance* substance
 );
 
 void Require(
 Name typeName,
 const typename UnorderedMotif< Property >::Contents* properties,
 const typename UnorderedMotif< State >::Contents* states
 );
 
 template < typename T >
 void Require()
 {
 Properties empty;
 States enabled;
 enabled.push_back(state::Enabled());
 Require(
 TypeName< T >(),
 empty,
 enabled
 );
 }
 
 template < typename T >
 void Require(const T* substance)
 {
 Require(
 TypeName< T >(),
 substance
 );
 }
 
 template < typename T >
 void Require(
 const typename UnorderedMotif< Property >::Contents* properties,
 const typename UnorderedMotif< State >::Contents* states
 )
 {
 Require(
 TypeName< T >(),
 properties,
 states
 );
 }
 
 virtual Products Process(Reactants* reactants) const
 {
 
 // YOUR CODE GOES HERE
 
 return Products(code::NotImplemented());
 }
 
 virtual bool ReactantsMeetRequirements(const Reactants* toCheck) const;
 
 virtual Products operator()(Reactants* reactants) const;
 
 static const Reaction* Initiate(StandardDimension id);
 
 template < typename T >
 static const T* Initiate()
 {
 const T* ret = ReactionPerspective::Instance().template GetTypeFromNameAs< T >(TypeName< T >());
 BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret,
 return ret,
 return NULL);
 }
 
 template < typename T >
 static Products Attempt(Reactants* reactants)
 {
 BIO_SANITIZE_WITH_CACHE(Initiate< T >(),
 return (*Cast< const T* >(RESULT))(reactants),
 return Products(
 code::NotImplemented(),
 reactants
 ));
 }
 
 template < typename T >
 static Products Attempt(Substances& substances)
 {
 Reactants reactants(substances);
 BIO_SANITIZE_WITH_CACHE(Initiate< T >(),
 return (*Cast< const T* >(RESULT))(&reactants),
 return Products(
 code::NotImplemented(),
 reactants
 ));
 }
 
 template < typename T >
 static Products Attempt(
 Substance* reactant1,
 Substance* reactant2 = NULL,
 Substance* reactant3 = NULL
 )
 {
 Substances substances;
 substances.push_back(reactant1);
 substances.push_back(reactant2);
 substances.push_back(reactant3);
 Reactants reactants(substances);
 return Attempt< T >(&reactants);
 }
 
protected:
 Reactants m_requiredReactants;
};
 
} //chemical namespace
} //bio namespace