Plasmid.cpp

Go to the documentation of this file.

/*
 * 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/genetic/Plasmid.h"
#include "bio/genetic/Expressor.h"
#include "bio/genetic/proteins/RNAPolymerase.h"
 
namespace bio {
namespace genetic {
 
Plasmid::~Plasmid()
{
 
}
 
molecular::Protein* Plasmid::GetRNAPolymerase()
{
    return GetProtein();
}
 
const molecular::Protein* Plasmid::GetRNAPolymerase() const
{
    return GetProtein();
}
 
void Plasmid::CtorCommon()
{
    m_protein = new RNAPolymerase(this);
}
 
RNA* Plasmid::TranscribeFor(Expressor* expressor) const
{
    std::string rnaName = "mRNA_";
    rnaName += GetName();
    RNA* ret = new RNA(rnaName.c_str());
    molecular::Protein* polymerase = ForceCast< molecular::Protein* >(GetRNAPolymerase()->Clone());
    StandardDimension bindingSite = polymerase->GetIdFromName("RNA Binding Site");
    polymerase->RecruitChaperones(expressor);
    polymerase->Fold();
    polymerase->RotateTo(bindingSite)->Bind(ret);
    polymerase->Activate();
    polymerase->RotateTo(bindingSite)->ReleaseAll();
    delete polymerase;
    return ret;
}
 
} //genetic namespace
} //bio namespace