double CCopasiSpringLayout::getPotential()
{
//here we need to add the different effects that contribute to the potential
double tmp = 0;
//repulsion between species nodes
unsigned int i, j;
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size() - 1; ++i)
for (j = i + 1; j < mpLayout->getListOfMetaboliteGlyphs().size(); ++j)
{
if (i != j)
tmp += 100000 * potSpeciesSpecies(*mpLayout->getListOfMetaboliteGlyphs()[i], *mpLayout->getListOfMetaboliteGlyphs()[j]);
}
// only if we have reactions!
if (mpLayout->getListOfReactionGlyphs().size() > 0)
{
//repulsion between species nodes and reaction nodes
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size(); ++i)
for (j = 0; j < mpLayout->getListOfReactionGlyphs().size(); ++j)
{
tmp += 100000 * potSpeciesReaction(*mpLayout->getListOfMetaboliteGlyphs()[i], *mpLayout->getListOfReactionGlyphs()[j]);
}
//repulsion between reaction nodes
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size() - 1; ++i)
for (j = i + 1; j < mpLayout->getListOfReactionGlyphs().size(); ++j)
{
if (i != j)
tmp += 100000 * potReactionReaction(*mpLayout->getListOfReactionGlyphs()[i], *mpLayout->getListOfReactionGlyphs()[j]);
}
}
//spring force for species references
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size(); ++i)
{
CLReactionGlyph* pRG = mpLayout->getListOfReactionGlyphs()[i];
for (j = 0; j < pRG->getListOfMetabReferenceGlyphs().size(); ++j)
{
tmp += 0.5 * potEdge(*pRG->getListOfMetabReferenceGlyphs()[j], *pRG);
}
}
/*
//forces at reaction nodes
for (i=0; i<mReactionNodes.size(); ++i)
{
tmp += 3000* potReaction(mReactionNodes[i]);
}
*/
//force to keep species in compartment
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size(); ++i)
{
CLMetabGlyph* tmpMG = mpLayout->getListOfMetaboliteGlyphs()[i];
std::map<CLBase*, CLCompartmentGlyph*>::const_iterator mapIt = mCompartmentMap.find(tmpMG);
if (mapIt == mCompartmentMap.end())
{
//there is no information in the map. Should not happen.
#ifdef COPASI_DEBUG
std::cout << "No compartment info for a species glyph!!!" << std::endl;
#endif
continue;
}
CLCompartmentGlyph* tmpCG = mapIt->second;
if (tmpCG) //the species glyph is inside a compartment glyph
tmp += 0.2 * potSpeciesCompartment(*tmpMG, *tmpCG);
}
//force to keep reaction nodes in compartment
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size(); ++i)
{
CLReactionGlyph* tmpRG = mpLayout->getListOfReactionGlyphs()[i];
std::map<CLBase*, CLCompartmentGlyph*>::const_iterator mapIt = mCompartmentMap.find(tmpRG);
if (mapIt == mCompartmentMap.end())
{
//there is no information in the map. Should not happen.
#ifdef COPASI_DEBUG
std::cout << "No compartment info for a reaction glyph!!!" << std::endl;
#endif
continue;
}
CLCompartmentGlyph* tmpCG = mapIt->second;
if (tmpCG) //the reaction glyph is inside a compartment glyph
tmp += 0.2 * potReactionCompartment(*tmpRG, *tmpCG);
}
/*
//force to shrink compartments
for (i=0; i<mCompartmentNodes.size(); ++i)
{
tmp += 0.2*(fabs(mCompartmentNodes[i].w-100)+fabs(mCompartmentNodes[i].h-100));
}
//repulsion between compartments
for (i=0; i<mCompartmentNodes.size(); ++i)
for (j=0; j<mCompartmentNodes.size(); ++j)
{
if (i!=j)
tmp += 100*potCompartmentCompartment(mCompartmentNodes[i], mCompartmentNodes[j]);
}
//centering force
for (i=0; i<mCompartmentNodes.size(); ++i)
{
tmp += 10*(fabs(mCompartmentNodes[i].x)+fabs(mCompartmentNodes[i].y));
}
*/
return tmp;
}
double CCopasiSpringLayout::getPotential()
{
//here we need to add the different effects that contribute to the potential
double tmp = 0;
//repulsion between species nodes
unsigned int i, j;
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size() - 1; ++i)
for (j = i + 1; j < mpLayout->getListOfMetaboliteGlyphs().size(); ++j)
{
if (i != j)
tmp += mpPar->values[0] * potSpeciesSpecies(mpLayout->getListOfMetaboliteGlyphs()[i], mpLayout->getListOfMetaboliteGlyphs()[j]);
}
// only if we have reactions!
if (mpLayout->getListOfReactionGlyphs().size() > 0)
{
//repulsion between species nodes and reaction nodes
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size(); ++i)
for (j = 0; j < mpLayout->getListOfReactionGlyphs().size(); ++j)
{
tmp += mpPar->values[0] * potSpeciesReaction(mpLayout->getListOfMetaboliteGlyphs()[i], mpLayout->getListOfReactionGlyphs()[j]);
}
//repulsion between reaction nodes
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size() - 1; ++i)
for (j = i + 1; j < mpLayout->getListOfReactionGlyphs().size(); ++j)
{
if (i != j)
tmp += mpPar->values[0] * potReactionReaction(mpLayout->getListOfReactionGlyphs()[i], mpLayout->getListOfReactionGlyphs()[j]);
}
}
//spring force for species references
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size(); ++i)
{
CLReactionGlyph* pRG = &mpLayout->getListOfReactionGlyphs()[i];
for (j = 0; j < pRG->getListOfMetabReferenceGlyphs().size(); ++j)
{
tmp += potEdge(pRG->getListOfMetabReferenceGlyphs()[j], *pRG);
//second order
CLMetabReferenceGlyph::Role role = pRG->getListOfMetabReferenceGlyphs()[j].getFunctionalRole();
if (role != CLMetabReferenceGlyph::SUBSTRATE && role != CLMetabReferenceGlyph::SIDESUBSTRATE)
continue;
double dist = role == CLMetabReferenceGlyph::SUBSTRATE ? mpPar->values[1] : mpPar->values[3];
size_t k;
for (k = 0; k < pRG->getListOfMetabReferenceGlyphs().size(); ++k)
{
CLMetabReferenceGlyph::Role role2 = pRG->getListOfMetabReferenceGlyphs()[k].getFunctionalRole();
if (role2 != CLMetabReferenceGlyph::PRODUCT && role2 != CLMetabReferenceGlyph::SIDEPRODUCT)
continue;
dist += role2 == CLMetabReferenceGlyph::PRODUCT ? mpPar->values[1] : mpPar->values[3];
tmp += mpPar->values[5] * potSecondOrderEdge(pRG->getListOfMetabReferenceGlyphs()[j], pRG->getListOfMetabReferenceGlyphs()[k], dist);
}
}
}
for (i = 0; i < mpLayout->getListOfGeneralGlyphs().size(); ++i)
{
CLGeneralGlyph* pRG = &mpLayout->getListOfGeneralGlyphs()[i];
for (j = 0; j < pRG->getListOfReferenceGlyphs().size(); ++j)
{
tmp += potGeneralEdge(pRG->getListOfReferenceGlyphs()[j], *pRG);
}
}
/*
//forces at reaction nodes
for (i=0; i<mReactionNodes.size(); ++i)
{
tmp += 3000* potReaction(mReactionNodes[i]);
}
*/
//force to keep species in compartment
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size(); ++i)
{
CLMetabGlyph* tmpMG = &mpLayout->getListOfMetaboliteGlyphs()[i];
std::map<CLBase*, CLCompartmentGlyph*>::const_iterator mapIt = mCompartmentMap.find(tmpMG);
if (mapIt == mCompartmentMap.end())
{
//there is no information in the map. Should not happen.
#ifdef COPASI_DEBUG
std::cout << "No compartment info for a species glyph!!!" << std::endl;
#endif
continue;
}
CLCompartmentGlyph* tmpCG = mapIt->second;
if (tmpCG) //the species glyph is inside a compartment glyph
tmp += mpPar->values[6] * potSpeciesCompartment(*tmpMG, *tmpCG);
}
//force to keep reaction nodes in compartment
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size(); ++i)
{
CLReactionGlyph* tmpRG = &mpLayout->getListOfReactionGlyphs()[i];
std::map<CLBase*, CLCompartmentGlyph*>::const_iterator mapIt = mCompartmentMap.find(tmpRG);
if (mapIt == mCompartmentMap.end())
{
//there is no information in the map. Should not happen.
#ifdef COPASI_DEBUG
std::cout << "No compartment info for a reaction glyph!!!" << std::endl;
#endif
continue;
}
CLCompartmentGlyph* tmpCG = mapIt->second;
if (tmpCG) //the reaction glyph is inside a compartment glyph
tmp += mpPar->values[7] * potReactionCompartment(*tmpRG, *tmpCG);
}
/*
//force to shrink compartments
for (i=0; i<mCompartmentNodes.size(); ++i)
{
tmp += 0.2*(fabs(mCompartmentNodes[i].w-100)+fabs(mCompartmentNodes[i].h-100));
}
//repulsion between compartments
for (i=0; i<mCompartmentNodes.size(); ++i)
for (j=0; j<mCompartmentNodes.size(); ++j)
{
if (i!=j)
tmp += 100*potCompartmentCompartment(mCompartmentNodes[i], mCompartmentNodes[j]);
}
//centering force
for (i=0; i<mCompartmentNodes.size(); ++i)
{
tmp += 10*(fabs(mCompartmentNodes[i].x)+fabs(mCompartmentNodes[i].y));
}
*/
return tmp;
}