private void addSpecificBindingProcess(IMoleculeBuilder drug, IReactionMapping compoundReactionMapping, CompoundProperties compoundProperties)
{
var compound = compoundProperties.Compound;
var process = compound.ProcessByName(compoundReactionMapping.ProcessName);
var complex = _moleculeBuilderFactory.Create(QuantityType.Complex, _moleculeBuildingBlock.FormulaCache)
.WithName(compoundReactionMapping.ProductName(CoreConstants.Molecule.Complex));
addMoleculeToBuildingBlock(complex, compoundProperties);
var complexReactionFrom = _processBuilderMapper.ComplexReactionFrom(process, drug, complex, compoundReactionMapping.MoleculeName, _allMoleculeNames, _reactionBuildingBlock.FormulaCache);
addReactionToBuildingBlock(complexReactionFrom, compound);
}
private void addMetabolismProcess(IMoleculeBuilder compoundBuilder, IReactionMapping compoundReactionMapping, CompoundProperties compoundProperties)
{
var compound = compoundProperties.Compound;
var process = compound.ProcessByName(compoundReactionMapping.ProcessName);
if (process == null)
{
return;
}
var metabolite = getOrCreateMetaboliteFor(compoundReactionMapping, compoundProperties);
var reaction = _processBuilderMapper.MetabolismReactionFrom(process, compoundBuilder, metabolite, compoundReactionMapping.MoleculeName, _allMoleculeNames, _reactionBuildingBlock.FormulaCache);
_interactionKineticUpdater.UpdateReaction(reaction, compoundReactionMapping.MoleculeName, compound.Name, _simulation, _reactionBuildingBlock.FormulaCache);
addReactionToBuildingBlock(reaction, compound);
}
private IMoleculeBuilder getOrCreateMetaboliteFor(IReactionMapping compoundReactionMapping, CompoundProperties compoundProperties)
{
IMoleculeBuilder metabolite = null;
var enzymaticProcess = compoundReactionMapping as EnzymaticProcessSelection;
if (enzymaticProcess != null)
{
metabolite = _moleculeBuildingBlock[enzymaticProcess.MetaboliteName];
}
if (metabolite != null)
{
return(metabolite);
}
metabolite = _moleculeBuilderFactory.Create(QuantityType.Metabolite, _moleculeBuildingBlock.FormulaCache)
.WithName(compoundReactionMapping.ProductName(CoreConstants.Molecule.Metabolite));
addMoleculeToBuildingBlock(metabolite, compoundProperties);
return(metabolite);
}
