private bool MatchByMass(IAtomContainer ac, double peak, double mzabs, double mzppm, out double matchedMass, out double hydrogenPenalty, out int hydrogensAdded)
{
matchedMass = 0;
hydrogenPenalty = 0;
hydrogensAdded = 0;
double mass;
//speed up and neutral loss matching!
if (ac.getProperty("FragmentMass") != null && (string)ac.getProperty("FragmentMass") != "")
{
mass = double.Parse(ac.getProperty("FragmentMass").ToString(), CultureInfo.InvariantCulture);
}
else
{
mass = MolecularFormulaTools.GetMonoisotopicMass(GetMolecularFormula(ac));
}
var peakLow = peak - mzabs - PpmTool.GetPPMDeviation(peak, mzppm);
var peakHigh = peak + mzabs + PpmTool.GetPPMDeviation(peak, mzppm);
//now try to add/remove neutral hydrogens ...at most the treedepth
var treeDepth = int.Parse((String)ac.getProperty("TreeDepth"));
for (var i = 0; i <= treeDepth; i++)
{
var hMass = i * hydrogenMass;
if ((mass + hMass) >= peakLow && (mass + hMass) <= peakHigh)
{
matchedMass = Math.Round(mass + hMass, 4);
//now add a bond energy equivalent to a H-C bond
hydrogenPenalty = (i * 1000);
hydrogensAdded = i;
return true;
}
if ((mass - hMass) >= peakLow && (mass - hMass) <= peakHigh)
{
matchedMass = Math.Round(mass - hMass, 4);
//now add a bond energy equivalent to a H-C bond
hydrogenPenalty = (i * 1000);
hydrogensAdded = -i;
return true;
}
}
return false;
}
/**
* Quick isomorphism check:
* ...if the fragment is isomorph to the ones already in the map
* ...only the atoms are compared and a list of bonds is stored in a
* map with sum formula to fragment
*
*
* @param fragment the fragment to be checked
*
* @return true, if successful
*
* @throws CDKException the CDK exception
*/
private bool isIdentical(IAtomContainer fragment, string currentSumFormula)
{
var isomorph = false;
List<IAtomContainer> fragsToCompare = null;
//iterate over list to check for isomorphism
if (sumformulaToFragMap.TryGetValue(currentSumFormula, out fragsToCompare))
{
isomorph = identicalAtoms(fragment, fragsToCompare);
if (isomorph)
{
//now replace fragment if its "bond energy is less"
var bondEnergy = Double.Parse((String)fragment.getProperty("BondEnergy"), CultureInfo.InvariantCulture);
foreach (var atomContainer in fragsToCompare)
{
if (Double.Parse((String)atomContainer.getProperty("BondEnergy"), CultureInfo.InvariantCulture) > bondEnergy)
{
addFragmentToListMapReplace(fragment, currentSumFormula);
}
}
}
//if not in map (with this formula) add it
else
{
addFragmentToListMap(fragment, currentSumFormula);
}
}
else
{
//sum formula has no entry in map yet
addFragmentToListMap(fragment, currentSumFormula);
}
return isomorph;
}
/**
* Gets the fragment mass subtracting the neutral loss from it.
* It also sets the new FragmentWeight property
*
* @param fragment the fragment
* @param mass the mass
*
* @return the fragment mass
*/
private double getFragmentMass(IAtomContainer fragment, double mass)
{
var massFinal = mass;
var nlMass = 0.0;
if (fragment.getProperty("FragmentMass") != null && (string)fragment.getProperty("FragmentMass") != "")
{
if (fragment.getProperty("NlMass") != null && (string)fragment.getProperty("NlMass") != "")
{
var tempNLMass = fragment.getProperty("NlMass").ToString().Split(',');
for (var i = 0; i < tempNLMass.Count(); i++)
{
nlMass += Convert.ToDouble(tempNLMass[i], CultureInfo.InvariantCulture);
}
}
}
massFinal = massFinal - nlMass;
fragment.setProperty("FragmentMass", massFinal.ToString(CultureInfo.InvariantCulture));
return massFinal;
}
/**
* Sets the bond energy.
*
* @param mol the mol
* @param bondEnergy the bond energy
*
* @return the i atom container
*/
private IAtomContainer setBondEnergy(IAtomContainer origMol, IAtomContainer mol, Double bondEnergy)
{
var props = mol.getProperties();
var bondEnergyOrig = (String)origMol.getProperty("BondEnergy");
if (bondEnergyOrig != null)
{
var sumEnergy = Convert.ToDouble(bondEnergyOrig, CultureInfo.InvariantCulture) + bondEnergy;
props.put("BondEnergy", sumEnergy.ToString(CultureInfo.InvariantCulture));
}
else
{
props.put("BondEnergy", bondEnergy.ToString(CultureInfo.InvariantCulture));
}
mol.setProperties(props);
return mol;
}
