private List <Fragment> recursiveFragGeneration(IndigoObject prefrag, List <fragmentationRule> _copyRules, string currName = "")
{
List <fragmentationRule> copyRules = new List <fragmentationRule>();
copyRules.AddRange(_copyRules);
List <Fragment> _frags = new List <Fragment>();
foreach (IndigoObject structure in prefrag.iterateComponents())
{
foreach (fragmentationRule rule in _copyRules)
{
IndigoObject temp = structure.clone();
try
{
temp.getBond(rule._bondId).remove();
if (rule._bondId2 != -1)
{
temp.getBond(rule._bondId2).remove();
}
currName = currName + "+" + rule.fragmentName;
if (_copyRules.Count == _rules.Count)
{
currName = rule.fragmentName;
}
Console.Out.WriteLine("RULE NAME " + currName);
for (int i = 0; i < temp.countComponents(); i++)
{
IndigoObject currFragment = temp.component(i).clone();
double totalMassShift = 0.00;
totalMassShift = calculateRgrpMassShift(rule, currFragment);
Fragment currFragAdd = new Fragment(rule);
Console.Out.WriteLine("MASS BEFORE " + totalMassShift);
foreach (IndigoObject atoms in temp.component(i).iterateAtoms())
{
if (atoms.componentIndex() == i)
{
if (atoms.index() == rule._atomId1)
{
totalMassShift = totalMassShift + rule._MassShift1;
}
if (atoms.index() == rule._atomId2)
{
totalMassShift = totalMassShift + rule._MassShift2;
}
}
}
currFragAdd.mass = (currFragment.monoisotopicMass() + totalMassShift);
currFragAdd.fragmentName = currName;
_frags.Add(currFragAdd);
copyRules.Remove(rule);
}
_frags.AddRange(recursiveFragGeneration(temp, copyRules, currName));
}
catch (Exception e)
{
Console.Out.WriteLine("That Atom doesn't exist in thsi structure!" + e);
}
}
}
// renderMolecule2(prefrag, prefrag.monoisotopicMass().ToString());
return(_frags);
}