//start naive
private List <Fragment> generateFragByNaive()
{
int percent = 0;
progressBar1.Maximum = _chemStructures[0].countBonds();
int PBar_Percent = 0;
progressBar1.Value = PBar_Percent;
progressBar1.Step = 1;
//Do this to preserve hydrogen numbers so that breaking bonds doesn't cause re-ordering.
foreach (IndigoObject atom in _chemStructures[0].iterateAtoms())
{
atom.countHydrogens();
}
List <Fragment> _frags = new List <Fragment>();
foreach (IndigoObject bond in _chemStructures[0].iterateBonds())
{
progressBar1.PerformStep();
IndigoObject tempStructure = _chemStructures[0].clone();
percent = (int)(progressBar1.Value / (progressBar1.Maximum * 100));
label3.Text = percent.ToString() + "%";
fragmentationRule naiveFragment = new fragmentationRule();
naiveFragment._atomId1 = bond.source().index();
naiveFragment._atomId2 = bond.destination().index();
naiveFragment._bondId = bond.index();
tempStructure.getBond(bond.index()).remove();
if (tempStructure.countComponents() > 1)
{
for (int i = 0; i < tempStructure.countComponents(); i++)
{
IndigoObject currFragment = tempStructure.component(i).clone();
double totalMassShift = 0.00;
//Get R Group Masses
foreach (IndigoObject rgroup in _chemStructures[0].iterateAtoms())
{
if (rgroup.symbol().Equals("R"))
{
if (rgroup.componentIndex() == i)
{
try
{
double RgrpMassShift = double.Parse(rmasses[rmasses.IndexOf(rmasses.Find(x => x.index == rgroup.index()))].interfaceText.Text);
Console.Out.WriteLine("BEFORE " + totalMassShift);
totalMassShift += RgrpMassShift;
Console.Out.WriteLine("AFTER " + totalMassShift);
}
catch (FormatException e)
{
MessageBox.Show("All R-Groups must have masses... R Group #" + rgroup.index() + " does not!");
}
//Console.Out.WriteLine(rgroup.index() + " has a mass of " +RgrpMassShift);
}
}
}
Fragment currFragAdd = new Fragment(naiveFragment);
currFragAdd.mass = (currFragment.monoisotopicMass() + totalMassShift);
_frags.Add(currFragAdd);
}
}
}
return(_frags);
}
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);
}