private void button6_Click(object sender, EventArgs e)
{
if (savedRule == false)
{
label8.Show();
}
else
{
savedRule = false;
comboBox1.DisplayMember = "fragmentName";
fragmentationRule f = new fragmentationRule();
comboBox1.Items.Add(f);
Console.WriteLine(comboBox1.SelectedValue);
comboBox1.SelectedIndex = comboBox1.Items.Count - 1;
label8.Hide();
}
}
public Fragment(fragmentationRule rule)
{
fragmentName = rule.fragmentName;
_bondId = rule._bondId;
_atomId1 = rule._atomId1;
_atomId2 = rule._atomId2;
_bondId2 = rule._bondId2;
_atomId3 = rule._atomId3;
_atomId4 = rule._atomId4;
_MassShift1 = rule._MassShift1;
_MassShift2 = rule._MassShift2;
_MassShift3 = rule._MassShift3;
_MassShift4 = rule._MassShift4;
mass = 0;
}
private double calculateRgrpMassShift(fragmentationRule rule, IndigoObject structure)
{
Console.Out.WriteLine(rule._MassShift1);
double mshift = 0.00;
foreach (IndigoObject atom in structure.iterateAtoms())
{
if (atom.symbol().Equals("R"))
{
try
{
double RgrpMassShift = double.Parse(rmasses[rmasses.IndexOf(rmasses.Find(x => x.index == atom.index()))].interfaceText.Text);
mshift += RgrpMassShift;
}
catch (FormatException e)
{
MessageBox.Show("All R-Groups must have masses... R Group #" + atom.index() + " does not!");
}
}
}
Console.Out.WriteLine("MASS SHIFT FINAL " + mshift);
return(mshift);
}
//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);
}