// The calculations for unlabeled and neucode components are the same, currently
public static List <Component> generate_neucode_components(double starter_mass)
{
List <Component> components = new List <Component>();
InputFile inFile = new ProteoformSuiteInternal.InputFile("somepath", Labeling.NeuCode, Purpose.Identification);
for (int i = 0; i < 2; i++)
{
Component light = new Component();
Component heavy = new Component();
light.input_file = inFile;
heavy.input_file = inFile;
light.id = 1.ToString();
heavy.id = 2.ToString();
light.weighted_monoisotopic_mass = starter_mass;
heavy.weighted_monoisotopic_mass = starter_mass + starter_lysine_count * Lollipop.NEUCODE_LYSINE_MASS_SHIFT;
light.intensity_sum_olcs = starter_intensity; //using the special intensity sum for overlapping charge states in a neucode pair
heavy.intensity_sum_olcs = starter_intensity / 2; //using the special intensity sum for overlapping charge states in a neucode pair
light.rt_apex = starter_rt;
heavy.rt_apex = starter_rt;
light.accepted = true;
heavy.accepted = true;
ChargeState light_charge_state = new ChargeState(1, light.intensity_sum_olcs, light.weighted_monoisotopic_mass, 1.00727645D);
ChargeState heavy_charge_state = new ChargeState(1, heavy.intensity_sum_olcs, heavy.weighted_monoisotopic_mass, 1.00727645D);
light.charge_states = new List <ChargeState> {
light_charge_state
};
heavy.charge_states = new List <ChargeState> {
heavy_charge_state
};
NeuCodePair n = new NeuCodePair(light, heavy);
n.lysine_count = starter_lysine_count;
n.calculate_properties();
components.Add(n);
}
return(components);
}
