double WeightWrapper::getWeight(const EmpiricalFormula & ef) const
{
if (weight_mode_ == WeightWrapper::MONO)
return ef.getMonoWeight();
else
return ef.getAverageWeight();
}
void TheoreticalSpectrumGenerator::addPrecursorPeaks(RichPeakSpectrum & spec, const AASequence & peptide, Int charge) const
{
RichPeak1D p;
// precursor peak
double mono_pos = peptide.getMonoWeight(Residue::Full, charge) / double(charge);
if (add_isotopes_)
{
IsotopeDistribution dist = peptide.getFormula(Residue::Full, charge).getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p.setMZ((double)(mono_pos + j * Constants::NEUTRON_MASS_U) / (double)charge);
p.setIntensity(pre_int_ * it->second);
if (add_metainfo_)
{
String name("[M+H]+");
if (charge == 2)
{
name = "[M+2H]++";
}
p.setMetaValue("IonName", name);
}
spec.push_back(p);
}
}
else
{
p.setMZ(mono_pos);
p.setIntensity(pre_int_);
if (add_metainfo_)
{
String name("[M+H]+");
if (charge == 2)
{
name = "[M+2H]++";
}
p.setMetaValue("IonName", name);
}
spec.push_back(p);
}
// loss peaks of the precursor
//loss of water
EmpiricalFormula ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("H2O");
mono_pos = ion.getMonoWeight() / double(charge);
if (add_isotopes_)
{
IsotopeDistribution dist = ion.getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p.setMZ((double)(mono_pos + j * Constants::NEUTRON_MASS_U) / (double)charge);
p.setIntensity(pre_int_H2O_ * it->second);
if (add_metainfo_)
{
String name("[M+H]-H2O+");
if (charge == 2)
{
name = "[M+2H]-H2O++";
}
p.setMetaValue("IonName", name);
}
spec.push_back(p);
}
}
else
{
p.setMZ(mono_pos);
p.setIntensity(pre_int_H2O_);
if (add_metainfo_)
{
String name("[M+H]-H2O+");
if (charge == 2)
{
name = "[M+2H]-H2O++";
}
p.setMetaValue("IonName", name);
}
spec.push_back(p);
}
//loss of ammonia
ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("NH3");
mono_pos = ion.getMonoWeight() / double(charge);
if (add_isotopes_)
{
IsotopeDistribution dist = ion.getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p.setMZ((double)(mono_pos + j * Constants::NEUTRON_MASS_U) / (double)charge);
p.setIntensity(pre_int_NH3_ * it->second);
if (add_metainfo_)
{
String name("[M+H]-NH3+");
if (charge == 2)
{
name = "[M+2H]-NH3++";
}
p.setMetaValue("IonName", name);
}
spec.push_back(p);
}
}
else
{
p.setMZ(mono_pos);
p.setIntensity(pre_int_NH3_);
if (add_metainfo_)
{
String name("[M+H]-NH3+");
if (charge == 2)
{
name = "[M+2H]-NH3++";
}
p.setMetaValue("IonName", name);
}
spec.push_back(p);
}
spec.sortByPosition();
}
e_ptr = new EmpiricalFormula;
TEST_NOT_EQUAL(e_ptr, e_nullPointer)
END_SECTION
START_SECTION(~EmpiricalFormula())
delete e_ptr;
END_SECTION
START_SECTION(EmpiricalFormula(const String& rhs))
e_ptr = new EmpiricalFormula("C4");
TEST_NOT_EQUAL(e_ptr, e_nullPointer)
EmpiricalFormula e0("C5(13)C4H2");
EmpiricalFormula e1("C5(13)C4");
EmpiricalFormula e2("(12)C5(13)C4");
EmpiricalFormula e3("C9");
TEST_REAL_SIMILAR(e1.getMonoWeight(), e2.getMonoWeight())
TEST_REAL_SIMILAR(e1.getMonoWeight(), 112.013419)
TEST_REAL_SIMILAR(e2.getMonoWeight(), 112.013419)
END_SECTION
START_SECTION(EmpiricalFormula(const EmpiricalFormula& rhs))
EmpiricalFormula ef(*e_ptr);
TEST_EQUAL(ef == *e_ptr, true)
END_SECTION
START_SECTION((EmpiricalFormula(SignedSize number, const Element* element, SignedSize charge=0)))
EmpiricalFormula ef(4, db->getElement("C"));
TEST_EQUAL(ef == *e_ptr, true)
TEST_EQUAL(ef.getCharge(), 0)
END_SECTION
ptr = new AccurateMassSearchEngine();
TEST_NOT_EQUAL(ptr, null_ptr)
}
END_SECTION
START_SECTION(virtual ~AccurateMassSearchEngine())
{
delete ptr;
}
END_SECTION
START_SECTION([EXTRA]AdductInfo)
{
EmpiricalFormula ef_empty;
// make sure an empty formula has no weight (we rely on that in AdductInfo's getMZ() and getNeutralMass()
TEST_EQUAL(ef_empty.getMonoWeight(), 0)
// now we test if converting from neutral mass to m/z and back recovers the input value using different adducts
{
// testing M;-2 // intrinsic doubly negative charge
AdductInfo ai("TEST_INTRINSIC", ef_empty, -2, 1);
double neutral_mass=1000; // some mass...
double mz = ai.getMZ(neutral_mass);
double neutral_mass_recon = ai.getNeutralMass(mz);
TEST_REAL_SIMILAR(neutral_mass, neutral_mass_recon);
}
{ // testing M+Na+H;+2
EmpiricalFormula simpleAdduct("HNa");
AdductInfo ai("TEST_WITHADDUCT", simpleAdduct, 2, 1);
double neutral_mass=1000; // some mass...
double mz = ai.getMZ(neutral_mass);
void TheoreticalSpectrumGenerator::addPrecursorPeaks(RichPeakSpectrum & spec, const AASequence & peptide, Int charge)
{
bool add_metainfo(param_.getValue("add_metainfo").toBool());
DoubleReal pre_int((DoubleReal)param_.getValue("precursor_intensity"));
DoubleReal pre_int_H2O((DoubleReal)param_.getValue("precursor_H2O_intensity"));
DoubleReal pre_int_NH3((DoubleReal)param_.getValue("precursor_NH3_intensity"));
bool add_isotopes(param_.getValue("add_isotopes").toBool());
int max_isotope((int)param_.getValue("max_isotope"));
// precursor peak
DoubleReal mono_pos = peptide.getMonoWeight(Residue::Full, charge) / DoubleReal(charge);
if (add_isotopes)
{
IsotopeDistribution dist = peptide.getFormula(Residue::Full, charge).getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(mono_pos + j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(pre_int * it->second);
if (add_metainfo)
{
String name("[M+H]+");
if (charge == 2)
{
name = "[M+2H]++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
}
else
{
p_.setMZ(mono_pos);
p_.setIntensity(pre_int);
if (add_metainfo)
{
String name("[M+H]+");
if (charge == 2)
{
name = "[M+2H]++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
// loss peaks of the precursor
//loss of water
EmpiricalFormula ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("H2O");
mono_pos = ion.getMonoWeight() / DoubleReal(charge);
if (add_isotopes)
{
IsotopeDistribution dist = ion.getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(mono_pos + j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(pre_int_H2O * it->second);
if (add_metainfo)
{
String name("[M+H]-H2O+");
if (charge == 2)
{
name = "[M+2H]-H2O++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
}
else
{
p_.setMZ(mono_pos);
p_.setIntensity(pre_int_H2O);
if (add_metainfo)
{
String name("[M+H]-H2O+");
if (charge == 2)
{
name = "[M+2H]-H2O++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
//loss of ammonia
ion = peptide.getFormula(Residue::Full, charge) - EmpiricalFormula("NH3");
mono_pos = ion.getMonoWeight() / DoubleReal(charge);
if (add_isotopes)
{
IsotopeDistribution dist = ion.getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(mono_pos + j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(pre_int_NH3 * it->second);
if (add_metainfo)
{
String name("[M+H]-NH3+");
if (charge == 2)
{
name = "[M+2H]-NH3++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
}
else
{
p_.setMZ(mono_pos);
p_.setIntensity(pre_int_NH3);
if (add_metainfo)
{
String name("[M+H]-NH3+");
if (charge == 2)
{
name = "[M+2H]-NH3++";
}
p_.setMetaValue("IonName", name);
}
spec.push_back(p_);
}
spec.sortByPosition();
}
