MassDistribution calculateDistributionFor2Isotopes(const MassDistribution& isotopeDistribution, int atomCount)
{
MassDistribution result;
if (isotopeDistribution.size() != 2)
throw runtime_error("only implemented for 2 isotopes");
double m0 = isotopeDistribution[0].mass;
double p0 = isotopeDistribution[0].abundance;
double m1 = isotopeDistribution[1].mass;
double p1 = isotopeDistribution[1].abundance;
double mass = m0 * atomCount;
double abundance = pow(p0, atomCount);
//for (int i=0; i<=atomCount; i++)
for (int i=0; i<=4; i++)
{
result.push_back(MassAbundance(mass, abundance));
mass += (m1-m0);
abundance *= p1/p0*(atomCount-i)/(i+1);
}
return result;
}
void test4()
{
const double p0 = .9;
const double p1 = .09;
const double p2 = .009;
const double p3 = 1 - (p0 + p1 + p2);
const double m0 = 10;
const double m1 = 11;
const double m2 = 12.33;
const double m3 = 13.13;
MassDistribution md;
md.push_back(MassAbundance(m0, p0));
md.push_back(MassAbundance(m1, p1));
md.push_back(MassAbundance(m2, p2));
md.push_back(MassAbundance(m3, p3));
cout << "test4 distribution:\n" << md << endl;
IsotopeTable table(md, 10, 1e-5);
compare(md, table.distribution(1));
MassDistribution test4_2 = table.distribution(2);
cout << "2 atoms:\n" << test4_2 << endl;
}
void compare(const MassDistribution& test, const MassDistribution& good)
{
unit_assert(test.size() == good.size());
for (unsigned int i=0; i<test.size(); i++)
{
unit_assert_equal(test[i].mass, good[i].mass, 1e-12);
unit_assert_equal(test[i].abundance, good[i].abundance, 1e-12);
}
}
void printEnvelope(const MassDistribution& md, int charge)
{
using namespace pwiz::calibration; // for Ion
for (MassDistribution::const_iterator it=md.begin(); it!=md.end(); ++it)
{
if (it->abundance < .0001) continue;
cout << Ion::mz(it->mass, charge) << " " << it->abundance << endl;
}
}
void test2()
{
const double p0 = .9;
const double p1 = 1 - p0;
MassDistribution md;
md.push_back(MassAbundance(10, p0));
md.push_back(MassAbundance(11, p1));
IsotopeTable table(md, 10, 0);
/*
for (int i=0; i<=10; i++)
cout << i << " atoms:\n" << table.distribution(i) << endl;
*/
// test manually for 1 atom
MassDistribution test1 = table.distribution(1);
unit_assert(test1.size() == 2);
unit_assert(test1[0] == md[0]);
unit_assert(test1[1] == md[1]);
// test manually for 10 atoms
const int n = 10;
MassDistribution good10;
double abundance = pow(p0, n);
double mass = 100;
for (int k=0; k<=n; k++)
{
good10.push_back(MassAbundance(mass, abundance));
abundance *= p1/p0*(n-k)/(k+1);
mass += 1;
}
sort(good10.begin(), good10.end(), hasGreaterAbundance);
MassDistribution test10 = table.distribution(10);
sort(test10.begin(), test10.end(), hasGreaterAbundance);
unit_assert((int)test10.size() == n+1);
for (int k=0; k<=n; k++)
unit_assert_equal(test10[k].abundance, good10[k].abundance, 1e-15);
// test cutoff
IsotopeTable table_cutoff(md, 10, 1e-8);
unit_assert(table_cutoff.distribution(10).size() == 9);
}
void test1()
{
MassDistribution md;
md.push_back(MassAbundance(10, 1));
IsotopeTable table(md, 10, 0);
for (int i=1; i<=10; i++)
{
MassDistribution temp = table.distribution(i);
unit_assert(temp.size() == 1);
unit_assert(temp[0] == MassAbundance(i*10, 1));
//cout << i << " atoms:\n" << temp << endl;
}
}
void test3()
{
const double p0 = .9;
const double p1 = .09;
const double p2 = 1 - (p0 + p1);
const double m0 = 10;
const double m1 = 11;
const double m2 = 12.33;
MassDistribution md;
md.push_back(MassAbundance(m0, p0));
md.push_back(MassAbundance(m1, p1));
md.push_back(MassAbundance(m2, p2));
// cout << "test3 distribution:\n" << md << endl;
IsotopeTable table(md, 10, 1e-5);
// compare distribution for 1 atom
compare(table.distribution(1), md);
// compare distribution for 2 atoms
MassDistribution good3_2;
good3_2.push_back(MassAbundance(m0*2, p0*p0));
good3_2.push_back(MassAbundance(m0+m1, p0*p1*2));
good3_2.push_back(MassAbundance(m0+m2, p0*p2*2));
good3_2.push_back(MassAbundance(m1+m2, p1*p2*2));
good3_2.push_back(MassAbundance(m1+m1, p1*p1));
good3_2.push_back(MassAbundance(m2+m2, p2*p2));
sort(good3_2.begin(), good3_2.end(), hasGreaterAbundance);
MassDistribution test3_2 = table.distribution(2);
sort(test3_2.begin(), test3_2.end(), hasGreaterAbundance);
// cout << "good:\n" << good3_2 << endl;
// cout << "test:\n" << test3_2 << endl;
compare(test3_2, good3_2);
}
void testNormalization(const IsotopeCalculator& calc)
{
if (os_) *os_ << "mass normalized:\n"
<< calc.distribution(Formula("C100"), 0,
IsotopeCalculator::NormalizeMass) << endl;
if (os_) *os_ << "abundance normalized:\n"
<< calc.distribution(Formula("C100"), 0,
IsotopeCalculator::NormalizeAbundance) << endl;
MassDistribution md = calc.distribution(Formula("C100"), 0,
IsotopeCalculator::NormalizeMass |
IsotopeCalculator::NormalizeAbundance);
if (os_) *os_ << "both normalized:\n" << md << endl;
double sumSquares = 0;
for (MassDistribution::iterator it=md.begin(); it!=md.end(); ++it)
sumSquares += it->abundance * it->abundance;
if (os_) *os_ << "sumSquares: " << sumSquares << endl;
unit_assert_equal(sumSquares, 1, 1e-12);
unit_assert(md[0].mass == 0);
}
void test()
{
using namespace Peptide;
cout.precision(12);
initializeIsotopes();
for (Element e=ElementBegin; e!=ElementEnd; ++e)
{
cout << e << ":\n";
copy(isotopes[e].begin(), isotopes[e].end(), ostream_iterator<MassAbundance>(cout, "\n"));
}
cout << endl;
for (Element e=ElementBegin; e!=ElementEnd; ++e)
{
if (isotopes[e].size() != 2) continue;
MassDistribution test = calculateDistributionFor2Isotopes(isotopes[e], 100);
cout << e << ":\n";
copy(test.begin(), test.end(), ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
}
}
MassDistribution multiply(const MassDistribution& m, const MassDistribution& n)
{
MassDistribution result;
for (MassDistribution::const_iterator i=m.begin(); i!=m.end(); ++i)
for (MassDistribution::const_iterator j=n.begin(); j!=n.end(); ++j)
result.push_back(MassAbundance(i->mass + j->mass, i->abundance * j->abundance));
return result;
}
void calculateIsotopeEnvelope(const PepDatum& peptide)
{
using namespace Peptide;
const string& name = peptide.first;
const Peptide::Formula f = peptide.second;
cout << name << endl << endl;
MassDistribution c = calculateDistributionFor2Isotopes(isotopes[C], f[C]);
cout << "C envelope:\n";
copy(c.begin(), c.end(), ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
MassDistribution n = calculateDistributionFor2Isotopes(isotopes[N], f[N]);
cout << "N envelope:\n";
copy(n.begin(), n.end(), ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
// calculate product of C and N envelopes
MassDistribution cn = multiply(c,n);
sort(cn.begin(), cn.end(), isMoreAbundant);
cout << "C*N envelope:\n";
copy(cn.begin(), cn.begin()+5, ostream_iterator<MassAbundance>(cout, "\n"));
cout << endl;
// hack to add back in H, O, S
Peptide::Formula hack(0, f[H], 0, f[O], f[S]);
double hackMass = hack.monoisotopicMass();
for (MassDistribution::iterator it=cn.begin(); it!=cn.end(); ++it)
it->mass += hackMass;
// print envelopes by charge state
for (int i=1; i<5; i++)
{
cout << "charge state " << i << endl;
printEnvelope(cn, i);
cout << endl;
}
}
