double WeightWrapper::getWeight(const AASequence & aa) const
{
if (weight_mode_ == WeightWrapper::MONO)
return aa.getMonoWeight();
else
return aa.getAverageWeight();
}
bool EnzymaticDigestionLogModel::isCleavageSite_(
const AASequence& protein, const AASequence::ConstIterator& iterator) const
{
if (enzyme_.getName() != "Trypsin") // no cleavage
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, String("EnzymaticDigestionLogModel: enzyme '") + enzyme_.getName() + " does not support logModel!");
}
else
{
if ((!enzyme_.getRegEx().hasSubstring(iterator->getOneLetterCode())) || *iterator == 'P') // wait for R or K
{
return false;
}
SignedSize pos = distance(AASequence::ConstIterator(protein.begin()),
iterator) - 4; // start position in sequence
double score_cleave = 0, score_missed = 0;
for (SignedSize i = 0; i < 9; ++i)
{
if ((pos + i >= 0) && (pos + i < (SignedSize)protein.size()))
{
BindingSite_ bs(i, protein[pos + i].getOneLetterCode());
Map<BindingSite_, CleavageModel_>::const_iterator pos_it =
model_data_.find(bs);
if (pos_it != model_data_.end()) // no data for non-std. amino acids
{
score_cleave += pos_it->second.p_cleave;
score_missed += pos_it->second.p_miss;
}
}
}
return score_missed - score_cleave > log_model_threshold_;
}
}
int main()
{
// construct a AASequence object, query a residue
// and output some of its properties
AASequence aas = AASequence::fromString("DECIANGER");
cout << aas[2].getName() << " "
<< aas[2].getFormula().toString() << " "
<< aas[2].getModificationName() << " "
<< aas[2].getMonoWeight() << endl;
// find a modification in ModificationsDB
// and output some of its properties
// getInstance() returns a pointer to a ModsDB instance
ResidueModification mod = ModificationsDB::getInstance()->getModification("Carbamidomethyl (C)");
cout << mod.getOrigin() << " "
<< mod.getFullId() << " "
<< mod.getDiffMonoMass() << " "
<< mod.getMonoMass() << endl;
// set the modification on a residue of a peptide
// and output some of its properties (the formula and mass have changed)
// in this case ModificationsDB is used in the background
// to relate the name of the mod to its attributes
aas.setModification(2, "Carbamidomethyl (C)");
cout << aas[2].getName() << " "
<< aas[2].getFormula().toString() << " "
<< aas[2].getModificationName() << " "
<< aas[2].getMonoWeight() << endl;
return 0;
} //end of main
Feature ICPLLabeler::mergeFeatures_(Feature& feature_to_merge, const AASequence& labeled_feature_sequence, Map<String, Feature>& feature_index) const
{
// merge with feature from first map (if it exists)
if (feature_index.count(labeled_feature_sequence.toString()) != 0)
{
// we only merge abundance and use feature from first map
Feature new_f = feature_index[labeled_feature_sequence.toString()];
new_f.setMetaValue(getChannelIntensityName(1), new_f.getIntensity());
new_f.setMetaValue(getChannelIntensityName(2), feature_to_merge.getIntensity());
new_f.setIntensity(new_f.getIntensity() + feature_to_merge.getIntensity());
mergeProteinAccessions_(new_f, feature_to_merge);
// remove feature from index
feature_index.erase(labeled_feature_sequence.toString());
return new_f;
}
else
{
// simply add feature from second channel, since we have no corresponding feature in the first channel
return feature_to_merge;
}
}
String ICPLLabeler::getUnmodifiedAASequence_(const Feature& feature, const String& label) const
{
AASequence unmodified = feature.getPeptideIdentifications()[0].getHits()[0].getSequence();
if (unmodified.getNTerminalModification() == label)
{
unmodified.setNTerminalModification(""); // remove terminal modification, if it is the channel specific one
}
return unmodified.toString();
}
Size EnzymaticDigestionLogModel::peptideCount(const AASequence& protein)
{
SignedSize count = 1;
AASequence::ConstIterator iterator = protein.begin();
while (nextCleavageSite_(protein, iterator), iterator != protein.end())
{
++count;
}
Size sum = count;
return sum;
}
String CompNovoIdentificationBase::getModifiedStringFromAASequence_(const AASequence & sequence)
{
String seq;
for (AASequence::ConstIterator it = sequence.begin(); it != sequence.end(); ++it)
{
if (residue_to_name_.has(&*it))
{
seq += residue_to_name_[&*it];
}
else
{
seq += it->getOneLetterCode();
}
}
return seq;
}
String IBSpectraFile::getModifString_(const AASequence& sequence)
{
String modif = sequence.getNTerminalModification();
for (AASequence::ConstIterator aa_it = sequence.begin();
aa_it != sequence.end();
++aa_it)
{
modif += ":" + aa_it->getModification();
}
if (sequence.getCTerminalModification() != "")
{
modif += ":" + sequence.getCTerminalModification();
}
return modif;
}
void EnzymaticDigestion::digest(const AASequence& protein, vector<AASequence>& output) const
{
// initialization
output.clear();
// naive cleavage sites
Size missed_cleavages = missed_cleavages_;
std::vector<Size> pep_positions = tokenize_(protein.toUnmodifiedString());
Size count = pep_positions.size();
Size begin = pep_positions[0];
for (Size i = 1; i < count; ++i)
{
output.push_back(protein.getSubsequence(begin, pep_positions[i] - begin));
begin = pep_positions[i];
}
output.push_back(protein.getSubsequence(begin, protein.size() - begin));
// missed cleavages
if (pep_positions.size() > 0 && missed_cleavages_ != 0) // there is at least one cleavage site!
{
// generate fragments with missed cleavages
for (Size i = 1; ((i <= missed_cleavages) && (count > i)); ++i)
{
begin = pep_positions[0];
for (Size j = 1; j < count - i; ++j)
{
output.push_back(protein.getSubsequence(begin, pep_positions[j + i] - begin));
begin = pep_positions[j];
}
output.push_back(protein.getSubsequence(begin, protein.size() - begin));
}
}
}
void ICPLLabeler::addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const
{
// check if proteinIdentification exists before accessing it
if (features.getProteinIdentifications().empty())
return;
for (std::vector<ProteinHit>::iterator protein_hit = features.getProteinIdentifications()[0].getHits().begin();
protein_hit != features.getProteinIdentifications()[0].getHits().end();
++protein_hit)
{
AASequence aa = AASequence::fromString(protein_hit->getSequence());
// modify only if the term is accessible
if (aa.getNTerminalModification() == "")
{
aa.setNTerminalModification(label);
protein_hit->setSequence(aa.toString());
}
}
}
Size ProteaseDigestion::peptideCount(const AASequence& protein)
{
// For unspecific cleavage every cutting position may be skipped. Thus, we get (n + 1) \choose 2 products.
if (enzyme_->getName() == UnspecificCleavage)
{
return (protein.size() + 1) * protein.size() / 2;
};
std::vector<int> pep_positions = tokenize_(protein.toUnmodifiedString());
Size count = pep_positions.size();
// missed cleavages
Size sum = count;
for (Size i = 1; i < count; ++i)
{
if (i > missed_cleavages_) break;
sum += count - i;
}
return sum;
}
void TheoreticalSpectrumGenerator::addIsotopeCluster_(RichPeakSpectrum & spectrum, const AASequence & ion, Residue::ResidueType res_type, Int charge, double intensity) const
{
double pos = ion.getMonoWeight(res_type, charge) / (double)charge;
RichPeak1D p;
IsotopeDistribution dist = ion.getFormula(res_type, charge).getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
// TODO: this is usually dominated by 13C-12C mass shift which deviates a bit from neutron mass
p.setMZ((double)(pos + (double)j * Constants::NEUTRON_MASS_U) / (double)charge);
p.setIntensity(intensity * it->second);
if (add_metainfo_ && j == 0)
{
String ion_name = String(residueTypeToIonLetter_(res_type)) + String(ion.size()) + String(charge, '+');
p.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p);
}
}
bool ProteaseDigestion::isValidProduct(const AASequence& protein,
int pep_pos,
int pep_length,
bool ignore_missed_cleavages,
bool allow_nterm_protein_cleavage,
bool allow_random_asp_pro_cleavage) const
{
String seq = protein.toUnmodifiedString();
return isValidProduct_(seq, pep_pos, pep_length, ignore_missed_cleavages, allow_nterm_protein_cleavage, allow_random_asp_pro_cleavage);
}
vector<Size> AScore::getSites_(const AASequence& without_phospho) const
{
vector<Size> tupel;
String unmodified = without_phospho.toUnmodifiedString();
for (Size i = 0; i < unmodified.size(); ++i)
{
if (unmodified[i] == 'Y' || unmodified[i] == 'T' || unmodified[i] == 'S')
{
tupel.push_back(i);
}
}
return tupel;
}
void EnzymaticDigestionLogModel::nextCleavageSite_(const AASequence& protein, AASequence::ConstIterator& iterator) const
{
while (iterator != protein.end())
{
if (isCleavageSite_(protein, iterator))
{
++iterator;
return;
}
++iterator;
}
return;
}
Size EnzymaticDigestion::peptideCount(const AASequence& protein)
{
std::vector<Size> pep_positions = tokenize_(protein.toUnmodifiedString());
Size count = pep_positions.size();
// missed cleavages
Size sum = count;
for (Size i = 1; i < count; ++i)
{
if (i > missed_cleavages_) break;
sum += count - i;
}
return sum;
}
void EnzymaticDigestionLogModel::digest(const AASequence& protein, vector<AASequence>& output) const
{
// initialization
output.clear();
AASequence::ConstIterator begin = protein.begin();
AASequence::ConstIterator end = protein.begin();
while (nextCleavageSite_(protein, end), end != protein.end())
{
output.push_back(protein.getSubsequence(begin - protein.begin(), end - begin));
begin = end;
}
output.push_back(protein.getSubsequence(begin - protein.begin(), end - begin));
}
void ConsensusIDAlgorithm::compareChargeStates_(Int& recorded_charge,
Int new_charge,
const AASequence& peptide)
{
if (recorded_charge == 0) // update recorded charge
{
recorded_charge = new_charge;
}
else if ((new_charge != 0) && (recorded_charge != new_charge))
{ // maybe TODO: calculate correct charge from prec. m/z and peptide mass?
String msg = "Conflicting charge states found for peptide '" +
peptide.toString() + "': " + String(recorded_charge) + ", " +
String(new_charge);
throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
msg, String(new_charge));
}
}
void SILACLabeler::applyLabelToProteinHit_(SimTypes::FeatureMapSim& channel, const String& arginine_label, const String& lysine_label) const
{
for (std::vector<ProteinHit>::iterator protein_hit = channel.getProteinIdentifications()[0].getHits().begin();
protein_hit != channel.getProteinIdentifications()[0].getHits().end();
++protein_hit)
{
AASequence aa = AASequence::fromString(protein_hit->getSequence());
for (AASequence::Iterator residue = aa.begin(); residue != aa.end(); ++residue)
{
if (*residue == 'R')
{
aa.setModification(residue - aa.begin(), arginine_label);
}
else if (*residue == 'K')
{
aa.setModification(residue - aa.begin(), lysine_label);
}
}
protein_hit->setSequence(aa.toString());
}
}
Size ProteaseDigestion::digest(const AASequence& protein, vector<AASequence>& output, Size min_length, Size max_length) const
{
// initialization
output.clear();
// disable max length filter by setting to maximum length
if (max_length == 0 || max_length > protein.size())
{
max_length = protein.size();
}
Size mc = (enzyme_->getName() == UnspecificCleavage) ? std::numeric_limits<Size>::max() : missed_cleavages_;
Size wrong_size(0);
// naive cleavage sites
std::vector<int> pep_positions = tokenize_(protein.toUnmodifiedString());
pep_positions.push_back(protein.size()); // positions now contains 0, x1, ... xn, end
Size count = pep_positions.size();
Size begin = pep_positions[0];
for (Size i = 1; i < count; ++i)
{
Size l = pep_positions[i] - begin;
if (l >= min_length && l <= max_length) output.push_back(protein.getSubsequence(begin, l));
else ++wrong_size;
begin = pep_positions[i];
}
// missed cleavages
if (pep_positions.size() > 1 && mc != 0) // there is at least one cleavage site (in addition to last position)!
{
// generate fragments with missed cleavages
for (Size mcs = 1; ((mcs <= mc) && (mcs < count - 1)); ++mcs)
{
begin = pep_positions[0];
for (Size j = 1; j < count - mcs; ++j)
{
Size l = pep_positions[j + mcs] - begin;
if (l >= min_length && l <= max_length) output.push_back(protein.getSubsequence(begin, l));
else ++wrong_size;
begin = pep_positions[j];
}
}
}
return wrong_size;
}
TEST_EQUAL(out[5].toString(),"PLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRK")
TEST_EQUAL(out[6].toString(),"VPQVSTPTLVEVSRSLGK")
TEST_EQUAL(out[7].toString(),"VGTRCCTK")
TEST_EQUAL(out[8].toString(),"PESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRR")
TEST_EQUAL(out[9].toString(),"PCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHK")
TEST_EQUAL(out[10].toString(),"PKATEEQLKTVMENFVAFDKCCAADDKEACFAVEGPKLVVSTQTALA")
END_SECTION
START_SECTION(( bool isValidProduct(const AASequence& protein, Size pep_pos, Size pep_length) ))
EnzymaticDigestion ed;
ed.setEnzyme(EnzymaticDigestion::ENZYME_TRYPSIN);
ed.setSpecificity(EnzymaticDigestion::SPEC_FULL); // require both sides
AASequence prot = AASequence("ABCDEFGKABCRAAAKAARPBBBB");
TEST_EQUAL(ed.isValidProduct(prot, 100, 3), false); // invalid position
TEST_EQUAL(ed.isValidProduct(prot, 10, 300), false); // invalid length
TEST_EQUAL(ed.isValidProduct(prot, 10, 0), false); // invalid size
TEST_EQUAL(ed.isValidProduct(AASequence(""), 10, 0), false); // invalid size
TEST_EQUAL(ed.isValidProduct(prot, 0, 3), false); // invalid N-term
TEST_EQUAL(ed.isValidProduct(prot, 0, 8), true); // valid N-term
TEST_EQUAL(ed.isValidProduct(prot, 8, 4), true); // valid fully-tryptic
TEST_EQUAL(ed.isValidProduct(prot, 8, 8), true); // valid fully-tryptic
TEST_EQUAL(ed.isValidProduct(prot, 0, 19), false); // invalid C-term - followed by proline
TEST_EQUAL(ed.isValidProduct(prot, 8, 3), false); // invalid C-term
TEST_EQUAL(ed.isValidProduct(prot, 3, 6), false); // invalid C+N-term
TEST_EQUAL(ed.isValidProduct(prot, 1, 7), false); // invalid N-term
TEST_EQUAL(ed.isValidProduct(prot, 0, prot.size()), true); // the whole thing
bool EnzymaticDigestion::isValidProduct(const AASequence& protein,
Size pep_pos, Size pep_length,
bool methionine_cleavage,
bool ignore_missed_cleavages) const
{
if (pep_pos >= protein.size())
{
LOG_WARN << "Error: start of peptide (" << pep_pos << ") is beyond end of protein '" << protein.toString() << "'!" << endl;
return false;
}
else if (pep_pos + pep_length > protein.size())
{
LOG_WARN << "Error: end of peptide (" << (pep_pos + pep_length) << ") is beyond end of protein '" << protein.toString() << "'!" << endl;
return false;
}
else if (pep_length == 0 || protein.size() == 0)
{
LOG_WARN << "Error: peptide or protein must not be empty!" << endl;
return false;
}
if (specificity_ == SPEC_NONE)
{
return true; // we don't care about terminal ends
}
else // either SPEC_SEMI or SPEC_FULL
{
bool spec_c = false, spec_n = false;
std::vector<Size> pep_positions = tokenize_(protein.toUnmodifiedString());
// initialize start and end
std::vector<Size>::const_iterator begin_pos, end_pos;
begin_pos = end_pos = pep_positions.end();
// test each end
if (pep_pos == 0 ||
(begin_pos = std::find(pep_positions.begin(), pep_positions.end(), pep_pos)) != pep_positions.end())
{
spec_n = true;
}
// if allow methionine cleavage at the protein start position
if (pep_pos == 1 && methionine_cleavage && protein.getResidue((Size)0).getOneLetterCode() == "M")
{
// methionine_cleavage:consider the first product for begin_pos
begin_pos = pep_positions.begin();
spec_n = true;
}
if (pep_pos + pep_length == protein.size() ||
(end_pos = std::find(pep_positions.begin(), pep_positions.end(), pep_pos + pep_length)) != pep_positions.end())
{
spec_c = true;
}
if (spec_n && spec_c)
{
if (ignore_missed_cleavages)
{
return true;
}
Size offset = std::distance(begin_pos, end_pos);
if (pep_pos + pep_length == protein.size())
{
return (pep_positions.size() <= getMissedCleavages() + 1);
}
else if (offset > getMissedCleavages() + 1)
{
return false;
}
else if (offset == 0)
{
// This corner case needs to be checked when peptide is at the start and the end of the protein.
// We check with the total number of cleavages.
return (pep_positions.size() >= getMissedCleavages() + 1);
}
else
{
return true;
}
}
else if ((specificity_ == SPEC_SEMI) && (spec_n || spec_c))
{
return true; // one only for SEMI
}
else
{
return false;
}
}
}
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();
}
void TheoreticalSpectrumGenerator::addPeaks(RichPeakSpectrum & spectrum, const AASequence & peptide, Residue::ResidueType res_type, Int charge) const
{
if (peptide.empty())
{
return;
}
spectrum.reserve(peptide.size());
// Generate the ion peaks:
// Does not generate peaks of full peptide (therefore "<").
// They are added via precursor mass (and neutral losses).
// Could be changed in the future.
switch (res_type)
{
case Residue::AIon:
{
Size i = 1;
if (!add_first_prefix_ion_)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
AASequence ion = peptide.getPrefix(i);
if (add_isotopes_) // add isotope cluster
{
addIsotopeCluster_(spectrum, ion, res_type, charge, a_intensity_);
}
else // add single peak
{
double pos = ion.getMonoWeight(Residue::AIon, charge) / static_cast<double>(charge);
addPeak_(spectrum, pos, a_intensity_, res_type, i, charge);
}
if (add_losses_)
{
addLosses_(spectrum, ion, a_intensity_, res_type, charge);
}
}
break;
}
case Residue::BIon:
{
Size i = 1;
if (!add_first_prefix_ion_)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
AASequence ion = peptide.getPrefix(i);
if (add_isotopes_)
{
addIsotopeCluster_(spectrum, ion, res_type, charge, b_intensity_);
}
else
{
double pos = ion.getMonoWeight(Residue::BIon, charge) / static_cast<double>(charge);
addPeak_(spectrum, pos, b_intensity_, res_type, i, charge);
}
if (add_losses_)
{
addLosses_(spectrum, ion, b_intensity_, res_type, charge);
}
}
break;
}
case Residue::CIon:
{
Size i = 1;
if (!add_first_prefix_ion_)
{
i = 2;
}
if (peptide.size() < 2)
{
//"Cannot create c ions of a monomer."
throw Exception::InvalidSize(__FILE__, __LINE__, __PRETTY_FUNCTION__, 1);
}
for (; i < peptide.size(); ++i)
{
AASequence ion = peptide.getPrefix(i);
if (add_isotopes_)
{
addIsotopeCluster_(spectrum, ion, res_type, charge, c_intensity_);
}
else
{
double pos = ion.getMonoWeight(Residue::CIon, charge) / static_cast<double>(charge);
addPeak_(spectrum, pos, c_intensity_, res_type, i, charge);
}
if (add_losses_)
{
addLosses_(spectrum, ion, c_intensity_, res_type, charge);
}
}
break;
}
case Residue::XIon:
{
Size i = 1;
if (!add_first_prefix_ion_)
{
i = 2;
}
if (peptide.size() < 2)
{
// "Cannot create c ions of a monomer."
throw Exception::InvalidSize(__FILE__, __LINE__, __PRETTY_FUNCTION__, 1);
}
for (; i < peptide.size(); ++i)
{
AASequence ion = peptide.getSuffix(i);
if (add_isotopes_)
{
addIsotopeCluster_(spectrum, ion, res_type, charge, x_intensity_);
}
else
{
double pos = ion.getMonoWeight(Residue::XIon, charge) / static_cast<double>(charge);
addPeak_(spectrum, pos, x_intensity_, res_type, i, charge);
}
if (add_losses_)
{
addLosses_(spectrum, ion, x_intensity_, res_type, charge);
}
}
break;
}
case Residue::YIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
AASequence ion = peptide.getSuffix(i);
if (add_isotopes_)
{
addIsotopeCluster_(spectrum, ion, res_type, charge, y_intensity_);
}
else
{
double pos = ion.getMonoWeight(Residue::YIon, charge) / static_cast<double>(charge);
addPeak_(spectrum, pos, y_intensity_, res_type, i, charge);
}
if (add_losses_)
{
addLosses_(spectrum, ion, y_intensity_, res_type, charge);
}
}
break;
}
case Residue::ZIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
AASequence ion = peptide.getSuffix(i);
if (add_isotopes_)
{
addIsotopeCluster_(spectrum, ion, res_type, charge, z_intensity_);
}
else
{
double pos = ion.getMonoWeight(Residue::ZIon, charge) / static_cast<double>(charge);
addPeak_(spectrum, pos, z_intensity_, res_type, i, charge);
}
if (add_losses_)
{
addLosses_(spectrum, ion, z_intensity_, res_type, charge);
}
}
break;
}
default:
cerr << "Cannot create peaks of that ion type" << endl;
}
spectrum.sortByPosition();
return;
}
void TheoreticalSpectrumGenerator::addLosses_(RichPeakSpectrum & spectrum, const AASequence & ion, double intensity, Residue::ResidueType res_type, int charge) const
{
RichPeak1D p;
set<String> losses;
for (AASequence::ConstIterator it = ion.begin(); it != ion.end(); ++it)
{
if (it->hasNeutralLoss())
{
vector<EmpiricalFormula> loss_formulas = it->getLossFormulas();
for (Size i = 0; i != loss_formulas.size(); ++i)
{
losses.insert(loss_formulas[i].toString());
}
}
}
if (!add_isotopes_)
{
p.setIntensity(intensity * rel_loss_intensity_);
}
for (set<String>::const_iterator it = losses.begin(); it != losses.end(); ++it)
{
EmpiricalFormula loss_ion = ion.getFormula(res_type, charge) - EmpiricalFormula(*it);
// thanks to Chris and Sandro
// check for negative element frequencies (might happen if losses are not allowed for specific ions)
bool negative_elements(false);
for (EmpiricalFormula::ConstIterator eit = loss_ion.begin(); eit != loss_ion.end(); ++eit)
{
if (eit->second < 0)
{
negative_elements = true;
break;
}
}
if (negative_elements)
{
continue;
}
double loss_pos = loss_ion.getMonoWeight() / (double)charge;
const String& loss_name = *it;
if (add_isotopes_)
{
IsotopeDistribution dist = loss_ion.getIsotopeDistribution(max_isotope_);
UInt j(0);
for (IsotopeDistribution::ConstIterator iso = dist.begin(); iso != dist.end(); ++iso)
{
p.setMZ((double)(loss_pos + j) / (double)charge);
p.setIntensity(intensity * rel_loss_intensity_ * iso->second);
if (add_metainfo_ && j == 0)
{
// note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal
String ion_name = String(residueTypeToIonLetter_(res_type)) + String(ion.size()) + "-" + loss_name + String(charge, '+');
p.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p);
}
}
else
{
p.setMZ(loss_pos);
if (add_metainfo_)
{
// note: important to construct a string from char. If omitted it will perform pointer arithmetics on the "-" string literal
String ion_name = String(residueTypeToIonLetter_(res_type)) + String(ion.size()) + "-" + loss_name + String(charge, '+');
p.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p);
}
}
}
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();
}
ww.setWeightMode(WeightWrapper::AVERAGE);
TEST_EQUAL(ww.getWeightMode(), WeightWrapper::AVERAGE)
}
END_SECTION
START_SECTION((WEIGHTMODE getWeightMode() const ))
{
WeightWrapper ww;
TEST_EQUAL(ww.getWeightMode(), WeightWrapper::MONO)
}
END_SECTION
START_SECTION((double getWeight(const AASequence &aa) const ))
{
WeightWrapper ww;
AASequence aa= AASequence::fromString("DFINAGER");
TEST_EQUAL(ww.getWeight(aa), aa.getMonoWeight())
WeightWrapper ww2(WeightWrapper::AVERAGE);
TEST_EQUAL(ww2.getWeight(aa), aa.getAverageWeight())
}
END_SECTION
START_SECTION((double getWeight(const EmpiricalFormula &ef) const ))
{
WeightWrapper ww;
EmpiricalFormula aa("C12H544");
TEST_EQUAL(ww.getWeight(aa), aa.getMonoWeight())
WeightWrapper ww2(WeightWrapper::AVERAGE);
TEST_EQUAL(ww2.getWeight(aa), aa.getAverageWeight())
}
END_SECTION
void TheoreticalSpectrumGenerator::addPeaks(RichPeakSpectrum & spectrum, const AASequence & peptide, Residue::ResidueType res_type, Int charge)
{
if (peptide.empty())
{
return;
}
Map<DoubleReal, AASequence> ions;
Map<DoubleReal, String> names;
AASequence ion;
DoubleReal intensity(0);
bool add_first_prefix_ion(param_.getValue("add_first_prefix_ion").toBool());
// generate the ion peaks
switch (res_type)
{
case Residue::AIon:
{
Size i = 1;
if (!add_first_prefix_ion)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
ion = peptide.getPrefix(i);
DoubleReal pos = ion.getMonoWeight(Residue::AIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "a" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("a_intensity");
break;
}
case Residue::BIon:
{
Size i = 1;
if (!add_first_prefix_ion)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
ion = peptide.getPrefix(i);
DoubleReal pos = ion.getMonoWeight(Residue::BIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "b" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("b_intensity");
break;
}
case Residue::CIon:
{
Size i = 1;
if (!add_first_prefix_ion)
{
i = 2;
}
for (; i < peptide.size(); ++i)
{
ion = peptide.getPrefix(i);
DoubleReal pos = ion.getMonoWeight(Residue::CIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "c" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("c_intensity");
break;
}
case Residue::XIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
ion = peptide.getSuffix(i);
DoubleReal pos = ion.getMonoWeight(Residue::XIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "x" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("x_intensity");
break;
}
case Residue::YIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
ion = peptide.getSuffix(i);
DoubleReal pos = ion.getMonoWeight(Residue::YIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "y" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("y_intensity");
break;
}
case Residue::ZIon:
{
for (Size i = 1; i < peptide.size(); ++i)
{
ion = peptide.getSuffix(i);
DoubleReal pos = ion.getMonoWeight(Residue::ZIon, charge) / (DoubleReal)charge;
ions[pos] = ion;
names[pos] = "z" + String(i) + String(charge, '+');
}
intensity = (DoubleReal)param_.getValue("z_intensity");
break;
}
default:
cerr << "Cannot create peaks of that ion type" << endl;
}
// get the params
bool add_losses(param_.getValue("add_losses").toBool());
bool add_metainfo(param_.getValue("add_metainfo").toBool());
bool add_isotopes(param_.getValue("add_isotopes").toBool());
Int max_isotope((Int)param_.getValue("max_isotope"));
DoubleReal rel_loss_intensity((DoubleReal)param_.getValue("relative_loss_intensity"));
for (Map<DoubleReal, AASequence>::ConstIterator cit = ions.begin(); cit != ions.end(); ++cit)
{
ion = cit->second;
DoubleReal pos = cit->first;
String ion_name = names[pos];
if (add_isotopes)
{
IsotopeDistribution dist = ion.getFormula(res_type, charge).getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator it = dist.begin(); it != dist.end(); ++it, ++j)
{
p_.setMZ((DoubleReal)(pos + (DoubleReal)j * Constants::NEUTRON_MASS_U) / (DoubleReal)charge);
p_.setIntensity(intensity * it->second);
if (add_metainfo && j == 0)
{
p_.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p_);
}
}
else
{
p_.setMZ(pos);
p_.setIntensity(intensity);
if (add_metainfo)
{
p_.setMetaValue("IonName", ion_name);
}
spectrum.push_back(p_);
}
if (add_losses)
{
set<String> losses;
for (AASequence::ConstIterator it = cit->second.begin(); it != cit->second.end(); ++it)
{
if (it->hasNeutralLoss())
{
vector<EmpiricalFormula> loss_formulas = it->getLossFormulas();
for (Size i = 0; i != loss_formulas.size(); ++i)
{
losses.insert(loss_formulas[i].toString());
}
}
}
if (!add_isotopes)
{
p_.setIntensity(intensity * rel_loss_intensity);
}
for (set<String>::const_iterator it = losses.begin(); it != losses.end(); ++it)
{
EmpiricalFormula loss_ion = ion.getFormula(res_type, charge) - EmpiricalFormula(*it);
// thanks to Chris and Sandro
// check for negative element frequencies (might happen if losses are not allowed for specific ions)
bool negative_elements(false);
for (EmpiricalFormula::ConstIterator eit = loss_ion.begin(); eit != loss_ion.end(); ++eit)
{
if (eit->second < 0)
{
negative_elements = true;
break;
}
}
if (negative_elements)
{
continue;
}
DoubleReal loss_pos = loss_ion.getMonoWeight() / (DoubleReal)charge;
String loss_name = *it;
if (add_isotopes)
{
IsotopeDistribution dist = loss_ion.getIsotopeDistribution(max_isotope);
UInt j(0);
for (IsotopeDistribution::ConstIterator iso = dist.begin(); iso != dist.end(); ++iso)
{
p_.setMZ((DoubleReal)(loss_pos + j) / (DoubleReal)charge);
p_.setIntensity(intensity * rel_loss_intensity * iso->second);
if (add_metainfo && j == 0)
{
p_.setMetaValue("IonName", ion_name + "-" + loss_name);
}
spectrum.push_back(p_);
}
}
else
{
p_.setMZ(loss_pos);
if (add_metainfo)
{
p_.setMetaValue("IonName", ion_name + "-" + loss_name);
}
spectrum.push_back(p_);
}
}
}
}
if (add_metainfo)
{
p_.setMetaValue("IonName", String(""));
}
spectrum.sortByPosition();
return;
}
bool ModificationDefinitionsSet::isCompatible(const AASequence & peptide) const
{
set<String> var_names(getVariableModificationNames()), fixed_names(getFixedModificationNames());
// no modifications present and needed
if (fixed_names.empty() && !peptide.isModified())
{
return true;
}
// check whether the fixed modifications are fulfilled
if (!fixed_names.empty())
{
for (set<String>::const_iterator it1 = fixed_names.begin(); it1 != fixed_names.end(); ++it1)
{
String origin = ModificationsDB::getInstance()->getModification(*it1).getOrigin();
// only single 1lc amino acids are allowed
if (origin.size() != 1)
{
continue;
}
for (AASequence::ConstIterator it2 = peptide.begin(); it2 != peptide.end(); ++it2)
{
if (origin == it2->getOneLetterCode())
{
// check whether the residue is modified (has to be)
if (!it2->isModified())
{
return false;
}
// check whether the modification is the same
if (ModificationsDB::getInstance()->getModification(*it1).getId() != it2->getModification())
{
return false;
}
}
}
}
}
// check wether other modifications than the variable are present
for (AASequence::ConstIterator it = peptide.begin(); it != peptide.end(); ++it)
{
if (it->isModified())
{
String mod = ModificationsDB::getInstance()->getModification(it->getOneLetterCode(), it->getModification(), ResidueModification::ANYWHERE).getFullId();
if (var_names.find(mod) == var_names.end() &&
fixed_names.find(mod) == fixed_names.end())
{
return false;
}
}
}
if (peptide.hasNTerminalModification())
{
String mod = ModificationsDB::getInstance()->getTerminalModification(peptide.getNTerminalModification(), ResidueModification::N_TERM).getFullId();
if (var_names.find(mod) == var_names.end() &&
fixed_names.find(mod) == fixed_names.end())
{
return false;
}
}
if (peptide.hasCTerminalModification())
{
String mod = ModificationsDB::getInstance()->getTerminalModification(peptide.getCTerminalModification(), ResidueModification::C_TERM).getFullId();
if (var_names.find(mod) == var_names.end() &&
fixed_names.find(mod) == fixed_names.end())
{
return false;
}
}
return true;
}