void Residue::setModification(const String & modification)
{
//modification_ = modification;
ModificationsDB * mod_db = ModificationsDB::getInstance();
ResidueModification mod = mod_db->getModification(one_letter_code_, modification, ResidueModification::ANYWHERE);
modification_ = mod.getId();
// update all the members
if (mod.getAverageMass() != 0)
{
average_weight_ = mod.getAverageMass();
}
if (mod.getMonoMass() != 0)
{
mono_weight_ = mod.getMonoMass();
}
bool updated_formula(false);
if (!mod.getDiffFormula().isEmpty())
{
updated_formula = true;
setFormula(getFormula() + mod.getDiffFormula());
}
if (mod.getFormula() != "" && !updated_formula)
{
updated_formula = true;
String formula = mod.getFormula();
formula.removeWhitespaces();
formula_ = EmpiricalFormula(formula);
}
if (updated_formula)
{
average_weight_ = formula_.getAverageWeight();
mono_weight_ = formula_.getMonoWeight();
}
else
{
if (mod.getAverageMass() != 0)
{
average_weight_ = mod.getAverageMass();
}
if (mod.getMonoMass() != 0)
{
mono_weight_ = mod.getMonoMass();
}
}
// neutral losses
loss_formulas_.clear();
loss_names_.clear();
if (mod.hasNeutralLoss())
{
loss_formulas_.push_back(mod.getNeutralLossDiffFormula());
loss_names_.push_back(mod.getNeutralLossDiffFormula().toString());
}
is_modified_ = true;
}
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
void MassDecompositionAlgorithm::updateMembers_()
{
// todo add accessor to tolerance, it is called very often in CID mode
Map<char, double> aa_to_weight;
set<const Residue *> residues = ResidueDB::getInstance()->getResidues((String)param_.getValue("residue_set"));
for (set<const Residue *>::const_iterator it = residues.begin(); it != residues.end(); ++it)
{
aa_to_weight[(*it)->getOneLetterCode()[0]] = (*it)->getMonoWeight(Residue::Internal);
}
// now handle the modifications
ModificationDefinitionsSet mod_set(param_.getValue("fixed_modifications"), param_.getValue("variable_modifications"));
set<ModificationDefinition> fixed_mods = mod_set.getFixedModifications();
for (set<ModificationDefinition>::const_iterator it = fixed_mods.begin(); it != fixed_mods.end(); ++it)
{
const ResidueModification& mod = it->getModification();
char aa = ' ';
if (mod.getOrigin() == 'X')
{
cerr << "MassDecompositionAlgorithm: Warning: cannot handle modification " << mod.getName() << ", because aa is ambiguous (" << mod.getOrigin() << "), ignoring modification!" << endl;
continue;
}
else
{
aa = mod.getOrigin();
}
if (mod.getMonoMass() != 0)
{
aa_to_weight[aa] = mod.getMonoMass();
}
else
{
if (mod.getDiffMonoMass() != 0)
{
aa_to_weight[aa] += mod.getDiffMonoMass();
}
else
{
cerr << "MassDecompositionAlgorithm: Warning: cannot handle modification " << mod.getName() << ", because no monoisotopic mass value was found! Ignoring modification!" << endl;
continue;
}
}
}
const StringList mod_names(ListUtils::create<String>("a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z"));
vector<String>::const_iterator actual_mod_name = mod_names.begin();
set<ModificationDefinition> var_mods = mod_set.getVariableModifications();
for (set<ModificationDefinition>::const_iterator it = var_mods.begin(); it != var_mods.end(); ++it)
{
ResidueModification mod = it->getModification();
//cerr << it->getModification() << " " << mod.getOrigin() << " " << mod.getId() << " " << mod.getFullId() << " " << mod.getUniModAccession() << " " << mod.getPSIMODAccession() << endl;
char aa = (*actual_mod_name)[0];
char origin_aa = ' ';
++actual_mod_name;
if (mod.getOrigin() == 'X')
{
cerr << "MassDecompositionAlgorithm: Warning: cannot handle modification " << mod.getName() << ", because aa is ambiguous (" << mod.getOrigin() << "), ignoring modification!" << endl;
continue;
}
else
{
origin_aa = mod.getOrigin();
}
if (mod.getMonoMass() != 0)
{
aa_to_weight[aa] = mod.getMonoMass();
}
else
{
if (mod.getDiffMonoMass() != 0)
{
aa_to_weight[aa] = aa_to_weight[origin_aa] + mod.getDiffMonoMass();
}
else
{
cerr << "Warning: cannot handle modification " << mod.getName() << ", because no monoisotopic mass value was found! Ignoring modification!" << endl;
continue;
}
}
}
if (alphabet_ != nullptr)
{
delete alphabet_;
}
if (decomposer_ != nullptr)
{
delete decomposer_;
}
// init mass decomposer
alphabet_ = new ims::IMSAlphabet();
for (Map<char, double>::ConstIterator it = aa_to_weight.begin(); it != aa_to_weight.end(); ++it)
{
alphabet_->push_back(String(it->first), it->second);
}
// initializes weights
ims::Weights weights(alphabet_->getMasses(), (double) param_.getValue("decomp_weights_precision"));
// optimize alphabet by dividing by gcd
weights.divideByGCD();
// decomposes real values
decomposer_ = new ims::RealMassDecomposer(weights);
return;
}
void CompNovoIdentificationBase::updateMembers_()
{
// init residue mass table
String residue_set(param_.getValue("residue_set"));
set<const Residue *> residues = ResidueDB::getInstance()->getResidues(residue_set);
for (set<const Residue *>::const_iterator it = residues.begin(); it != residues.end(); ++it)
{
aa_to_weight_[(*it)->getOneLetterCode()[0]] = (*it)->getMonoWeight(Residue::Internal);
}
max_number_aa_per_decomp_ = param_.getValue("max_number_aa_per_decomp");
tryptic_only_ = param_.getValue("tryptic_only").toBool();
fragment_mass_tolerance_ = (DoubleReal)param_.getValue("fragment_mass_tolerance");
max_number_pivot_ = param_.getValue("max_number_pivot");
decomp_weights_precision_ = (DoubleReal)param_.getValue("decomp_weights_precision");
min_mz_ = (DoubleReal)param_.getValue("min_mz");
max_mz_ = (DoubleReal)param_.getValue("max_mz");
max_decomp_weight_ = (DoubleReal)param_.getValue("max_decomp_weight");
max_subscore_number_ = param_.getValue("max_subscore_number");
max_isotope_ = param_.getValue("max_isotope");
name_to_residue_.clear();
residue_to_name_.clear();
// now handle the modifications
ModificationDefinitionsSet mod_set((StringList)param_.getValue("fixed_modifications"), (StringList)param_.getValue("variable_modifications"));
set<ModificationDefinition> fixed_mods = mod_set.getFixedModifications();
for (set<ModificationDefinition>::const_iterator it = fixed_mods.begin(); it != fixed_mods.end(); ++it)
{
ResidueModification mod = ModificationsDB::getInstance()->getModification(it->getModification());
char aa = ' ';
if (mod.getOrigin().size() != 1 || mod.getOrigin() == "X")
{
cerr << "Warning: cannot handle modification " << it->getModification() << ", because aa is ambiguous (" << mod.getOrigin() << "), ignoring modification!" << endl;
continue;
}
else
{
aa = mod.getOrigin()[0];
}
if (mod.getMonoMass() != 0)
{
aa_to_weight_[aa] = mod.getMonoMass();
}
else
{
if (mod.getDiffMonoMass() != 0)
{
aa_to_weight_[aa] += mod.getDiffMonoMass();
}
else
{
cerr << "Warning: cannot handle modification " << it->getModification() << ", because no monoisotopic mass value was found! Ignoring modification!" << endl;
continue;
}
}
//cerr << "Setting fixed modification " << it->getModification() << " of amino acid '" << aa << "'; weight = " << aa_to_weight_[aa] << endl;
const Residue * res = ResidueDB::getInstance()->getModifiedResidue(it->getModification());
name_to_residue_[aa] = res;
residue_to_name_[res] = aa;
}
const StringList mod_names(StringList::create("a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z"));
vector<String>::const_iterator actual_mod_name = mod_names.begin();
set<ModificationDefinition> var_mods = mod_set.getVariableModifications();
for (set<ModificationDefinition>::const_iterator it = var_mods.begin(); it != var_mods.end(); ++it)
{
ResidueModification mod = ModificationsDB::getInstance()->getModification(it->getModification());
char aa = (*actual_mod_name)[0];
char origin_aa = ' ';
++actual_mod_name;
if (mod.getOrigin().size() != 1 || mod.getOrigin() == "X")
{
cerr << "CompNovoIdentificationBase: Warning: cannot handle modification " << it->getModification() << ", because aa is ambiguous (" << mod.getOrigin() << "), ignoring modification!" << endl;
continue;
}
else
{
origin_aa = mod.getOrigin()[0];
}
if (mod.getMonoMass() != 0)
{
aa_to_weight_[aa] = mod.getMonoMass();
}
else
{
if (mod.getDiffMonoMass() != 0)
{
aa_to_weight_[aa] = aa_to_weight_[origin_aa] + mod.getDiffMonoMass();
}
else
{
cerr << "CompNovoIdentificationBase: Warning: cannot handle modification " << it->getModification() << ", because no monoisotopic mass value was found! Ignoring modification!" << endl;
continue;
}
}
//cerr << "Mapping variable modification " << it->getModification() << " to letter '" << aa << "' (@" << origin_aa << "); weight = " << aa_to_weight_[aa] << endl;
const Residue * res = ResidueDB::getInstance()->getModifiedResidue(it->getModification());
name_to_residue_[aa] = res;
residue_to_name_[res] = aa;
}
/*
cerr << "Following masses are used for identification: " << endl;
for (Map<char, DoubleReal>::const_iterator it = aa_to_weight_.begin(); it != aa_to_weight_.end(); ++it)
{
cerr << it->first << " " << precisionWrapper(it->second) << endl;
}*/
initIsotopeDistributions_();
Param decomp_param(mass_decomp_algorithm_.getParameters());
decomp_param.setValue("tolerance", fragment_mass_tolerance_);
decomp_param.setValue("fixed_modifications", (StringList)param_.getValue("fixed_modifications"));
decomp_param.setValue("variable_modifications", (StringList)param_.getValue("variable_modifications"));
mass_decomp_algorithm_.setParameters(decomp_param);
min_aa_weight_ = numeric_limits<DoubleReal>::max();
for (Map<char, DoubleReal>::const_iterator it = aa_to_weight_.begin(); it != aa_to_weight_.end(); ++it)
{
if (min_aa_weight_ > it->second)
{
min_aa_weight_ = it->second;
}
}
return;
}