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development version 1.3.7
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Jiri Novak committed Nov 8, 2018
1 parent 5015469 commit 0744d78
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Showing 26 changed files with 953 additions and 275 deletions.
9 changes: 9 additions & 0 deletions CycloBranch/core/cFragmentIons.cpp
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Expand Up @@ -1855,6 +1855,15 @@ void cFragmentIons::recalculateFragments(bool cyclicnterminus, bool cyclicctermi
fragmentions[ms_NH4plus].multiplier = 1;
fragmentions[ms_NH4plus].summary = "NH4+";

// initialize ion [M+Cl]-
fragmentions[ms_Clminus].nterminal = true;
fragmentions[ms_Clminus].cterminal = true;
fragmentions[ms_Clminus].name = "[M+Cl]-";
fragmentions[ms_Clminus].massdifference = Cl + e;
fragmentions[ms_Clminus].positive = false;
fragmentions[ms_Clminus].multiplier = 1;
fragmentions[ms_Clminus].summary = "Cl+-1";

// initialize ion [M]+
fragmentions[ms_plus].nterminal = true;
fragmentions[ms_plus].cterminal = true;
Expand Down
1 change: 1 addition & 0 deletions CycloBranch/core/cFragmentIons.h
View file
Expand Up @@ -986,6 +986,7 @@ enum eFragmentIonType {
ms_3MFe4H,
ms_3M2Fe7H,
ms_NH4plus,
ms_Clminus,
ms_plus,
ms_minus,
ms_liplus,
Expand Down
210 changes: 198 additions & 12 deletions CycloBranch/core/cParameters.cpp
View file
Expand Up @@ -48,8 +48,11 @@ void cParameters::clear() {
reportunmatchedtheoreticalpeaks = false;
generateisotopepattern = false;
minimumpatternsize = 1;
minimumfeaturesize = 1;
allionsmustbepresent = false;
cyclicnterminus = false;
cycliccterminus = false;
internalfragments = false;
enablescrambling = false;
similaritysearch = false;
regularblocksorder = false;
Expand Down Expand Up @@ -746,10 +749,9 @@ int cParameters::checkAndPrepare(bool& terminatecomputation) {

// calculate combinations of neutral losses
if (!error) {
errtype = calculateNeutralLosses(terminatecomputation);
errtype = calculateNeutralLosses(terminatecomputation, errormessage);
if (errtype == -1) {
error = true;
errormessage = "Aborted by user.\n";
}
}

Expand All @@ -770,6 +772,64 @@ int cParameters::checkAndPrepare(bool& terminatecomputation) {
}


bool cParameters::checkModifications(cSequence& sequence, int& startmodifid, int& endmodifid, int& middlemodifid, string& errormessage) {
startmodifid = 0;
endmodifid = 0;
middlemodifid = 0;
errormessage = "";

if ((sequence.getPeptideType() == linear) || (sequence.getPeptideType() == branched) || (sequence.getPeptideType() == branchcyclic) || (sequence.getPeptideType() == linearpolyketide)) {

if ((sequence.getPeptideType() == linear) || (sequence.getPeptideType() == branched) || (sequence.getPeptideType() == linearpolyketide)) {
startmodifid = -1;
endmodifid = -1;
}

if ((sequence.getPeptideType() == branched) || (sequence.getPeptideType() == branchcyclic)) {
middlemodifid = -1;
}

for (int i = 0; i < (int)searchedmodifications.size(); i++) {

if ((sequence.getPeptideType() == linear) || (sequence.getPeptideType() == branched) || (sequence.getPeptideType() == linearpolyketide)) {
if (searchedmodifications[i].name.compare(sequence.getNTterminalModification()) == 0) {
startmodifid = i;
}

if (searchedmodifications[i].name.compare(sequence.getCTterminalModification()) == 0) {
endmodifid = i;
}
}

if ((sequence.getPeptideType() == branched) || (sequence.getPeptideType() == branchcyclic)) {
if (searchedmodifications[i].name.compare(sequence.getBranchModification()) == 0) {
middlemodifid = i;
}
}

}

if (startmodifid == -1) {
errormessage = "The N-terminal modification in the sequence " + sequence.getSequence() + " is not defined: " + sequence.getNTterminalModification();
return false;
}

if (endmodifid == -1) {
errormessage = "The C-terminal modification in the sequence " + sequence.getSequence() + " is not defined: " + sequence.getCTterminalModification();
return false;
}

if (middlemodifid == -1) {
errormessage = "The branch modification in the sequence " + sequence.getSequence() + " is not defined: " + sequence.getBranchModification();
return false;
}

}

return true;
}


string cParameters::printToString() {
string s = "";

Expand Down Expand Up @@ -840,9 +900,6 @@ string cParameters::printToString() {
s += "FWHM: " + to_string(fwhm) + "\n";
s += "Building Blocks Database File: " + bricksdatabasefilename + "\n";
s += "Maximum Number of Combined Blocks (start, middle, end): " + to_string(maximumbricksincombinationbegin) + ", " + to_string(maximumbricksincombinationmiddle) + ", " + to_string(maximumbricksincombinationend) + "\n";
s += "Maximum Cumulative Mass of Blocks: " + to_string(maximumcumulativemass) + "\n";

s += "N-/C-terminal Modifications File: " + modificationsfilename + "\n";

s += "Incomplete Paths in De Novo Graph: ";
switch (blindedges) {
Expand All @@ -860,20 +917,27 @@ string cParameters::printToString() {
}
s += "\n";

s += "Cyclic N-terminus: ";
s += cyclicnterminus ? "on" : "off";
s += "Maximum Cumulative Mass of Blocks: " + to_string(maximumcumulativemass) + "\n";
s += "N-/C-terminal Modifications File: " + modificationsfilename + "\n";

s += "Disable Precursor Mass Filter: ";
s += similaritysearch ? "on" : "off";
s += "\n";

s += "Cyclic C-terminus: ";
s += cycliccterminus ? "on" : "off";
s += "Internal Fragments: ";
s += internalfragments ? "on" : "off";
s += "\n";

s += "Enable Scrambling: ";
s += enablescrambling ? "on" : "off";
s += "\n";

s += "Disable Precursor Mass Filter: ";
s += similaritysearch ? "on" : "off";
s += "Cyclic N-terminus: ";
s += cyclicnterminus ? "on" : "off";
s += "\n";

s += "Cyclic C-terminus: ";
s += cycliccterminus ? "on" : "off";
s += "\n";

s += "Regular Order of Ketide Blocks: ";
Expand Down Expand Up @@ -942,6 +1006,12 @@ string cParameters::printToString() {

s += "Minimum Pattern Size: " + to_string(minimumpatternsize) + "\n";

s += "Minimum Feature Size: " + to_string(minimumfeaturesize) + "\n";

s += "All Ions Must be Annotated: ";
s += allionsmustbepresent ? "on" : "off";
s += "\n";

s += "Searched Sequence: " + originalsearchedsequence + "\n";
s += "N-terminal Modification: " + searchedsequenceNtermmodif + "\n";
s += "C-terminal Modification: " + searchedsequenceCtermmodif + "\n";
Expand All @@ -968,10 +1038,11 @@ void cParameters::updateFragmentDefinitions() {
}


int cParameters::calculateNeutralLosses(bool& terminatecomputation) {
int cParameters::calculateNeutralLosses(bool& terminatecomputation, string& errormessage) {
neutrallossesdefinitions.clear();
neutrallossesfortheoreticalspectra.clear();
numberofgeneratedneutrallosses = 0;
errormessage = "";

if (maximumcombinedlosses == 0) {
return 0;
Expand Down Expand Up @@ -1011,6 +1082,7 @@ int cParameters::calculateNeutralLosses(bool& terminatecomputation) {
tmpbrick.setComposition(to_string(numberofbasicbricks + 1), false);
tmpbrick.setMass(tmpformula.getMass());
tmpbrick.setSummary(originalneutrallossesdefinitions[originalneutrallossesfortheoreticalspectra[i]].summary);
tmpbrick.createSummaryMap();

neutrallossesbrickdatabase.push_back(tmpbrick);

Expand All @@ -1024,16 +1096,123 @@ int cParameters::calculateNeutralLosses(bool& terminatecomputation) {
combarray.push_back(0);
}

map<string, int> atoms;
map<int, int> counts;
vector<int> max_counts;
bool skipcombination;
bool bruteforce = false;

if (mode == singlecomparison) {

bruteforce = true;
for (i = 0; i < neutrallossesbrickdatabase.size(); i++) {
if (neutrallossesbrickdatabase[i].getSummaryMap().size() == 1) {
auto it = neutrallossesbrickdatabase[i].getSummaryMap().begin();
if (it->second != 1) {
bruteforce = false;
break;
}
}
else {
bruteforce = false;
break;
}
}

// calculate molecular formula of searched sequence
if (bruteforce) {

*os << "Brute force fragmentation enabled. Maximum numbers of elements: " << endl;

string upperboundsequence = searchedsequence;

if (!checkRegex(peptidetype, upperboundsequence, errormessage)) {
return -1;
}

if (!bricksdatabase.replaceAcronymsByIDs(upperboundsequence, errormessage)) {
return -1;
}

cSequence tmpsequence;
tmpsequence.setNTterminalModification(searchedsequenceNtermmodif);
tmpsequence.setCTterminalModification(searchedsequenceCtermmodif);
tmpsequence.setBranchModification(searchedsequenceTmodif);
tmpsequence.setPeptideType(peptidetype);

int startmodifid, endmodifid, middlemodifid;
if (!checkModifications(tmpsequence, startmodifid, endmodifid, middlemodifid, errormessage)) {
return -1;
}

int branchstart, branchend;
vector<string> v;
cCandidate c;
vector<nodeEdge> netmp;

parseBranch(peptidetype, upperboundsequence, v, branchstart, branchend);
// startmodifid, endmodifid and middlemodifid were filled up by checkModifications
c.setCandidate(v, netmp, fragmentIonTypeEnd, startmodifid, endmodifid, middlemodifid, branchstart, branchend);
cSummaryFormula formula = c.calculateSummaryFormula(*this, peptidetype, precursormass);

string formulastr = formula.getSummary();
addStringFormulaToMap(formulastr, atoms);

string tmpstr;
for (i = 0; i < neutrallossesbrickdatabase.size(); i++) {
tmpstr = neutrallossesbrickdatabase[i].getSummary();
if (atoms.count(tmpstr) == 1) {
max_counts.push_back(atoms[tmpstr]);
}
else {
max_counts.push_back(0);
}
*os << tmpstr << ": " << max_counts[i] << endl;
}

}

}

i = 0;
compressformulas = false;
while (neutrallossesbrickdatabase.nextCombination(combarray, numberofbasicbricks, maximumcombinedlosses, 0, uncharge(precursormass, precursorcharge) - minimummz)) {
if (terminatecomputation) {
neutrallossesdefinitions.clear();
neutrallossesfortheoreticalspectra.clear();
numberofgeneratedneutrallosses = 0;
errormessage = "Aborted by user.";
return -1;
}

if (bruteforce) {
counts.clear();
int cnt = 0;
for (int j = 0; j < maximumcombinedlosses; j++) {
if (combarray[j] == 0) {
break;
}
if (counts.count(combarray[j]) > 0) {
counts[combarray[j]]++;
}
else {
counts[combarray[j]] = 1;
}
}

skipcombination = false;
for (auto& it : counts) {
if (it.second > max_counts[it.first - 1]) {
skipcombination = true;
break;
}
}

if (skipcombination) {
continue;
}
}

getNameOfCompositionFromIntVector(compositionname, combarray);

tmpbrick.clear();
Expand Down Expand Up @@ -1143,6 +1322,7 @@ int cParameters::calculateNeutralLosses(bool& terminatecomputation) {
neutrallossesdefinitions.clear();
neutrallossesfortheoreticalspectra.clear();
numberofgeneratedneutrallosses = 0;
errormessage = "Aborted by user.";
return -1;
}
}
Expand Down Expand Up @@ -1207,8 +1387,11 @@ void cParameters::store(ofstream& os) {
os.write((char *)&reportunmatchedtheoreticalpeaks, sizeof(bool));
os.write((char *)&generateisotopepattern, sizeof(bool));
os.write((char *)&minimumpatternsize, sizeof(int));
os.write((char *)&minimumfeaturesize, sizeof(int));
os.write((char *)&allionsmustbepresent, sizeof(bool));
os.write((char *)&cyclicnterminus, sizeof(bool));
os.write((char *)&cycliccterminus, sizeof(bool));
os.write((char *)&internalfragments, sizeof(bool));
os.write((char *)&enablescrambling, sizeof(bool));
os.write((char *)&similaritysearch, sizeof(bool));
os.write((char *)&regularblocksorder, sizeof(bool));
Expand Down Expand Up @@ -1334,8 +1517,11 @@ void cParameters::load(ifstream& is) {
is.read((char *)&reportunmatchedtheoreticalpeaks, sizeof(bool));
is.read((char *)&generateisotopepattern, sizeof(bool));
is.read((char *)&minimumpatternsize, sizeof(int));
is.read((char *)&minimumfeaturesize, sizeof(int));
is.read((char *)&allionsmustbepresent, sizeof(bool));
is.read((char *)&cyclicnterminus, sizeof(bool));
is.read((char *)&cycliccterminus, sizeof(bool));
is.read((char *)&internalfragments, sizeof(bool));
is.read((char *)&enablescrambling, sizeof(bool));
is.read((char *)&similaritysearch, sizeof(bool));
is.read((char *)&regularblocksorder, sizeof(bool));
Expand Down

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