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fix a bug related createcomplexreport: failure for multi-queries is s…
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…olved
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@Woosub-Kim
Woosub-Kim committed Aug 12, 2023
1 parent aae423b commit 71f07e7
Showing 1 changed file with 38 additions and 25 deletions.
63 changes: 38 additions & 25 deletions src/strucclustutils/createcomplexreport.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,16 @@
#include "LDDT.h"
#include "CalcProbTP.h"
#include <map>
#include <map>

#ifdef OPENMP
#include <omp.h>
#endif

void getComplexNameChainName(std::string & chainName, std::pair<std::string, std::string> &compAndChainName) {
typedef std::pair<std::string, std::string> compNameChainName_t;
typedef std::pair<unsigned int, std::string> ComplexAlignmentKey_t;

void getComplexNameChainName(std::string &chainName, compNameChainName_t &compAndChainName) {
size_t pos = chainName.rfind('_');
std::string comp = chainName.substr(0, pos);
std::string chain = chainName.substr(pos + 1);
Expand All @@ -34,7 +38,7 @@ void getResult (std::vector<std::string> &qChainVector, std::vector<std::string>
std::string tComplexName;
std::string qChainString;
std::string tChainString;
std::pair<std::string, std::string> compAndChainName;
compNameChainName_t compAndChainName;
getComplexNameChainName(qChainVector[0], compAndChainName);
qComplexName = compAndChainName.first;
qChainString = compAndChainName.second;
Expand All @@ -54,6 +58,19 @@ void getResult (std::vector<std::string> &qChainVector, std::vector<std::string>
complexResVec.emplace_back(ComplexResult(assId, result));
}

struct ComplexAlignment {
ComplexAlignment(){};
ComplexAlignment(std::string qChain, std::string tChain, double qTMscore, double tTMscore) : qTMScore(qTMscore),tTMScore(tTMscore){
qChainVector = {qChain};
tChainVector = {tChain};
};
std::vector<std::string> qChainVector;
std::vector<std::string> tChainVector;
double qTMScore;
double tTMScore;
};


int createcomplexreport(int argc, const char **argv, const Command &command) {
LocalParameters &par = LocalParameters::getLocalInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
Expand All @@ -69,8 +86,8 @@ int createcomplexreport(int argc, const char **argv, const Command &command) {
tDbrHeader = &qDbrHeader;
} else{
tDbrHeader = new IndexReader(par.db2, par.threads, IndexReader::SRC_HEADERS, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0);
}
}

DBReader<unsigned int> alnDbr(par.db3.c_str(), par.db3Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA);
alnDbr.open(DBReader<unsigned int>::LINEAR_ACCCESS);

Expand All @@ -87,13 +104,9 @@ int createcomplexreport(int argc, const char **argv, const Command &command) {
TranslateNucl translateNucl(static_cast<TranslateNucl::GenCode>(par.translationTable));
Debug::Progress progress(alnDbr.getSize());
std::vector<ComplexResult> complexResVec;
unsigned int prevAssId;
std::vector<std::string> qChainVector;
std::vector<std::string> tChainVector;
std::vector<std::string> tVec;
std::vector<std::string> uVec;
double qTMScore;
double tTMScore;
Matcher::result_t res;
auto complexDataHandler = ComplexDataHandler();
std::map<ComplexAlignmentKey_t, ComplexAlignment> complexAlignmentsWithAssId;

#pragma omp parallel num_threads(localThreads)
{
Expand All @@ -107,10 +120,10 @@ int createcomplexreport(int argc, const char **argv, const Command &command) {
const unsigned int queryKey = alnDbr.getDbKey(i);
size_t qHeaderId = qDbrHeader.sequenceReader->getId(queryKey);
const char *qHeader = qDbrHeader.sequenceReader->getData(qHeaderId, thread_idx);
compNameChainName_t qCompAndChainName;
std::string queryId = Util::parseFastaHeader(qHeader);
getComplexNameChainName(queryId, qCompAndChainName);
char *data = alnDbr.getData(i, thread_idx);
Matcher::result_t res;
auto complexDataHandler = ComplexDataHandler();
while (*data != '\0') {
bool isValid = parseScoreComplexResult(data, res, complexDataHandler);
if (!isValid) {
Expand All @@ -120,21 +133,21 @@ int createcomplexreport(int argc, const char **argv, const Command &command) {
size_t tHeaderId = tDbrHeader->sequenceReader->getId(res.dbKey);
const char *tHeader = tDbrHeader->sequenceReader->getData(tHeaderId, thread_idx);
std::string targetId = Util::parseFastaHeader(tHeader);
unsigned int currAssId = complexDataHandler.assId;
if (!qChainVector.empty() && !tChainVector.empty() && currAssId != prevAssId) {
getResult(qChainVector, tChainVector, complexResVec, qTMScore, tTMScore, prevAssId);
qChainVector.clear();
tChainVector.clear();
unsigned int assId = complexDataHandler.assId;
auto key = ComplexAlignmentKey_t(assId, qCompAndChainName.first);
if (complexAlignmentsWithAssId.find(key) == complexAlignmentsWithAssId.end()){
complexAlignmentsWithAssId.insert({key, ComplexAlignment(queryId, targetId, complexDataHandler.qTmScore, complexDataHandler.tTmScore)});
} else {
complexAlignmentsWithAssId[key].qChainVector.emplace_back(queryId);
complexAlignmentsWithAssId[key].tChainVector.emplace_back(targetId);
}
prevAssId = currAssId;
qTMScore = complexDataHandler.qTmScore;
tTMScore = complexDataHandler.tTmScore;
qChainVector.emplace_back(queryId);
tChainVector.emplace_back(targetId);
} // while end
} // for end
}
getResult(qChainVector, tChainVector, complexResVec, qTMScore, tTMScore, prevAssId);
std::map<ComplexAlignmentKey_t, ComplexAlignment>::iterator iter;
for (iter = complexAlignmentsWithAssId.begin(); iter != complexAlignmentsWithAssId.end(); iter++) {
getResult(iter->second.qChainVector, iter->second.tChainVector, complexResVec, iter->second.qTMScore, iter->second.tTMScore, iter->first.first);
}
SORT_SERIAL(complexResVec.begin(), complexResVec.end(), compareComplexResult);
for (size_t i=0; i < complexResVec.size(); i++) {
resultWriter.writeData(complexResVec[i].result.c_str(), complexResVec[i].result.length(), 0, localThreads - 1, false, false);
Expand All @@ -148,4 +161,4 @@ int createcomplexreport(int argc, const char **argv, const Command &command) {
delete tDbrHeader;
}
return EXIT_SUCCESS;
}
}

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