Fix warning

data/structurecluster.sh

@@ -46,7 +46,6 @@ buildMergedDb() {
 [ "$#" -ne 3 ] && echo "Please provide <sequenceDB> <outDB> <tmp>" && exit 1;
 # check if files exist
 [ ! -f "$1.dbtype" ] && echo "$1.dbtype not found!" && exit 1;
-[   -f "$2.dbtype" ] && echo "$2.dbtype exists already!" && exit 1;
 [ ! -d "$3" ] && echo "tmp directory $3 not found!" && mkdir -p "$3";
 
 INPUT="$1"

lib/mmseqs/src/prefiltering/QueryMatcher.cpp

@@ -319,6 +319,14 @@ size_t QueryMatcher::match(Sequence *seq, float *compositionBias) {
     outer:
     indexPointer[indexTo + 1] = databaseHits + numMatches;
     // fill the output
+    if((foundDiagonalsSize - overflowHitCount) < 0.1 * foundDiagonalsSize){
+        foundDiagonalsSize *= 1.5;
+        foundDiagonals = (CounterResult*) realloc(foundDiagonals, foundDiagonalsSize * sizeof(CounterResult));
+        if(foundDiagonals == NULL){
+            Debug(Debug::ERROR) << "Out of memory in QueryMatcher::match\n";
+            EXIT(EXIT_FAILURE);
+        }
+    }
     size_t hitCount = findDuplicates(indexPointer, foundDiagonals + overflowHitCount,
                                      foundDiagonalsSize - overflowHitCount, indexStart, indexTo, (diagonalScoring == false));
     if (overflowHitCount != 0) {

src/commons/TMaligner.cpp

@@ -26,6 +26,7 @@ TMaligner::TMaligner(unsigned int maxSeqLen, bool tmAlignFast, bool tmScoreOnly)
     querySecStruc  = new char[maxSeqLen];
     targetSecStruc = new char[maxSeqLen];
     invmap = new int[maxSeqLen];
+    allocatedLength = maxSeqLen;
 }
 
 TMaligner::~TMaligner(){
@@ -64,7 +65,7 @@ TMaligner::TMscoreResult TMaligner::computeTMscore(float *x, float *y, float *z,
             tPos++;
         }
     }
-
+    std::cout << targetLen << std::endl;
     memcpy(target_x, x, sizeof(float) * targetLen);
     memcpy(target_y, y, sizeof(float) * targetLen);
     memcpy(target_z, z, sizeof(float) * targetLen);
@@ -101,6 +102,7 @@ TMaligner::TMscoreResult TMaligner::computeTMscore(float *x, float *y, float *z,
 }
 
 void TMaligner::initQuery(float *x, float *y, float *z, char * querySeq, unsigned int queryLen){
+    // reallocate memory if necessary
     memset(querySecStruc, 0, sizeof(char) * queryLen);
     memcpy(query_x, x, sizeof(float) * queryLen);
     memcpy(query_y, y, sizeof(float) * queryLen);
@@ -112,7 +114,6 @@ void TMaligner::initQuery(float *x, float *y, float *z, char * querySeq, unsigne
     queryCaCords.y = query_y;
     queryCaCords.z = query_z;
     make_sec(queryCaCords, queryLen, querySecStruc); // secondary structure assignment
-
 }
 
 Matcher::result_t TMaligner::align(unsigned int dbKey, float *x, float *y, float *z, char * targetSeq, unsigned int targetLen, float &TM1){

src/commons/TMaligner.h

@@ -60,6 +60,7 @@ class TMaligner{
     bool tmAlignFast;
     Coordinates xtm, ytm, xt, r1, r2;
     int * invmap;
+    size_t allocatedLength;
 };
 
 #endif //FOLDSEEK_TMALIGNER_H

src/strucclustutils/createcomplexreport.cpp

@@ -65,7 +65,11 @@ int createcomplexreport(int argc, const char **argv, const Command &command) {
     IndexReader qDbr(par.db1, par.threads,  IndexReader::SRC_SEQUENCES, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0, dbaccessMode);
     IndexReader qDbrHeader(par.db1, par.threads, IndexReader::SRC_HEADERS , (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0);
     IndexReader *tDbrHeader;
-    tDbrHeader = sameDB ? &qDbrHeader : tDbrHeader = new IndexReader(par.db2, par.threads, IndexReader::SRC_HEADERS, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0);
+    if(sameDB){
+        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);
 

src/strucclustutils/scorecomplex.cpp

@@ -558,26 +558,34 @@ class ComplexScorer {
             unsigned int qKey = alnDbr.getId(qChainKey);
             if (qKey == NOT_AVAILABLE_CHAIN_KEY)
                 continue;
+
             char *data = alnDbr.getData(qKey, thread_idx);
             if (*data == '\0') continue;
-            Matcher::result_t qAlnResult = Matcher::parseAlignmentRecord(data);
             size_t qId = qCaDbr->sequenceReader->getId(qChainKey);
+            unsigned int qLen = q3diDbr->sequenceReader->getSeqLen(qId);
             char *qCaData = qCaDbr->sequenceReader->getData(qId, thread_idx);
             size_t qCaLength = qCaDbr->sequenceReader->getEntryLen(qId);
-            float *queryCaData = qCoords.read(qCaData, qAlnResult.qLen, qCaLength);
+            float *queryCaData = qCoords.read(qCaData, qLen, qCaLength);
             Chain qChain = Chain(qComplexId, qChainKey);
-            tmAligner->initQuery(queryCaData, &queryCaData[qAlnResult.qLen], &queryCaData[qAlnResult.qLen * 2], NULL, qAlnResult.qLen);
+            tmAligner->initQuery(queryCaData, &queryCaData[qLen], &queryCaData[qLen * 2], NULL, qLen);
             while (*data != '\0') {
-                char dbKeyBuffer[255 + 1];
-                Util::parseKey(data, dbKeyBuffer);
-                const auto dbKey = (unsigned int) strtoul(dbKeyBuffer, NULL, 10);
-                const unsigned int dbComplexId = dbChainKeyToComplexIdLookup.at(dbKey);
                 Matcher::result_t alnResult = Matcher::parseAlignmentRecord(data);
-                size_t tCaId = tCaDbr->sequenceReader->getId(dbKey);
+                const unsigned int dbComplexId = dbChainKeyToComplexIdLookup.at(alnResult.dbKey);
+                size_t tCaId = tCaDbr->sequenceReader->getId(alnResult.dbKey);
                 char *tCaData = tCaDbr->sequenceReader->getData(tCaId, thread_idx);
                 size_t tCaLength = tCaDbr->sequenceReader->getEntryLen(tCaId);
                 float *targetCaData = tCoords.read(tCaData, alnResult.dbLen, tCaLength);
-                Chain dbChain = Chain(dbComplexId, dbKey);
+                Chain dbChain = Chain(dbComplexId, alnResult.dbKey);
+                if(qChainKey == 49 && alnResult.dbKey == 685) {
+                    for(unsigned int i = 0; i < alnResult.qLen; i++) {
+                        std::cout << queryCaData[i] << " " << queryCaData[alnResult.qLen + i] << " " << queryCaData[alnResult.qLen + alnResult.qLen + i] << std::endl;
+                    }
+                    std::cout << std::endl;
+                    for(unsigned int i = 0; i < alnResult.dbLen; i++) {
+                        std::cout << targetCaData[i] << " " << targetCaData[alnResult.dbLen + i] << " " << targetCaData[alnResult.dbLen + alnResult.dbLen + i] << std::endl;
+                    }
+                    std::cout << std::endl;
+                }
                 TMaligner::TMscoreResult tmResult = tmAligner->computeTMscore(targetCaData, &targetCaData[alnResult.dbLen], &targetCaData[alnResult.dbLen + alnResult.dbLen], alnResult.dbLen, alnResult.qStartPos, alnResult.dbStartPos, Matcher::uncompressAlignment(alnResult.backtrace), alnResult.alnLength);
                 ChainToChainAln chainAln(qChain, dbChain, queryCaData, targetCaData, alnResult, tmResult);
                 parsedAlns.emplace_back(chainAln);
@@ -772,7 +780,6 @@ int scorecomplex(int argc, const char **argv, const Command &command) {
         // for each q complex
         for (size_t queryIdx = 0; queryIdx < complexScorer.qComplexIdVec.size(); queryIdx++) {
             progress.updateProgress();
-
             unsigned int qComplexId = complexScorer.qComplexIdVec[queryIdx];
             std::vector<unsigned int> qChainKeys = complexScorer.getQueryChainKeys(qComplexId);
             std::vector<Complex> qComplexes = complexScorer.getQComplexes(qComplexId, qChainKeys);