Fix issue #312

alntmscore is now normalized by the backtrace length
steineggerlab · Aug 29, 2024 · b40729c · b40729c
1 parent 69d397b
commit b40729c
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Showing 4 changed files with 18 additions and 17 deletions.
diff --git a/src/strucclustutils/aln2tmscore.cpp b/src/strucclustutils/aln2tmscore.cpp
@@ -101,10 +101,11 @@ int aln2tmscore(int argc, const char **argv, const Command& command) {
                 float* tdata = tcoords.read(tcadata, targetLen, tCaLength);
 
                 // Matching residue index collection
+                unsigned int normLen = std::min(res.dbLen, res.qLen);
                 TMaligner::TMscoreResult tmres = tmaln.computeTMscore(tdata, &tdata[targetLen], &tdata[targetLen + targetLen], targetLen,
-                                                                      res.qStartPos, res.dbStartPos, res.backtrace,
-                                                                      std::min(static_cast<unsigned int>(res.backtrace.length()), std::min(res.dbLen, res.qLen)));
-
+                                                                      res.qStartPos, res.dbStartPos, res.backtrace, normLen);
+                tmres.tmscore = (tmres.tmscore / static_cast<double>(normLen))
+                                * static_cast<double>(res.backtrace.size());
                 //std::cout << TMalnScore << std::endl;
                 resultsStr.append(SSTR(dbKey));
                 resultsStr.push_back(' ');

diff --git a/src/strucclustutils/structurealign.cpp b/src/strucclustutils/structurealign.cpp
@@ -380,6 +380,7 @@ int structurealign(int argc, const char **argv, const Command& command) {
                             size_t tCaLength = tcadbr->sequenceReader->getEntryLen(tId);
                             float* targetCaData = tcoords.read(tcadata, res.dbLen, tCaLength);
                             if(needTMaligner) {
+                                unsigned int normLen = std::min(res.dbLen, res.qLen);
                                 tmres = tmaligner->computeTMscore(targetCaData,
                                                                   &targetCaData[res.dbLen],
                                                                   &targetCaData[res.dbLen +
@@ -388,7 +389,9 @@ int structurealign(int argc, const char **argv, const Command& command) {
                                                                   res.qStartPos,
                                                                   res.dbStartPos,
                                                                   res.backtrace,
-                                                                  std::min(static_cast<unsigned int>(res.backtrace.size()), std::min(res.dbLen, res.qLen)));
+                                                                  normLen);
+                                tmres.tmscore = (tmres.tmscore / static_cast<double>(normLen))
+                                                    * static_cast<double>(res.backtrace.size());
                                 if (tmres.tmscore < par.tmScoreThr) {
                                     continue;
                                 }

diff --git a/src/strucclustutils/structureconvertalis.cpp b/src/strucclustutils/structureconvertalis.cpp
@@ -653,12 +653,12 @@ R"html(<!DOCTYPE html>
                 }
                 if(needTMaligner){
                     tmaligner->initQuery(queryCaData, &queryCaData[res.qLen], &queryCaData[res.qLen+res.qLen], NULL, res.qLen);
+                    unsigned int normlen= std::min(res.qLen, res.dbLen);
                     tmpBt = Matcher::uncompressAlignment(res.backtrace);
                     tmres = tmaligner->computeTMscore(targetCaData, &targetCaData[res.dbLen], &targetCaData[res.dbLen+res.dbLen], res.dbLen,
-                                                      res.qStartPos, res.dbStartPos, tmpBt,
-                                                      std::min(std::min(res.dbLen, res.qLen), static_cast<unsigned int>(tmpBt.size())));
+                                                      res.qStartPos, res.dbStartPos, tmpBt,normlen);
+                    tmres.tmscore = tmres.tmscore / normlen;
                     rmsd = tmres.rmsd;
-
                 }
                 LDDTCalculator::LDDTScoreResult lddtres;
                 if(needLDDT) {
@@ -885,19 +885,13 @@ R"html(<!DOCTYPE html>
                                         result.append(SSTR(tmres.t[2]));
                                         break;
                                     case LocalParameters::OUTFMT_ALNTMSCORE:
-                                        result.append(SSTR(tmres.tmscore));
+                                        result.append(SSTR(tmres.tmscore * tmpBt.size()));
                                         break;
                                     case LocalParameters::OUTFMT_QTMSCORE:
-                                        tmres = tmaligner->computeTMscore(targetCaData, &targetCaData[res.dbLen], &targetCaData[res.dbLen+res.dbLen], res.dbLen,
-                                                                          res.qStartPos, res.dbStartPos, Matcher::uncompressAlignment(res.backtrace),
-                                                                          res.qLen);
-                                        result.append(SSTR(tmres.tmscore));
+                                        result.append(SSTR(tmres.tmscore * res.qLen));
                                         break;
                                     case LocalParameters::OUTFMT_TTMSCORE:
-                                        tmres = tmaligner->computeTMscore(targetCaData, &targetCaData[res.dbLen], &targetCaData[res.dbLen+res.dbLen], res.dbLen,
-                                                                          res.qStartPos, res.dbStartPos, Matcher::uncompressAlignment(res.backtrace),
-                                                                          res.dbLen);
-                                        result.append(SSTR(tmres.tmscore));
+                                        result.append(SSTR(tmres.tmscore * res.dbLen));
                                         break;
                                     case LocalParameters::OUTFMT_RMSD:
                                         result.append(SSTR(rmsd));

diff --git a/src/strucclustutils/structurerescorediagonal.cpp b/src/strucclustutils/structurerescorediagonal.cpp
@@ -342,9 +342,12 @@ int structureungappedalign(int argc, const char **argv, const Command& command)
                         char *tcadata = tcadbr->sequenceReader->getData(tId, thread_idx);
                         size_t tCaLength = tcadbr->sequenceReader->getEntryLen(tId);
                         float* targetCaData = tcoords.read(tcadata, res.dbLen, tCaLength);
+                        unsigned int normLen = std::min(res.dbLen, res.qLen);
                         TMaligner::TMscoreResult tmres = tmaligner->computeTMscore(targetCaData, &targetCaData[res.dbLen], &targetCaData[res.dbLen+res.dbLen], res.dbLen,
                                                                                    res.qStartPos, res.dbStartPos, Matcher::uncompressAlignment(res.backtrace),
-                                                                                   std::min(static_cast<unsigned int>(res.backtrace.length()), std::min(res.dbLen, res.qLen)));
+                                                                                   normLen);
+                        tmres.tmscore = (tmres.tmscore / static_cast<double>(normLen))
+                                        * static_cast<double>(res.backtrace.size());
                         if(tmres.tmscore < par.tmScoreThr){
                             continue;
                         }