Merge branch 'steineggerlab:master' into master

steineggerlab · Nov 26, 2024 · 7a3a9db · 7a3a9db
2 parents b011b8e + 214886b
commit 7a3a9db
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Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/.github/workflows/mac-arm64.yml b/.github/workflows/mac-arm64.yml
@@ -8,16 +8,20 @@ on:
 
 jobs:
   build:
-    runs-on: [self-hosted, macOS, ARM64]
+    runs-on: macos-latest
     steps:
       - uses: actions/checkout@v3
         with:
           submodules: true
 
+      - name: Dependencies
+        run: |
+          brew install -f --overwrite cmake libomp rustup
+          rustup-init --profile minimal -q -y
+
       - name: Build
         run: |
           mkdir -p build
-          rustup update
           cd build
           LIBOMP=$(brew --prefix libomp)
           cmake \

diff --git a/src/FoldseekBase.cpp b/src/FoldseekBase.cpp
@@ -495,15 +495,15 @@ std::vector<DatabaseDownload> externalDownloads = {
         {
                 "BFVD",
                 "BFVD Big fantastic virus database (predicted viral protein structures based on the viral sequence representatives of the UniRef30 clusters",
-                "Kim R et al. BFVD - a large repository of predicted viral protein structures. bioRxiv, 2024.09.08.611582v1 (2024)",
+                "Kim R et al. BFVD - a large repository of predicted viral protein structures. Nucleic Acids Research, gkae1119 (2024)",
                 "https://bfvd.steineggerlab.workers.dev",
                 true, Parameters::DBTYPE_AMINO_ACIDS, structdatabases_sh, structdatabases_sh_len,
                 {}
         },
         {
                 "ProstT5",
                 "Protein language model to predict 3Di directly from sequence.",
-                "Heinzinger et al. Bilingual Language Model for Protein Sequence and Structure. bioRxiv, 2023.07.23.550085v2 (2024)",
+                "Heinzinger et al. Bilingual language model for protein sequence and structure. NAR Genomics and Bioinformatics, lqae150 (2024)",
                 "https://huggingface.co/Rostlab/ProstT5",
                 false, Parameters::DBTYPE_AMINO_ACIDS, structdatabases_sh, structdatabases_sh_len,
                 {}

diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
@@ -283,7 +283,7 @@ LocalParameters::LocalParameters() :
     filtInterfaceLddtThr = 0.0;
     citations.emplace(CITATION_FOLDSEEK, "van Kempen, M., Kim, S.S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C.L.M., Söding, J., and Steinegger, M. Fast and accurate protein structure search with Foldseek. Nature Biotechnology, doi:10.1038/s41587-023-01773-0 (2023)");
     citations.emplace(CITATION_FOLDSEEK_MULTIMER, "Kim, W., Mirdita, M., Levy Karin, E., Gilchrist, C.L.M., Schweke, H., Söding, J., Levy, E., and Steinegger, M. Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer. bioRxiv, doi:10.1101/2024.04.14.589414 (2024)");
-    citations.emplace(CITATION_PROSTT5, "Heinzinger, M., Weissenow, K., Gomez Sanchez, J., Henkel, A., Mirdita, M., Steinegger, M., Steinegger, M., and Burkhard, R. Bilingual Language Model for Protein Sequence and Structure. bioRxiv, doi:10.1101/2023.07.23.550085 (2024)");
+    citations.emplace(CITATION_PROSTT5, "Heinzinger, M., Weissenow, K., Gomez Sanchez, J., Henkel, A., Mirdita, M., Steinegger, M., and Burkhard, R. Bilingual Language Model for Protein Sequence and Structure. NAR Genomics and Bioinformatics, doi:10.1093/nargab/lqae150 (2024)");
 
     //rewrite param vals.
     PARAM_FORMAT_OUTPUT.description = "Choose comma separated list of output columns from: query,target,evalue,gapopen,pident,fident,nident,qstart,qend,qlen\ntstart,tend,tlen,alnlen,raw,bits,cigar,qseq,tseq,qheader,theader,qaln,taln,mismatch,qcov,tcov\nqset,qsetid,tset,tsetid,taxid,taxname,taxlineage,\nlddt,lddtfull,qca,tca,t,u,qtmscore,ttmscore,alntmscore,rmsd,prob\ncomplexqtmscore,complexttmscore,complexu,complext,complexassignid\n";

diff --git a/src/strucclustutils/MultimerUtil.h b/src/strucclustutils/MultimerUtil.h
@@ -216,8 +216,8 @@ static ComplexDataHandler parseScoreComplexResult(const char *data, Matcher::res
     float qCov = SmithWaterman::computeCov(qStartPos==-1 ? 0 : qStartPos, qEndPos, qLen);
     float dbCov = SmithWaterman::computeCov(dbStartPos==-1 ? 0 : dbStartPos, dbEndPos, dbLen);
     size_t alnLength = Matcher::computeAlnLength(qStartPos==-1 ? 0 : qStartPos, qEndPos, dbStartPos==-1 ? 0 : dbStartPos, dbEndPos);
-    double qTmScore = std::stod(entry[11]);
-    double tTmScore = std::stod(entry[12]);
+    double qTmScore = strtod(entry[11], NULL);
+    double tTmScore = strtod(entry[12], NULL);
     std::string uString = std::string(entry[13], entry[14] - entry[13]-1);
     std::string tString = std::string(entry[14], entry[15] - entry[14]-1);
     auto assId = Util::fast_atoi<unsigned int>(entry[15]);