From d60563224ad2cf976af580cc48b1568bd35b4716 Mon Sep 17 00:00:00 2001 From: Martin Steinegger Date: Thu, 7 Nov 2024 14:36:48 +0100 Subject: [PATCH 1/4] Fix convertalis for FS multimer --- src/strucclustutils/MultimerUtil.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/strucclustutils/MultimerUtil.h b/src/strucclustutils/MultimerUtil.h index dea547b5..eba164e8 100644 --- 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(entry[15]); From 8485aaf93ace5202a7a6580eea6b1d9fb42301b9 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Sat, 23 Nov 2024 20:29:01 +0900 Subject: [PATCH 2/4] Switch mac arm test to github hosted runner --- .github/workflows/mac-arm64.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/mac-arm64.yml b/.github/workflows/mac-arm64.yml index 4c02e260..2c9b9c3a 100644 --- a/.github/workflows/mac-arm64.yml +++ b/.github/workflows/mac-arm64.yml @@ -8,12 +8,16 @@ 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 cmake libomp rust + - name: Build run: | mkdir -p build From d295eec6ba4c3ab26ef2f7ab8847d58f8373833c Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Sat, 23 Nov 2024 20:56:17 +0900 Subject: [PATCH 3/4] Replace rust with rustup in github CI --- .github/workflows/mac-arm64.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mac-arm64.yml b/.github/workflows/mac-arm64.yml index 2c9b9c3a..38e9ee39 100644 --- a/.github/workflows/mac-arm64.yml +++ b/.github/workflows/mac-arm64.yml @@ -16,12 +16,12 @@ jobs: - name: Dependencies run: | - brew install -f cmake libomp rust + 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 \ From 214886bb3e5742348ff5bb325b6a5dd7420d12ce Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Sun, 24 Nov 2024 13:07:48 +0900 Subject: [PATCH 4/4] Update citations --- src/FoldseekBase.cpp | 4 ++-- src/commons/LocalParameters.cpp | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/FoldseekBase.cpp b/src/FoldseekBase.cpp index 2e356641..7621ad66 100644 --- a/src/FoldseekBase.cpp +++ b/src/FoldseekBase.cpp @@ -495,7 +495,7 @@ std::vector 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, {} @@ -503,7 +503,7 @@ std::vector externalDownloads = { { "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 index 16dd72c4..645ae0b2 100644 --- 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";