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update examplex of foldseek multimer
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| Original file line number | Diff line number | Diff line change |
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@@ -260,9 +260,9 @@ std::vector<Command> foldseekCommands = { | |
| {"scoremultimer", scoremultimer, &localPar.scoremultimer, COMMAND_ALIGNMENT, | ||
| "Get complex level alignments from alignmentDB", | ||
| "# Get complex level alignments (chain assignments and tm-scores) from alignmentDB.\n" | ||
| "foldseek scorecomplex queryDB targetDB alignmentDB complexDB\n" | ||
| "foldseek scoremultimer queryDB targetDB alignmentDB complexDB\n" | ||
| "# simple tsv output format" | ||
| "foldseek createcomplexreport queryDB targetDB complexDB result.tsv" | ||
| "foldseek createmultimerreport queryDB targetDB complexDB result.tsv" | ||
| "# output files with convertalis" | ||
| "foldseek convertalis queryDB targetDB complexDB result.m8\n\n", | ||
| "Woosub Kim <[email protected]>", | ||
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@@ -280,13 +280,13 @@ std::vector<Command> foldseekCommands = { | |
| {"multimersearch", multimersearch, &localPar.multimersearchworkflow, COMMAND_MAIN, | ||
| "Complex level search", | ||
| "# Search a single/multiple PDB file against a set of PDB files and get complex level alignments\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp\n" | ||
| "foldseek multimersearch queryDB targetDB result tmp\n" | ||
| "# Format output differently\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp --format-output query,target,qstart,tstart,cigar\n" | ||
| "foldseek multimersearch queryDB targetDB result tmp --format-output query,target,qstart,tstart,cigar\n" | ||
| "# Align with TMalign (global)\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp --alignment-type 1\n" | ||
| "foldseek multimersearch queryDB targetDB result tmp --alignment-type 1\n" | ||
| "# Skip prefilter and perform an exhaustive alignment (slower but more sensitive)\n" | ||
| "foldseek complexsearch queryDB targetDB result tmp --exhaustive-search 1\n\n", | ||
| "foldseek multimersearch queryDB targetDB result tmp --exhaustive-search 1\n\n", | ||
| "Woosub Kim <[email protected]>", | ||
| "<i:queryDB> <i:targetDB> <o:alignmentDB> <tmpDir>", | ||
| CITATION_FOLDSEEK_MULTIMER, { | ||
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@@ -302,13 +302,13 @@ std::vector<Command> foldseekCommands = { | |
| {"easy-multimersearch", easymultimersearch, &localPar.easymultimersearchworkflow, COMMAND_EASY, | ||
| "Complex level search", | ||
| "# Search a single/multiple PDB file against a set of PDB files and get complex level alignments\n" | ||
| "foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp\n" | ||
| "foldseek easy-multimersearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp\n" | ||
| "# Format output differently\n" | ||
| "foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --format-output query,target,qstart,tstart,cigar\n" | ||
| "foldseek easy-multimersearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --format-output query,target,qstart,tstart,cigar\n" | ||
| "# Align with TMalign (global)\n" | ||
| "foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --alignment-type 1\n" | ||
| "foldseek easy-multimersearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --alignment-type 1\n" | ||
| "# Skip prefilter and perform an exhaustive alignment (slower but more sensitive)\n" | ||
| "foldseek easy-complexsearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --exhaustive-search 1\n\n", | ||
| "foldseek easy-multimersearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --exhaustive-search 1\n\n", | ||
| "Woosub Kim <[email protected]>", | ||
| "<i:PDB|mmCIF[.gz]> ... <i:PDB|mmCIF[.gz]>|<i:stdin> <i:targetFastaFile[.gz]>|<i:targetDB> <o:outputFileName> <tmpDir>", | ||
| CITATION_FOLDSEEK_MULTIMER, { | ||
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@@ -329,7 +329,7 @@ std::vector<Command> foldseekCommands = { | |
| "# (5,6) tm score based on query and target residue length,\n" | ||
| "# (8,9) u and t,\n" | ||
| "# (9) assignment id\n" | ||
| "foldseek createcomplexreport queryDB targetDB complexDB result.tsv\n", | ||
| "foldseek createmultimerreport queryDB targetDB complexDB result.tsv\n", | ||
| "Woosub Kim <[email protected]>", | ||
| "<i:queryDb> <i:targetDb> <i:complexDB> <o:complexFile>", | ||
| CITATION_FOLDSEEK_MULTIMER, { | ||
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