FoldseekBase.cpp update (#306)

* explanation complex -> multimer

* explanation complex -> multimer

src/FoldseekBase.cpp

@@ -258,8 +258,8 @@ std::vector<Command> foldseekCommands = {
                 CITATION_FOLDSEEK, {{"Db", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA|DbType::NEED_HEADER, &DbValidator::sequenceDb },
                                            {"pdbFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}}},
         {"scoremultimer", scoremultimer, &localPar.scoremultimer, COMMAND_ALIGNMENT,
-                "Get complex level alignments from alignmentDB",
-                "# Get complex level alignments (chain assignments and tm-scores) from alignmentDB.\n"
+                "Get multimer level alignments from alignmentDB",
+                "# Get multimer level alignments (chain assignments and tm-scores) from alignmentDB.\n"
                 "foldseek scoremultimer queryDB targetDB alignmentDB complexDB\n"
                 "# simple tsv output format"
                 "foldseek createmultimerreport queryDB targetDB complexDB result.tsv"
@@ -278,8 +278,8 @@ std::vector<Command> foldseekCommands = {
                 "", NULL, "", "", CITATION_FOLDSEEK_MULTIMER, {{"",DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, NULL}}
         },
         {"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"
+                "Multimer level search",
+                "# Search a single/multiple PDB file against a set of PDB files and get multimer level alignments\n"
                 "foldseek multimersearch queryDB targetDB result tmp\n"
                 "# Format output differently\n"
                 "foldseek multimersearch queryDB targetDB result tmp --format-output query,target,qstart,tstart,cigar\n"
@@ -300,8 +300,8 @@ std::vector<Command> foldseekCommands = {
                 "", NULL, "", "", CITATION_FOLDSEEK_MULTIMER, {{"",DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, NULL}}
         },
         {"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"
+                "Multimer level search",
+                "# Search a single/multiple PDB file against a set of PDB files and get multimer level alignments\n"
                 "foldseek easy-multimersearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp\n"
                 "# Format output differently\n"
                 "foldseek easy-multimersearch example/1tim.pdb.gz example/8tim.pdb.gz result tmp --format-output query,target,qstart,tstart,cigar\n"
@@ -324,8 +324,8 @@ std::vector<Command> foldseekCommands = {
         {"createmultimerreport", createmultimerreport, &localPar.createmultimerreport, COMMAND_FORMAT_CONVERSION,
                 "Convert complexDB to tsv format",
                 "# Create output in tsv format (9 columns):  qComplexName.c_str(), tComplexName.c_str(), qChainString.c_str(), tChainString.c_str(), qTMScore, tTMScore, u, t, assId\n"
-                "#  (1,2) identifiers for query and target complex,\n"
-                "#  (3,4) chains of query complex and target complex,\n"
+                "#  (1,2) identifiers for query and target multimers,\n"
+                "#  (3,4) chains of query multimer and target multimer,\n"
                 "#  (5,6) tm score based on query and target residue length,\n"
                 "#  (8,9) u and t,\n"
                 "#  (9) assignment id\n"
@@ -343,7 +343,7 @@ std::vector<Command> foldseekCommands = {
                 "", NULL, "", "", CITATION_FOLDSEEK_MULTIMER, {{"",DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, NULL}}
         },
         {"expandmultimer", expandmultimer, &localPar.expandmultimer, COMMAND_PREFILTER,
-                "Re-prefilter to ensure complete alignment between complexes",
+                "Re-prefilter to ensure complete alignment between multimers",
                 NULL,
                 "Woosub Kim <[email protected]>",
                 "<i:queryDB> <i:targetDB> <i:alignmentDB> <o:prefilterDB>",