fix explanation of complex related tools

steineggerlab · Dec 26, 2023 · 592ffa8 · 592ffa8
1 parent a6a712c
commit 592ffa8
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 10 deletions.
diff --git a/src/FoldseekBase.cpp b/src/FoldseekBase.cpp
@@ -268,7 +268,7 @@ std::vector<Command> foldseekCommands = {
                 "# 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"
                 "# Format output differently\n"
-                "foldseek easy-complexsearch queryDB targetDB result tmp --format-output query,target,qstart,tstart,cigar\n"
+                "foldseek complexsearch 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"
                 "# Skip prefilter and perform an exhaustive alignment (slower but more sensitive)\n"
@@ -302,7 +302,7 @@ std::vector<Command> foldseekCommands = {
                                    }
         },
         {"createcomplexreport", createcomplexreport, &localPar.createcomplexreport, COMMAND_FORMAT_CONVERSION,
-                "Convert complex DB to tsv format\"",
+                "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"
@@ -319,8 +319,8 @@ std::vector<Command> foldseekCommands = {
                                            {"complexFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}
                                    }
         },
-        {"expandcomplex", expandcomplex, &localPar.expandcomplex, COMMAND_ALIGNMENT,
-        "expand complex",
+        {"expandcomplex", expandcomplex, &localPar.expandcomplex, COMMAND_PREFILTER,
+        "Re-prefilter to ensure complete alignment between complexes",
         NULL,
         "Woosub Kim <[email protected]>",
         "<i:queryDB> <i:targetDB> <i:alignmentDB> <o:prefilterDB>",

diff --git a/src/strucclustutils/scorecomplex.cpp b/src/strucclustutils/scorecomplex.cpp
@@ -342,15 +342,12 @@ class DBSCANCluster {
             }
         }
 
-//        if (maxClusterSize == idealClusterSize) {
-//            bestClusters = currClusters;
-//            prevMaxClusterSize = maxClusterSize;
-//            return finishDBSCAN();
-//        } else
         if (maxClusterSize < prevMaxClusterSize)
             return finishDBSCAN();
-        else if (maxClusterSize == prevMaxClusterSize && currClusters.size() < bestClusters.size())
+
+        if (maxClusterSize == prevMaxClusterSize && currClusters.size() < bestClusters.size())
             return finishDBSCAN();
+
         bestClusters = currClusters;
         prevMaxClusterSize = maxClusterSize;
         eps += LEARNING_RATE;