From 2a187342f637cd3b6c5eae64bf4b61c9dce0d61a Mon Sep 17 00:00:00 2001
From: Woosub-Kim <woosubgo@gmail.com>
Date: Fri, 5 Jan 2024 13:20:02 +0900
Subject: [PATCH] complexsearch initial search parameter adjustment

---
 src/strucclustutils/scorecomplex.cpp | 15 +++------------
 src/workflow/ComplexSearch.cpp       | 15 ++++++++++-----
 2 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/src/strucclustutils/scorecomplex.cpp b/src/strucclustutils/scorecomplex.cpp
index 46622159..c75ee5f1 100644
--- a/src/strucclustutils/scorecomplex.cpp
+++ b/src/strucclustutils/scorecomplex.cpp
@@ -424,7 +424,8 @@ class DBSCANCluster {
 
     unsigned int finishDBSCAN() {
         initializeAlnLabels();
-        if (prevMaxClusterSize < minClusterSize || bestClusters.empty()) return UNCLUSTERED;
+        if (prevMaxClusterSize < minClusterSize || bestClusters.empty())
+            return UNCLUSTERED;
         cLabel = CLUSTERED;
         for (auto &cluster: bestClusters) {
             for (auto alnIdx: cluster) {
@@ -440,22 +441,12 @@ class DBSCANCluster {
         for (size_t alnIdx=0; alnIdx<searchResult.alnVec.size(); alnIdx++) {
             neighbors.emplace_back(alnIdx);
         }
-        if (checkChainRedundancy())
+        if (bestClusters.empty() || checkChainRedundancy())
             return UNCLUSTERED;
         prevMaxClusterSize = neighbors.size();
         bestClusters.emplace_back(neighbors);
         return finishDBSCAN();
     }
-
-//    void free() {
-//        neighbors.clear();
-//        neighborsOfCurrNeighbor.clear();
-//        qFoundChainKeys.clear();
-//        dbFoundChainKeys.clear();
-//        distMap.clear();
-//        currClusters.clear();
-//        bestClusters.clear();
-//    }
 };
 
 class ComplexScorer {
diff --git a/src/workflow/ComplexSearch.cpp b/src/workflow/ComplexSearch.cpp
index 201eebdc..eda56517 100644
--- a/src/workflow/ComplexSearch.cpp
+++ b/src/workflow/ComplexSearch.cpp
@@ -53,11 +53,11 @@ int complexsearch(int argc, const char **argv, const Command &command) {
         par.greedyBestHits) {
         needBacktrace = true;
     }
-    if (needBacktrace) {
-        Debug(Debug::INFO) << "Alignment backtraces will be computed, since they were requested by output format.\n";
-        par.addBacktrace = true;
-        par.PARAM_ADD_BACKTRACE.wasSet = true;
-    }
+//    if (needBacktrace) {
+//        Debug(Debug::INFO) << "Alignment backtraces will be computed, since they were requested by output format.\n";
+//        par.addBacktrace = true;
+//        par.PARAM_ADD_BACKTRACE.wasSet = true;
+//    }
     if (needLookup) {
         par.writeLookup = true;
     }
@@ -101,6 +101,11 @@ int complexsearch(int argc, const char **argv, const Command &command) {
     cmd.addVariable("QUERYDB", par.filenames.back().c_str());
     cmd.addVariable("LEAVE_INPUT", par.dbOut ? "TRUE" : NULL);
     par.filenames.pop_back();
+
+    // initial search speed up!
+    par.addBacktrace = par.exhaustiveSearch;
+    par.alignmentType = par.exhaustiveSearch ? par.alignmentType : LocalParameters::ALIGNMENT_TYPE_3DI_AA;
+
     cmd.addVariable("SEARCH_PAR", par.createParameterString(par.structuresearchworkflow, true).c_str());
     cmd.addVariable("SCORECOMPLEX_PAR", par.createParameterString(par.scorecomplex).c_str());
     cmd.addVariable("THREADS_PAR", par.createParameterString(par.onlythreads).c_str());