add report-paths argument to toggle paths in msa2lddt output

steineggerlab · Jul 30, 2024 · dc66166 · dc66166
1 parent e19eb74
commit dc66166
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/src/commons/FoldmasonParameters.cpp b/src/commons/FoldmasonParameters.cpp
@@ -19,6 +19,7 @@ FoldmasonParameters::FoldmasonParameters() :
         PARAM_BITFACTOR_3DI(PARAM_BITFACTOR_3DI_ID, "--bitfactor-3di", "3Di matrix bit factor", "3Di matrix bit factor", typeid(float), (void *) &bitFactor3Di, "^([0-9]*\\.[0-9]*)$"),
         PARAM_PAIR_THRESHOLD(PARAM_PAIR_THRESHOLD_ID, "--pair-threshold", "LDDT pair threshold", "% of pair subalignments with LDDT information [0.0,1.0]",typeid(float), (void *) &pairThreshold, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
         PARAM_REPORT_COMMAND(PARAM_REPORT_COMMAND_ID, "--report-command", "", "", typeid(std::string), (void *) &reportCommand, ""),
+        PARAM_REPORT_PATHS(PARAM_REPORT_PATHS_ID, "--report-paths", "", "", typeid(bool), (void *) &reportPaths, ""),
         PARAM_REFINE_SEED(PARAM_REFINE_SEED_ID, "--refine-seed", "Random number generator seed", "Random number generator seed", typeid(int), (void *) &refinementSeed, "^([-]?[0-9]*)$")
 {
     // structuremsa
@@ -59,6 +60,7 @@ FoldmasonParameters::FoldmasonParameters() :
     msa2lddt.push_back(&PARAM_GUIDE_TREE);
     msa2lddt.push_back(&PARAM_V);
     msa2lddt.push_back(&PARAM_REPORT_COMMAND);
+    msa2lddt.push_back(&PARAM_REPORT_PATHS);
 
     // refinemsa
     refinemsa = combineList(refinemsa, structuremsa);
@@ -81,6 +83,7 @@ FoldmasonParameters::FoldmasonParameters() :
     matchRatio = 0.51;
     guideTree = "";
     reportCommand = "";
+    reportPaths = true;
     recomputeScores = false;
     regressive = false;
     precluster = false;

diff --git a/src/commons/FoldmasonParameters.h b/src/commons/FoldmasonParameters.h
@@ -46,6 +46,7 @@ class FoldmasonParameters : public LocalParameters {
     PARAMETER(PARAM_BITFACTOR_3DI)
     PARAMETER(PARAM_PAIR_THRESHOLD)
     PARAMETER(PARAM_REPORT_COMMAND)
+    PARAMETER(PARAM_REPORT_PATHS)
     PARAMETER(PARAM_REFINE_SEED)
 
     MultiParam<PseudoCounts> pcaAa;
@@ -62,6 +63,7 @@ class FoldmasonParameters : public LocalParameters {
     float bitFactorAa;
     float bitFactor3Di;
     std::string reportCommand;
+    bool reportPaths;
     float pairThreshold;
     int refinementSeed;
 };

diff --git a/src/strucclustutils/msa2lddt.cpp b/src/strucclustutils/msa2lddt.cpp
@@ -512,11 +512,15 @@ R"html(<!DOCTYPE html>
             end.append(tree);            
             end.append("\",");
         }
-        end.append("\"statistics\": {\"db\":\"");
-        end.append(par.db1);
-        end.append("\",\"msaFile\":\"");
-        end.append(par.db2);
-        end.append("\",\"msaLDDT\":");
+        end.append("\"statistics\": {");
+        if (par.reportPaths) {
+            end.append("\"db\":\"");
+            end.append(par.db1);
+            end.append("\",\"msaFile\":\"");
+            end.append(par.db2);
+            end.append("\",");
+        }
+        end.append("\"msaLDDT\":");
         end.append(std::to_string(lddtScore));
 
         if (par.reportCommand != "") {