schrodinger#51 Issue: Update clear() method

sketcherMinimizer.cpp

@@ -27,7 +27,9 @@
 #include "sketcherMinimizerMaths.h"
 #include "sketcherMinimizerRing.h"
 #include "sketcherMinimizerStretchInteraction.h"
-
+#include "sketcherMinimizerAtom.h"
+#include "sketcherMinimizerBond.h"
+#include "sketcherMinimizerFragment.h"
 using namespace std;
 using namespace schrodinger;
 
@@ -54,7 +56,7 @@ sketcherMinimizer::sketcherMinimizer(float precision)
 
 sketcherMinimizer::~sketcherMinimizer()
 {
-    clear();
+    void clear();
 }
 
 void sketcherMinimizer::setScoreResidueInteractions(bool b)
@@ -161,11 +163,13 @@ void sketcherMinimizer::canonicalOrdering(sketcherMinimizerMolecule* minMol)
     }
 }
 
-void sketcherMinimizer::initialize(
-    sketcherMinimizerMolecule* minMol) // min mol is split into molecules if
-                                       // needed and then added to the minimizer
-{
-    clear();
+void sketcherMinimizer::initialize(sketcherMinimizerMolecule* minMol) {
+// min mol is split into molecules if
+// needed and then added to the minimizer
+    void clear();
+    m_proximityRelations.clear();
+
+    m_proximityRelations.clear();
     m_referenceAtoms = minMol->_atoms;
     m_referenceBonds = minMol->_bonds;
 
@@ -335,7 +339,7 @@ void sketcherMinimizer::flagCrossAtoms()
     }
 }
 
-void sketcherMinimizer::clear()
+void sketcherMinimizer :: clear()
 {
     for (auto& _referenceAtom : m_referenceAtoms) {
         delete _referenceAtom;
@@ -367,10 +371,29 @@ void sketcherMinimizer::clear()
     }
 
     m_molecules.clear();
+
+    for(auto& _atoms : m_atoms) {
+        delete _atoms;
+    }
+    m_atoms.clear();
+
+    for(auto& _bonds : m_bonds) {
+        delete _bonds;
+    }
+    m_bonds.clear();
+
+    for(auto& _residueInteractions : m_residueInteractions) {
+        delete _residueInteractions;
+    }
+    m_residueInteractions.clear();
+
+    for(auto& _independentFragments : m_independentFragments) {
+        delete _independentFragments;
+    }
+    m_independentFragments.clear();
 }
 
-void sketcherMinimizer::splitIntoMolecules(
-    sketcherMinimizerMolecule* mol, vector<sketcherMinimizerMolecule*>& mols)
+void sketcherMinimizer::splitIntoMolecules(sketcherMinimizerMolecule* mol, vector<sketcherMinimizerMolecule*>& mols)
 {
 
     if (mol->_atoms.empty()) {

sketcherMinimizer.h

@@ -81,7 +81,7 @@ class CoordgenTemplates
 class EXPORT_COORDGEN sketcherMinimizer
 {
 
-  public:
+public:
     sketcherMinimizer(float precision = SKETCHER_STANDARD_PRECISION);
     ~sketcherMinimizer();
 
@@ -283,9 +283,10 @@ class EXPORT_COORDGEN sketcherMinimizer
     static void loadTemplates();
     static CoordgenTemplates m_templates;
 
-private:
     /*all non-terminal bonds to a metal atom are treated as if they were zero order bonds (this usually results
      in a longer bond*/
+
+private:
     bool m_treatNonterminalBondsToMetalAsZOBs = true;
 
     CoordgenFragmentBuilder m_fragmentBuilder;
@@ -302,7 +303,6 @@ class EXPORT_COORDGEN sketcherMinimizer
     std::vector<sketcherMinimizerBond*> m_proximityRelations;
     std::vector<sketcherMinimizerBond*> m_extraBonds;
     std::vector<sketcherMinimizerMolecule*> m_molecules;
-
     /* return the position of res, which is part of SSE, given that the first
      * residue of SSE is placed at startF and consecutive residues are placed
      * increment away from each other. All distances are expressed in floats,
@@ -322,7 +322,6 @@ class EXPORT_COORDGEN sketcherMinimizer
 
     /* clear data and free memory */
     void clear();
-
     /* flag atoms that will be drawn with 90° angles (e.g. phosphate P) */
     void flagCrossAtoms();
 
@@ -439,8 +438,7 @@ class EXPORT_COORDGEN sketcherMinimizer
                          sketcherMinimizerResidue* residue);
 
     /* assign coordinates to residues */
-    void placeResidues(const std::vector<sketcherMinimizerAtom*>& atoms =
-                           std::vector<sketcherMinimizerAtom*>(0));
+    void placeResidues(const std::vector<sketcherMinimizerAtom*>& atoms = std::vector<sketcherMinimizerAtom*>(0));
 
     /* assign coordinates to residues in the context of a protein-protein
      interaction diagram */