From 7a4e342e8cedcfc514dd4d5b74af4d45c1930e1a Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Sat, 1 Nov 2014 04:03:38 +0100
Subject: [PATCH] basic smiles memory consumption

---
 Code/GraphMol/SmilesParse/SmilesParse.cpp    |  1 +
 Code/GraphMol/SmilesParse/SmilesParseOps.cpp | 17 +++++++++++++++++
 Code/GraphMol/SmilesParse/SmilesParseOps.h   |  1 +
 3 files changed, 19 insertions(+)

diff --git a/Code/GraphMol/SmilesParse/SmilesParse.cpp b/Code/GraphMol/SmilesParse/SmilesParse.cpp
index f04efb818..0106a25cc 100644
--- a/Code/GraphMol/SmilesParse/SmilesParse.cpp
+++ b/Code/GraphMol/SmilesParse/SmilesParse.cpp
@@ -153,6 +153,7 @@ namespace RDKit{
 	if(res->hasAtomBookmark(ci_RIGHTMOST_ATOM)){
 	  res->clearAtomBookmark(ci_RIGHTMOST_ATOM);
 	}
+	SmilesParseOps::CleanupAfterParsing(res);
         molVect[0]=0; // NOTE: to avoid leaks on failures, this should occur last in this if.
       }
     } catch (SmilesParseException &e) {
diff --git a/Code/GraphMol/SmilesParse/SmilesParseOps.cpp b/Code/GraphMol/SmilesParse/SmilesParseOps.cpp
index bc51077f6..882be8269 100644
--- a/Code/GraphMol/SmilesParse/SmilesParseOps.cpp
+++ b/Code/GraphMol/SmilesParse/SmilesParseOps.cpp
@@ -475,4 +475,21 @@ namespace SmilesParseOps{
     }
   };
 
+  void CleanupAfterParsing(RWMol *mol){
+    PRECONDITION(mol,"no molecule");
+    for(RWMol::AtomIterator atomIt=mol->beginAtoms();
+        atomIt!=mol->endAtoms();++atomIt){
+      if((*atomIt)->hasProp("_RingClosures"))
+        (*atomIt)->clearProp("_RingClosures");
+      if((*atomIt)->hasProp("_SmilesStart"))
+        (*atomIt)->clearProp("_SmilesStart");
+    }
+    for(RWMol::BondIterator bondIt=mol->beginBonds();
+        bondIt!=mol->endBonds();++bondIt){
+      if((*bondIt)->hasProp("_unspecifiedOrder"))
+        (*bondIt)->clearProp("_unspecifiedOrder");
+    }
+  }
+
+
 } // end of namespace SmilesParseOps
diff --git a/Code/GraphMol/SmilesParse/SmilesParseOps.h b/Code/GraphMol/SmilesParse/SmilesParseOps.h
index 3ceab7b9f..f9c7ac768 100644
--- a/Code/GraphMol/SmilesParse/SmilesParseOps.h
+++ b/Code/GraphMol/SmilesParse/SmilesParseOps.h
@@ -27,6 +27,7 @@ namespace SmilesParseOps {
 					       const RDKit::Atom *atom2);
   void CloseMolRings(RDKit::RWMol *mol,bool toleratePartials);
   void AdjustAtomChiralityFlags(RDKit::RWMol *mol);
+  void CleanupAfterParsing(RDKit::RWMol *mol);
 };
 
 #endif