From eebad845f551b6b15f0655589a5ab67e52f8f53f Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Thu, 21 Mar 2024 12:56:41 +0100
Subject: [PATCH] fix a leak in the new DCLV code (#7279)

---
 Code/GraphMol/Descriptors/DCLV.cpp               | 16 ++++++++++++++++
 Code/GraphMol/Descriptors/DCLV.h                 |  3 ++-
 .../Descriptors/Wrap/rdMolDescriptors.cpp        |  1 +
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/Code/GraphMol/Descriptors/DCLV.cpp b/Code/GraphMol/Descriptors/DCLV.cpp
index d6894291a60..8572f8e45ca 100644
--- a/Code/GraphMol/Descriptors/DCLV.cpp
+++ b/Code/GraphMol/Descriptors/DCLV.cpp
@@ -352,12 +352,27 @@ struct State {
   void freeAtomList(AtomList* ptr) {
     while (ptr) {
       AtomList* next = ptr->next;
+#if 0
       ptr->next = freeList;
       freeList = ptr;
+#else
+      free(ptr);
+#endif
       ptr = next;
     }
   }
 
+  void freeGrid() {
+    for (unsigned int x = 0; x < VOXORDER; x++) {
+      for (unsigned int y = 0; y < VOXORDER; y++) {
+        for (unsigned int z = 0; z < VOXORDER; z++) {
+          freeAtomList(grid[x][y][z]);
+          grid[x][y][z] = nullptr;
+        }
+      }
+    }
+  }
+
   ElemStruct* getAtomElem(std::string atmName, bool typeFlag) {
     const char* name = atmName.c_str();
 
@@ -856,6 +871,7 @@ DoubleCubicLatticeVolume::DoubleCubicLatticeVolume(const ROMol& mol,
   vdwVolume = s.calculateVolume(0.0, memberAtoms);
   compactness = calculateCompactness(surfaceArea, totalVolume);
   packingDensity = (vdwVolume / totalVolume);
+  s.freeGrid();
 }
 
 }  // namespace Descriptors
diff --git a/Code/GraphMol/Descriptors/DCLV.h b/Code/GraphMol/Descriptors/DCLV.h
index f4138f2701a..9b45f00c866 100644
--- a/Code/GraphMol/Descriptors/DCLV.h
+++ b/Code/GraphMol/Descriptors/DCLV.h
@@ -32,7 +32,8 @@ class RDKIT_DESCRIPTORS_EXPORT DoubleCubicLatticeVolume {
 
     \param mol: input molecule or protein
     \param isProtein: flag to identify input as protein vs unbound ligand
-    (default=true, Protein as input)
+    (default=true, Protein as input) NOTE that the results for isProtein=false
+    are currently not correct
     \param includeLigand: flag to trigger
     inclusion of bound ligand in surface area and volume calculations where
     molecule is a protein [default false]
diff --git a/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp b/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
index b635f8ca2a0..edaf86a175f 100644
--- a/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
+++ b/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
@@ -1657,6 +1657,7 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
   docString =
       R"DOC(ARGUMENTS:
       "   - mol: molecule or protein under consideration
+      "   - isProtein: flag to indicate if the input is a protein (default=True). NOTE that results with isProtein=False are currently not correct.
       "   - includeLigand: flag to include or exclude a bound ligand when input is a protein (default=False)
       "   - probeRadius: radius of the solvent probe (default=1.4)
       "   - depth: control of number of dots per atom (default=2)