From 1a67fefcc60f162dacab57c35234c3724c3bad57 Mon Sep 17 00:00:00 2001
From: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
Date: Wed, 19 Feb 2025 23:59:30 -0500
Subject: [PATCH] mem fixes (#8276)

---
 Code/GraphMol/DistGeomHelpers/Embedder.cpp    | 19 ++++++------
 .../Fingerprints/fpgen_catch_tests.cpp        |  3 +-
 External/INCHI-API/inchi.cpp                  | 31 +++++++------------
 3 files changed, 23 insertions(+), 30 deletions(-)

diff --git a/Code/GraphMol/DistGeomHelpers/Embedder.cpp b/Code/GraphMol/DistGeomHelpers/Embedder.cpp
index 772817b7b..1b368030d 100644
--- a/Code/GraphMol/DistGeomHelpers/Embedder.cpp
+++ b/Code/GraphMol/DistGeomHelpers/Embedder.cpp
@@ -837,16 +837,19 @@ bool embedPoints(RDGeom::PointPtrVect *positions, detail::EmbedArgs eargs,
     embedParams.basinThresh = 1e8;
   }
 
+  std::unique_ptr<RDKit::rng_type> generator;
+  std::unique_ptr<RDKit::uniform_double> distrib;
+  std::unique_ptr<RDKit::double_source_type> rngMgr;
+
   RDKit::double_source_type *rng = nullptr;
-  RDKit::rng_type *generator = nullptr;
-  RDKit::uniform_double *distrib = nullptr;
   CHECK_INVARIANT(seed >= -1,
                   "random seed must either be positive, zero, or negative one");
   if (seed > -1) {
-    generator = new RDKit::rng_type(42u);
+    generator.reset(new RDKit::rng_type(42u));
     generator->seed(seed);
-    distrib = new RDKit::uniform_double(0.0, 1.0);
-    rng = new RDKit::double_source_type(*generator, *distrib);
+    distrib.reset(new RDKit::uniform_double(0.0, 1.0));
+    rngMgr.reset(new RDKit::double_source_type(*generator, *distrib));
+    rng = rngMgr.get();
   } else {
     rng = &RDKit::getDoubleRandomSource();
   }
@@ -987,11 +990,7 @@ bool embedPoints(RDGeom::PointPtrVect *positions, detail::EmbedArgs eargs,
     }
 
   }  // while
-  if (seed > -1) {
-    delete rng;
-    delete generator;
-    delete distrib;
-  }
+
   return gotCoords;
 }
 
diff --git a/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp b/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp
index 6e66d3822..d85ac91d2 100644
--- a/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp
+++ b/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp
@@ -464,7 +464,8 @@ TEST_CASE("github #6679: suspicious value for atom pair code calculation") {
         {"C[I]", 7918328},  {"C[Te]", 7918456}, {"C[Sb]", 7918584},
         {"C[Sn]", 7918200}, {"C[Xe]", 7918200}, {"C[Li]", 7918200},
     };
-    auto fpg = AtomPair::getAtomPairGenerator<std::uint64_t>();
+    std::unique_ptr<FingerprintGenerator<std::uint64_t>> fpg{
+        AtomPair::getAtomPairGenerator<std::uint64_t>()};
     for (const auto &pr : data) {
       auto mol = v2::SmilesParse::MolFromSmiles(pr.first);
       REQUIRE(mol);
diff --git a/External/INCHI-API/inchi.cpp b/External/INCHI-API/inchi.cpp
index 191e1fab0..14b6a9ad1 100644
--- a/External/INCHI-API/inchi.cpp
+++ b/External/INCHI-API/inchi.cpp
@@ -1760,7 +1760,7 @@ std::string MolToInchi(const ROMol &mol, ExtraInchiReturnValues &rv,
   unsigned int nBonds = m->getNumBonds();
 
   // Make array of inchi_atom (storage space)
-  auto *inchiAtoms = new inchi_Atom[nAtoms];
+  std::unique_ptr<inchi_Atom[]> inchiAtoms(new inchi_Atom[nAtoms]);
   // and a vector for stereo0D
   std::vector<inchi_Stereo0D> stereo0DEntries;
 
@@ -2048,24 +2048,23 @@ std::string MolToInchi(const ROMol &mol, ExtraInchiReturnValues &rv,
   }
 
   // create stereo0D
-  inchi_Stereo0D *stereo0Ds;
+  std::unique_ptr<inchi_Stereo0D[]> stereo0Ds;
   if (stereo0DEntries.size()) {
-    stereo0Ds = new inchi_Stereo0D[stereo0DEntries.size()];
+    stereo0Ds.reset(new inchi_Stereo0D[stereo0DEntries.size()]);
     for (unsigned int i = 0; i < stereo0DEntries.size(); i++) {
       stereo0Ds[i] = stereo0DEntries[i];
     }
-  } else {
-    stereo0Ds = nullptr;
   }
 
   // create input
   inchi_Input input;
-  input.atom = inchiAtoms;
-  input.stereo0D = stereo0Ds;
+  input.atom = inchiAtoms.get();
+  input.stereo0D = stereo0Ds.get();
+  std::unique_ptr<char[]> _options;
   if (options) {
-    char *_options = new char[strlen(options) + 1];
-    fixOptionSymbol(options, _options);
-    input.szOptions = _options;
+    _options.reset(new char[strlen(options) + 1]);
+    fixOptionSymbol(options, _options.get());
+    input.szOptions = _options.get();
   } else {
     input.szOptions = nullptr;
   }
@@ -2098,14 +2097,6 @@ std::string MolToInchi(const ROMol &mol, ExtraInchiReturnValues &rv,
     // clean up
     FreeINCHI(&output);
   }
-  if (input.szOptions) {
-    delete[] input.szOptions;
-  }
-
-  delete[] inchiAtoms;
-  if (stereo0Ds) {
-    delete[] stereo0Ds;
-  }
 
   return inchi;
 }
@@ -2153,7 +2144,9 @@ std::string InchiToInchiKey(const std::string &inchi) {
   char inchiKey[29];
   char xtra1[65], xtra2[65];
   int ret = 0;
-  { ret = GetINCHIKeyFromINCHI(inchi.c_str(), 0, 0, inchiKey, xtra1, xtra2); }
+  {
+    ret = GetINCHIKeyFromINCHI(inchi.c_str(), 0, 0, inchiKey, xtra1, xtra2);
+  }
   std::string error;
   switch (ret) {
     case INCHIKEY_OK: