Fix (most of) mem problems (#2123)

* do not use new on loggers

* del pointers in testDistGeom

* Update Dict hasNonPOD status on bulk update

* delete new Dicts in memtest1.cpp

* fixes in MolSuppliers and testFMCS

* PeriodicTable singleton as unique_ptr

* fix EEM_arrays leak

* fix leaks in testPBF

* fix ParamCollection leak in test UFF

* fix leaks in MMFF

* clear prop dict before read in in pickler

* fix leaks in testFreeSASA

* fix leaks in test3D

* modernize Dict.h & SmilesParse.cpp

* fix leaks in testQuery

* fix leaks in testCrystalFF

* fix leaks in cxsmilesTest

* fix leaks in Catalog & mol cat test

* fix leaks in ShapeUtils & tests

* fix leaks in testSubgraphs1

* fix leaks testFingerprintGenerators

* fix leaks in Catalog/FilterCatalog

* fix leaks in graphmolqueryTest

* these changes reduce bison parse leaks

* fixed leaks in testChirality.cpp

* fix leaks + 2 tests in testMolWriter

* fix 4m leaks in substructLibraryTest

* small improvements to molTautomerTest; still leaks

* fix leaks in testRGroupDecomp

* fix leaks in test; parser still leaks

* fix leaks in itertest

* fix 4m leaks in testDepictor

* fixes in smatest; still leaking due to parser

* fixes in testSLNParse; still leaking due to parser

* flex/bison: always add atoms with ownership; smarts error cleanup

* fix leaks in testReaction

* fix leaks in testSubstructMatch

* fix leaks in resMolSupplierTest

* fix leaks in testChemTransforms + bug in ChemTransforms

* fix leaks in testPickler

* fix leaks in testMolTransform

* fix leaks in testFragCatalog

* fix leak in testSLNParse. Still leaks due to Smiles

* fixed most leaks in testMolSupplier

* pre bison fix

* fix some atom & bond parse problems; others still fail

* bison smiles & smarts, atoms & bonds more or less fixed

* fix leaks in molopstest.cpp

* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp

* fix leaks in moldraw2Dtest1

* fix leaks in testDescriptors

* fix leaks in testInchi

* fix leaks in testUFFForceFieldHelpers

* fix leaks in hanoiTest & new_canon.h

* fix leaks in testMMFFForceField

* fix leaks in graphmolTest1

* fix leaks in testMMFFForceFieldHelpers

* fix leaks in testDistGeomHelpers

* fix leaks in testMolAlign

* initialize occupancy & temp facto with default values

* fix leak in TautomerTransform

* updated suppressions

* fix testStructChecker

* fix logging & py tests

* fix TautomerTransform class/struct issue

* remove misplaced delete in testSLNParse

* deinit in testAvalonLib1

* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp

* fix random testMolWriter/Supplier fails

- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.

* use reset in FFs Params.cpp

* comments on testMMFFForceField

* unrequired 'if's added to mol suppliers

* correct cast in FilterCatalog.h

* use unique_ptr in MACCS Patterns

* remove unrequred if in new_canon

* update & move suppressions

Code/Query/test.cpp

@@ -43,8 +43,10 @@ void test1() {
   CHECK_INVARIANT(newQ->Match(1.001), "");
   CHECK_INVARIANT(!newQ->Match(1.1), "");
   CHECK_INVARIANT(!newQ->Match(-2), "");
+  delete newQ;
 }
 
+
 void test2() {
   cout << "Set" << endl;
   SetQuery<int> q;
@@ -63,6 +65,7 @@ void test2() {
   CHECK_INVARIANT(newQ->Match(1), "");
   CHECK_INVARIANT(newQ->Match(3), "");
   CHECK_INVARIANT(!newQ->Match(-3), "");
+  delete newQ;
 }
 
 void test3() {
@@ -87,6 +90,9 @@ void test3() {
   CHECK_INVARIANT(newQ->Match(1), "");
   CHECK_INVARIANT(newQ->Match(3), "");
   CHECK_INVARIANT(!newQ->Match(-3), "");
+
+  delete newQ;
+  delete q;
 }
 
 void test4() {
@@ -111,6 +117,9 @@ void test4() {
   CHECK_INVARIANT(newQ->Match(1), "");
   CHECK_INVARIANT(newQ->Match(3), "");
   CHECK_INVARIANT(newQ->Match(-3), "");
+
+  delete newQ;
+  delete q;
 }
 
 void test5() {
@@ -137,6 +146,9 @@ void test5() {
   CHECK_INVARIANT(!newQ->Match(1), "");
   CHECK_INVARIANT(!newQ->Match(3), "");
   CHECK_INVARIANT(newQ->Match(-3), "");
+
+  delete newQ;
+  delete q;
 }
 
 int foofun(double bar) { return int(floor(bar)); };
@@ -166,6 +178,9 @@ void test6() {
   CHECK_INVARIANT(newQ3->Match(6.0), "");
   CHECK_INVARIANT(newQ3->Match(6.1), "");
   CHECK_INVARIANT(!newQ3->Match(5.0), "");
+
+  delete newQ;
+  delete newQ3;
 }
 
 bool matchF(int v) { return v == 3; }
@@ -275,6 +290,8 @@ void test7() {
   CHECK_INVARIANT(newQ->Match("1"), "");
   CHECK_INVARIANT(newQ->Match("3"), "");
   CHECK_INVARIANT(!newQ->Match("-3"), "");
+
+  delete newQ;
 }
 
 int main() {