Decrease volumeTolerance threshold to calculate chirality on molecules

Code/GraphMol/Chirality.cpp

@@ -452,7 +452,7 @@ namespace Chirality {
 
 std::optional<Atom::ChiralType> atomChiralTypeFromBondDirPseudo3D(
     const ROMol &mol, const Bond *bond, const Conformer *conf,
-    double pseudo3DOffset = 0.1, double volumeTolerance = 0.01) {
+    double pseudo3DOffset = 0.1, double volumeTolerance = 1e-3) {
   PRECONDITION(bond, "no bond");
   PRECONDITION(conf, "no conformer");
   auto bondDir = bond->getBondDir();

Code/GraphMol/catch_chirality.cpp

@@ -5380,3 +5380,51 @@ M  END)CTAB"_ctab;
   CHECK(cAt0->getProp<std::string>(common_properties::_CIPCode) ==
         cAt1->getProp<std::string>(common_properties::_CIPCode));
 }
+
+TEST_CASE(
+    "GitHub Issue #7070: zero final chiral volume on scaled molecules") {
+  const auto mlarge = R"CTAB(
+  MM V3K  01017000002D
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 5 4 0 0 1
+M  V30 BEGIN ATOM
+M  V30 1 C 264.49 -311.16 0 0
+M  V30 2 C 278.9 -311.16 0 0
+M  V30 3 O 286.1 -298.69 0 0
+M  V30 4 C 286.1 -323.63 0 0
+M  V30 5 C 278.9 -336.1 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3 CFG=3
+M  V30 3 1 2 4
+M  V30 4 1 4 5
+M  V30 END BOND
+M  V30 END CTAB
+M  END)CTAB"_ctab;
+  const auto mscaled = R"CTAB(
+  MM V3K  01017000002D
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 5 4 0 0 1
+M  V30 BEGIN ATOM
+M  V30 1 C 26.449 -31.116 0 0
+M  V30 2 C 27.89 -31.116 0 0
+M  V30 3 O 28.61 -29.869 0 0
+M  V30 4 C 28.61 -32.363 0 0
+M  V30 5 C 27.89 -33.61 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3 CFG=3
+M  V30 3 1 2 4
+M  V30 4 1 4 5
+M  V30 END BOND
+M  V30 END CTAB
+M  END)CTAB"_ctab;
+  CHECK(MolToSmiles(*mlarge) == "CC[C@H](C)O");
+  CHECK(MolToSmiles(*mscaled) == "CC[C@H](C)O");
+}

rdkit/Chem/UnitTestInchi.py

@@ -167,9 +167,9 @@ def test0InchiWritePubChem(self):
 
       fmt = "\n{0}InChI write Summary: {1} identical, {2} suffix variance, {3} reasonable{4}"
       print(fmt.format(COLOR_GREEN, same, diff, reasonable, COLOR_RESET))
-      self.assertEqual(same, 1160)
+      self.assertEqual(same, 1162)
       self.assertEqual(diff, 0)
-      self.assertEqual(reasonable, 21)
+      self.assertEqual(reasonable, 19)
 
   def test1InchiReadPubChem(self):
     for f in self.dataset.values():