Fixes rdkit#8023 (rdkit#8024)

e-kwsm · Nov 21, 2024 · a0a21e6 · a0a21e6
1 parent 614116a
commit a0a21e6
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Showing 4 changed files with 39 additions and 9 deletions.
diff --git a/Code/GraphMol/FileParsers/MolFileWriter.cpp b/Code/GraphMol/FileParsers/MolFileWriter.cpp
@@ -546,9 +546,10 @@ bool hasNonDefaultValence(const Atom *atom) {
       SmilesWrite ::inOrganicSubset(atom->getAtomicNum())) {
     // for the ones we "know", we may have to specify the valence if it's
     // not the default value
+    auto effAtomicNum = atom->getAtomicNum() - atom->getFormalCharge();
     return atom->getNoImplicit() &&
            (atom->getExplicitValence() !=
-            PeriodicTable::getTable()->getDefaultValence(atom->getAtomicNum()));
+            PeriodicTable::getTable()->getDefaultValence(effAtomicNum));
   }
   return true;
 }
@@ -1225,7 +1226,11 @@ std::string getV3000CTAB(const ROMol &tmol,
   return res;
 }
 }  // namespace FileParserUtils
-enum class MolFileFormat { V2000, V3000, unspecified };
+enum class MolFileFormat {
+  V2000,
+  V3000,
+  unspecified
+};
 
 //------------------------------------------------
 //

diff --git a/Code/GraphMol/FileParsers/file_parsers_catch.cpp b/Code/GraphMol/FileParsers/file_parsers_catch.cpp
@@ -7155,7 +7155,7 @@ class FragTest {
         expectedResult(expectedResultInit),
         reapplyMolBlockWedging(reapplyMolBlockWedgingInit),
         origSgroupCount(origSgroupCountInit),
-        newSgroupCount(newSgroupCountInit){};
+        newSgroupCount(newSgroupCountInit) {};
 };
 
 void testFragmentation(const FragTest &fragTest) {
@@ -7412,3 +7412,28 @@ TEST_CASE("Github #7306: bad crossed bonds in large aromatic rings") {
     CHECK(ctab.find("2  3\n") == std::string::npos);
   }
 }
+
+TEST_CASE(
+    "Github #8023: explicit valence for charged organic atoms in mol block") {
+  SECTION("as reported 1") {
+    auto m = "C[NH3+]"_smiles;
+    REQUIRE(m);
+    auto ctab = MolToMolBlock(*m);
+    CHECK(ctab.find("N   0  0  0  0  0  0  0") != std::string::npos);
+    ctab = MolToV3KMolBlock(*m);
+    CHECK(ctab.find("CHG=1") != std::string::npos);
+    CHECK(ctab.find("VAL=4") == std::string::npos);
+  }
+  SECTION("nitro-type") {
+    auto m = "C[N+](=S)[O-]"_smiles;
+    REQUIRE(m);
+    auto ctab = MolToMolBlock(*m);
+    CHECK(ctab.find("N   0  0  0  0  0  0  0") != std::string::npos);
+    CHECK(ctab.find("O   0  0  0  0  0  0  0") != std::string::npos);
+    ctab = MolToV3KMolBlock(*m);
+    CHECK(ctab.find("CHG=1") != std::string::npos);
+    CHECK(ctab.find("VAL=4") == std::string::npos);
+    CHECK(ctab.find("CHG=-1") != std::string::npos);
+    CHECK(ctab.find("VAL=1") == std::string::npos);
+  }
+}
diff --git a/Code/GraphMol/MarvinParse/test_data/Na_Mg_Al_OH.expected.sdf b/Code/GraphMol/MarvinParse/test_data/Na_Mg_Al_OH.expected.sdf
@@ -5,17 +5,17 @@
 M  V30 BEGIN CTAB
 M  V30 COUNTS 12 3 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 O 0.000000 1.750000 0.000000 0 CHG=-1 VAL=1
-M  V30 2 O 2.299038 0.000000 0.000000 0 CHG=-1 VAL=1
-M  V30 3 O 0.000000 2.750000 0.000000 0 CHG=-1 VAL=1
-M  V30 4 O 3.299038 0.000000 0.000000 0 CHG=-2 VAL=-1
+M  V30 1 O 0.000000 1.750000 0.000000 0 CHG=-1
+M  V30 2 O 2.299038 0.000000 0.000000 0 CHG=-1
+M  V30 3 O 0.000000 2.750000 0.000000 0 CHG=-1
+M  V30 4 O 3.299038 0.000000 0.000000 0 CHG=-2
 M  V30 5 Na 0.000000 3.750000 0.000000 0 CHG=1 VAL=-1
 M  V30 6 Mg 4.299038 0.000000 0.000000 0 CHG=2 VAL=-1
 M  V30 7 Al 0.000000 4.750000 0.000000 0 CHG=3 VAL=-1
 M  V30 8 Si 5.299038 0.000000 0.000000 0 VAL=-1
 M  V30 9 O 1.299038 0.750000 0.000000 0
 M  V30 10 C 0.000000 0.000000 0.000000 0
-M  V30 11 O -1.299038 0.750000 0.000000 0 CHG=-1 VAL=1
+M  V30 11 O -1.299038 0.750000 0.000000 0 CHG=-1
 M  V30 12 O -0.000000 -1.500000 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND

diff --git a/Code/GraphMol/MarvinParse/test_data/Smiles1.expected.sdf b/Code/GraphMol/MarvinParse/test_data/Smiles1.expected.sdf
@@ -7,7 +7,7 @@ M  V30 COUNTS 9 9 0 0 0
 M  V30 BEGIN ATOM
 M  V30 1 N 3.750000 -1.299038 0.000000 0
 M  V30 2 C 3.000000 0.000000 0.000000 0
-M  V30 3 O 3.750000 1.299038 0.000000 0 CHG=-1 VAL=1
+M  V30 3 O 3.750000 1.299038 0.000000 0 CHG=-1
 M  V30 4 C 1.500000 0.000000 0.000000 0
 M  V30 5 C 0.750000 -1.299038 0.000000 0
 M  V30 6 C -0.750000 -1.299038 0.000000 0