Fix #7311: problem with InChI for phosphinic acid (#7419)

* backup * remove default valence for Tl
rdkit · May 3, 2024 · 31f1195 · 31f1195
1 parent 757d3ed
commit 31f1195
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Showing 3 changed files with 34 additions and 2 deletions.
diff --git a/Code/GraphMol/atomic_data.cpp b/Code/GraphMol/atomic_data.cpp
@@ -128,7 +128,7 @@ const std::string periodicTableAtomData =
 78	Pt	1.36	1.3	2.05	195.078	10	195	194.9647911	-1
 79	Au	1.36	1.34	2.1	196.967	11	197	196.9665687	-1
 80	Hg	1.32	1.49	2.05	200.59	2	202	201.970643	-1
-81	Tl	1.45	1.48	2.2	204.383	3	205	204.9744275	3
+81	Tl	1.45	1.48	2.2	204.383	3	205	204.9744275	-1
 82	Pb	1.46	1.48	2.3	207.2	4	208	207.9766521	2	4
 83	Bi	1.48	1.45	2.3	208.98	5	209	208.9803987	3	5	7
 84	Po	1.40	1.46	2.0	209	6	209	208.9824304	2	4	6

diff --git a/External/INCHI-API/inchi.cpp b/External/INCHI-API/inchi.cpp
@@ -1806,7 +1806,21 @@ std::string MolToInchi(const ROMol& mol, ExtraInchiReturnValues& rv,
     inchiAtoms[i].charge = atom->getFormalCharge();
 
     // number of iso H
-    inchiAtoms[i].num_iso_H[0] = -1;
+    int nHs = -1;
+    switch (atom->getAtomicNum()) {
+      case 6:
+      case 7:
+      case 8:
+      case 9:
+      case 17:
+      case 35:
+      case 53:
+        nHs = -1;
+        break;
+      default:
+        nHs = atom->getTotalNumHs();
+    }
+    inchiAtoms[i].num_iso_H[0] = nHs;
     inchiAtoms[i].num_iso_H[1] = 0;
     inchiAtoms[i].num_iso_H[2] = 0;
     inchiAtoms[i].num_iso_H[3] = 0;

diff --git a/External/INCHI-API/test.cpp b/External/INCHI-API/test.cpp
@@ -575,6 +575,7 @@ void testGithubIssue614() {
     m->removeAtom(3);
     ExtraInchiReturnValues tmp;
     std::string inchi = MolToInchi(*m, tmp);
+    std::cerr << " inchi: " << inchi << std::endl;
     TEST_ASSERT(inchi == "InChI=1S/C3H6/c1-3-2/h3H,1H2,2H3");
     delete m;
   }
@@ -896,6 +897,22 @@ void testGithub6172() {
     std::unique_ptr<ROMol> m{InchiToMol(inchi, tmp)};
     TEST_ASSERT(!m);
   }
+  BOOST_LOG(rdInfoLog) << "done" << std::endl;
+}
+
+void testGithub5311() {
+  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "testing github #5311" << std::endl;
+
+  {
+    auto m = "O[PH2]=O"_smiles;
+    TEST_ASSERT(m);
+    ExtraInchiReturnValues tmp;
+    auto inchi = MolToInchi(*m, tmp);
+    std::cerr << "!!! " << inchi << std::endl;
+    TEST_ASSERT(inchi == "InChI=1S/H3O2P/c1-3-2/h3H2,(H,1,2)");
+    BOOST_LOG(rdInfoLog) << "done" << std::endl;
+  }
 }
 //-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
 //
@@ -920,4 +937,5 @@ int main() {
   testGithub3645();
   test_clean_up_on_kekulization_error();
   testGithub6172();
+  testGithub5311();
 }