Fixes: rdkit#3415 (rdkit#3416)

* Fixes: rdkit#3415

* add another test

Author: greglandrum

Code/GraphMol/FileParsers/MolSGroupParsing.cpp

@@ -737,12 +737,31 @@ void ParseV3000SAPLabel(RWMol *mol, SubstanceGroup &sgroup,
 std::string ParseV3000StringPropLabel(std::stringstream &stream) {
   std::string strValue;
 
-  // TODO: this should be improved to be able to handle escaped quotes
-
   auto nextChar = stream.peek();
   if (nextChar == '"') {
+    // skip the opening quote:
     stream.get();
-    std::getline(stream, strValue, '"');
+
+    // this is a bit gross because it's legal to include a \" in a value,
+    // but the way that's done is by doubling it. So
+    // FIELDINFO=""""
+    // should assign the value \" to FIELDINFO
+    char chr;
+    while (stream.get(chr)) {
+      if (chr == '"') {
+        nextChar = stream.peek();
+
+        // if the next element in the stream is a \" then we have a quoted \".
+        // Otherwise we're done
+        if (nextChar != '"') {
+          break;
+        } else {
+          // skip the second \"
+          stream.get();
+        }
+      }
+      strValue += chr;
+    }
   } else if (nextChar == '\'') {
     std::getline(stream, strValue, '\'');
   } else {

Code/GraphMol/FileParsers/file_parsers_catch.cpp

@@ -1974,3 +1974,86 @@ M  END)CTAB"_ctab;
     CHECK(m->getNumBonds() == 0);
   }
 }
+
+TEST_CASE("github #3415: problem parsing SGroup data containing \" ", "[bug]") {
+  SECTION("basics") {
+    auto m = R"CTAB(
+  Mrv2014 09172018222D          
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 6 6 1 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 1.3337 2.31 0 0
+M  V30 2 C 2.6674 1.54 0 0
+M  V30 3 C 2.6674 -0 0 0
+M  V30 4 C 1.3337 -0.77 0 0
+M  V30 5 C 0 0 0 0
+M  V30 6 C 0 1.54 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 3 4
+M  V30 4 1 4 5
+M  V30 5 2 5 6
+M  V30 6 1 1 6
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Tempstruct FIELDINFO="""" -
+M  V30 FIELDDISP="    2.1037    1.5400    DA    ALL  0       0" QUERYOP="""" -
+M  V30 FIELDDATA=Foo1
+M  V30 END SGROUP
+M  V30 END CTAB
+M  END
+)CTAB"_ctab;
+    REQUIRE(m);
+    CHECK(m->getNumAtoms() == 6);
+    CHECK(m->getNumBonds() == 6);
+    auto sgs = getSubstanceGroups(*m);
+    REQUIRE(sgs.size() == 1);
+    CHECK(sgs[0].getProp<std::string>("TYPE") == "DAT");
+    CHECK(sgs[0].getProp<std::string>("FIELDINFO") == "\"");
+    CHECK(sgs[0].getProp<std::string>("QUERYOP") == "\"");
+  }
+  SECTION("empty string") {
+    auto m = R"CTAB(
+  Mrv2014 09172018222D          
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 6 6 1 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 1.3337 2.31 0 0
+M  V30 2 C 2.6674 1.54 0 0
+M  V30 3 C 2.6674 -0 0 0
+M  V30 4 C 1.3337 -0.77 0 0
+M  V30 5 C 0 0 0 0
+M  V30 6 C 0 1.54 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 3 4
+M  V30 4 1 4 5
+M  V30 5 2 5 6
+M  V30 6 1 1 6
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Tempstruct FIELDINFO="" -
+M  V30 FIELDDISP="    2.1037    1.5400    DA    ALL  0       0" QUERYOP="""" -
+M  V30 FIELDDATA=Foo1
+M  V30 END SGROUP
+M  V30 END CTAB
+M  END
+)CTAB"_ctab;
+    REQUIRE(m);
+    CHECK(m->getNumAtoms() == 6);
+    CHECK(m->getNumBonds() == 6);
+    auto sgs = getSubstanceGroups(*m);
+    REQUIRE(sgs.size() == 1);
+    CHECK(sgs[0].getProp<std::string>("TYPE") == "DAT");
+    CHECK(sgs[0].getProp<std::string>("FIELDINFO").empty());
+    CHECK(sgs[0].getProp<std::string>("QUERYOP") == "\"");
+  }
+}