Zero-order edges produce incorrect assembly indices #64

Author: LouieSlocombe

unitTests/graphioTester.cpp

@@ -194,6 +194,10 @@ int main()
         "extra type\n2\n1 2\nC C\n1 2\n",
         "expected 1 bond label, found 2"
     );
+    expectRejected(
+        "zero type\n2\n1 2\nC C\n0\n",
+        "zero-order bonds are not supported"
+    );
     expectRejected(
         "negative type\n2\n1 2\nC C\n-1\n",
         "bond label must be between 0 and"

unitTests/molfileParserTester.cpp

@@ -153,6 +153,30 @@ int main(int argc, char **argv)
     }
     assert(rejected);
 
+    string zeroOrderBond = validMolfile;
+    const size_t zeroOrderPosition = zeroOrderBond.find("  4  5  1");
+    assert(zeroOrderPosition != string::npos);
+    zeroOrderBond.replace(zeroOrderPosition, 9, "  4  5  0");
+    molGraph zeroOrderDestination;
+    string zeroOrderSentinel = "zero-order-sentinel";
+    zeroOrderDestination.addAtom(zeroOrderSentinel);
+    istringstream zeroOrderInput(zeroOrderBond);
+    rejected = false;
+    try
+    {
+        molfileParser(zeroOrderInput, zeroOrderDestination);
+    }
+    catch (const runtime_error &error)
+    {
+        rejected = string(error.what()).find(
+            "zero-order bonds are not supported"
+        ) != string::npos;
+    }
+    assert(rejected);
+    assert(zeroOrderDestination.mg.size() == 1);
+    assert(zeroOrderDestination.mg.front().type == zeroOrderSentinel);
+    assert(zeroOrderDestination.totalBonds == 0);
+
     string negativeBondOrder = validMolfile;
     const size_t negativeBondPosition = negativeBondOrder.find("  4  5  1");
     assert(negativeBondPosition != string::npos);

v5/graphio.h

@@ -215,6 +215,12 @@ inline void graphio(std::istream &ifs, molGraph &mg)
                 std::to_string(std::numeric_limits<short>::max())
             );
         }
+        if (value == 0)
+        {
+            throw std::runtime_error(
+                "invalid native graph: zero-order bonds are not supported"
+            );
+        }
         bondLabels.push_back(static_cast<short>(value));
     }
 

v5/molfileParser.h

@@ -158,6 +158,10 @@ void molfileParser(std::istream &molfile, molGraph &mg)
             throw std::runtime_error(
                 "invalid molfile: bond order must be nonnegative"
             );
+        if (bondOrder == 0)
+            throw std::runtime_error(
+                "invalid molfile: zero-order bonds are not supported"
+            );
         parsed.addBond(atomA - 1, atomB - 1, bondOrder);
     }
     if (removeHydrogens)