use SP3 params as default for sulfur; add tests for #485;

Fixes #485

Code/GraphMol/PartialCharges/CMakeLists.txt

@@ -5,4 +5,8 @@ rdkit_library(PartialCharges
 rdkit_headers(GasteigerCharges.h
               GasteigerParams.h DEST GraphMol/PartialCharges)
 
+rdkit_test(testPartialCharges test1.cpp LINK_LIBRARIES  PartialCharges
+SmilesParse GraphMol RDGeometryLib RDGeneral DataStructs 
+${RDKit_THREAD_LIBS} )
+
 add_subdirectory(Wrap)

Code/GraphMol/PartialCharges/GasteigerCharges.cpp

@@ -158,6 +158,9 @@ namespace RDKit {
             mode = "so2";
           } else if (no == 1) {
             mode = "so";
+          } else {
+            // some other sulfur state. Default to sp3
+            mode = "sp3";
           }
         }
       }

Code/GraphMol/PartialCharges/test1.cpp

@@ -0,0 +1,59 @@
+//
+//  Copyright (C) 2015 Greg Landrum
+//
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+//
+//
+
+// std bits
+#include <iostream>
+
+// RD bits
+#include <GraphMol/RDKitBase.h>
+#include "GasteigerCharges.h"
+#include "GasteigerParams.h"
+
+#include <GraphMol/SmilesParse/SmilesParse.h>
+
+using namespace RDKit;
+
+void testGitHubIssue485(){
+  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdErrorLog) << "    Test GitHub issue 485: Gasteiger charge calculation fails with hexavalent sulfur" << std::endl;
+
+  {
+    std::string smi="CC.S(F)(F)(F)(F)(F)F";
+    ROMol *mol = SmilesToMol(smi);
+    std::vector<double> charges(mol->getNumAtoms(),0);
+    computeGasteigerCharges(*mol,charges,12,true);
+    TEST_ASSERT(charges[0]==charges[0]); // test for nan
+    TEST_ASSERT(charges[2]==charges[2]); // test for nan
+    
+    delete mol;
+  }
+  {
+    std::string smi="CCS(F)(F)(F)(F)F";
+    ROMol *mol = SmilesToMol(smi);
+    std::vector<double> charges(mol->getNumAtoms(),0);
+    computeGasteigerCharges(*mol,charges,12,true);
+    TEST_ASSERT(charges[0]==charges[0]); // test for nan
+    TEST_ASSERT(charges[2]==charges[2]); // test for nan
+    
+    delete mol;
+  }
+  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
+}
+
+
+
+int main(int argc,char *argv[])
+{
+  testGitHubIssue485();
+  return 0;
+}
+
+