SDMolSupplier: don't throw on errors parsing molecules. This allows the parsing of further mols to continue.

Conformer.cpp: make sure we don't ask for space for zero atoms.

Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.

molopstest.cpp: bad smiles corrected in one test.exe

ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)

Wrap/MolOps.cpp: docs for replacesubstructs.

Code/GraphMol/Conformer.cpp

@@ -16,8 +16,12 @@ namespace RDKit {
 
   Conformer::Conformer(unsigned int numAtoms) {
     dp_mol = 0;
-    d_positions.resize(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0));
-    
+    if(numAtoms){
+      d_positions.resize(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0));
+    } else {
+      d_positions.resize(0);
+      d_positions.clear();
+    }
   }
 
   Conformer::Conformer(const Conformer &conf) {

Code/GraphMol/FileParsers/SDMolSupplier.cpp

@@ -150,6 +150,7 @@ namespace RDKit {
     std::string tempStr = getLine(dp_inStream);
     // FIX: report files missing the $$$$ marker
     while(!(dp_inStream->eof()) && tempStr.find("$$$$") != 0){
+      tempStr = strip(tempStr);
       if(tempStr!=""){
         if (tempStr[0] == '>') { // data header line: start of a data item
             // ignore all other crap and seek for for a data label enclosed
@@ -242,10 +243,6 @@ namespace RDKit {
         d_line++;
         tempStr = getLine(dp_inStream);
       }
-      // be sure to check to see if we hit EOF so that future
-      // calls into this supplier don't die.
-      this->checkForEnd();
-      throw fe;
     }
     catch (MolSanitizeException &se) {
       // We couldn't sanitize a molecule we got - write out an error message and move to
@@ -258,7 +255,7 @@ namespace RDKit {
       }
     } catch (...) {
       BOOST_LOG(rdErrorLog) << "Unexpected error hit on line " << d_line << std::endl;
-      BOOST_LOG(rdErrorLog) << "ERROR: moving to the begining of the next moelcule\n";
+      BOOST_LOG(rdErrorLog) << "ERROR: moving to the begining of the next molecule\n";
     }
     d_last++;
     unsigned int posHold=dp_inStream->tellg();

Code/GraphMol/Kekulize.cpp

@@ -409,7 +409,7 @@ namespace RDKit {
     
       for (bi = mol.beginBonds(); bi != mol.endBonds(); bi++) {
 	// by now the bondtype should have already changed from aromatic
-	if ((*bi)->getBondType() == Bond::AROMATIC) {
+	if (markAtomsBonds && (*bi)->getBondType() == Bond::AROMATIC) {
 	  std::ostringstream errout;
 	  errout << "Kekulization somehow did not convert bond " << (*bi)->getIdx();
 	  std::string msg = errout.str();

Code/GraphMol/ROMol.cpp

@@ -353,6 +353,7 @@ ROMol::BOND_ITER_PAIR ROMol::getEdges() const {return boost::edges(d_graph);}
 
 
 unsigned int ROMol::addAtom(Atom *atom_pin,bool updateLabel,bool takeOwnership){
+  PRECONDITION(atom_pin,"null atom passed in");
   Atom *atom_p;
   if(!takeOwnership) atom_p = atom_pin->copy();
   else atom_p = atom_pin;
@@ -377,6 +378,7 @@ unsigned int ROMol::addAtom(Atom::ATOM_SPTR atom_sp,bool updateLabel)
   return addAtom(atom_sp.get(),updateLabel,false);
 }
 unsigned int ROMol::addBond(Bond *bond_pin,bool takeOwnership){
+  PRECONDITION(bond_pin,"null bond passed in");
   RANGE_CHECK(0,bond_pin->getBeginAtomIdx(),getNumAtoms()-1);
   RANGE_CHECK(0,bond_pin->getEndAtomIdx(),getNumAtoms()-1);
   Bond *bond_p;

Code/GraphMol/RWMol.cpp

@@ -199,6 +199,7 @@ namespace RDKit{
 
   unsigned int RWMol::addBond(Atom *atom1,Atom *atom2,
 			      Bond::BondType bondType){
+    PRECONDITION(atom1&&atom2,"NULL atom passed in");
     return addBond(atom1->getIdx(),atom2->getIdx(),bondType);
   }
 

Code/GraphMol/Wrap/MolOps.cpp

@@ -229,7 +229,7 @@ namespace RDKit{
       See below for examples.\n\
       Default value is 0 (remove the atoms whether or not the entire fragment matches)\n\
 \n\
-  RETURNS: a new molecule with the Hs removed\n\
+  RETURNS: a new molecule with the substructure removed\n\
 \n\
   NOTES:\n\
 \n\
@@ -254,6 +254,39 @@ namespace RDKit{
 		  docString.c_str(),
 		  python::return_value_policy<python::manage_new_object>());
 
+      // ------------------------------------------------------------------------
+      docString="Replaces atoms matching a substructure query in a molecule\n\
+\n\
+  ARGUMENTS:\n\
+\n\
+    - mol: the molecule to be modified\n\
+\n\
+    - query: the molecule to be used as a substructure query\n\
+\n\
+    - replacement: the molecule to be used as the replacement\n\
+\n\
+    - replaceAll: (optional) if this toggle is set, all substructures matching\n\
+      the query will be replaced in a single result, otherwise each result will\n\
+      contain a separate replacement.\n\
+      Default value is False (return multiple replacements)\n\
+\n\
+  RETURNS: a tuple of new molecules with the substructures replaced removed\n\
+\n\
+  NOTES:\n\
+\n\
+    - The original molecule is *not* modified.\n\
+\n\
+  EXAMPLES:\n\
+\n\
+   The following examples substitute SMILES/SMARTS strings for molecules, you'd have\n\
+   to actually use molecules:\n\
+\n\
+    - ReplaceSubstructs('CCOC','OC','NC') -> ('CCNC',)\n\
+\n\
+    - ReplaceSubstructs('COCCOC','OC','NC') -> ('COCCNC','CNCCOC')\n\
+\n\
+    - ReplaceSubstructs('COCCOC','OC','NC',True) -> ('CNCCNC',)\n\
+\n";
       python::def("ReplaceSubstructs", replaceSubstructures,
                   (python::arg("mol"),python::arg("query"),
 		   python::arg("replacement"),

Code/GraphMol/molopstest.cpp

@@ -785,7 +785,7 @@ void test11()
   TEST_ASSERT(!(m->getAtomWithIdx(1)->hasProp("_CIPCode")));
 
   delete m;
-  smi = "F[C@]1C(Cl)CC1";
+  smi = "F[C@H]1C(Cl)CC1";
   m = SmilesToMol(smi);
   TEST_ASSERT(m);
   MolOps::assignAtomChiralCodes(*m,true);