merge back in changes from ChemTransforms (r30:51);

the makefile for linux is still missing (I have one, I just need to retrieve it) but otherwise this is in pretty good shape. err, I think so at least.
2026-06-03 21:44:30 +08:00 · 2006-09-15 16:44:38 +00:00
parent 9f5ed2186a
commit a890611a22
26 changed files with 2366 additions and 523 deletions
--- a/Code/Geometry/Wrap/Point.cpp
+++ b/Code/Geometry/Wrap/Point.cpp
@@ -82,6 +82,8 @@ namespace RDGeom {
        .def(python::self -= python::self)
        .def(python::self + python::self)
        .def(python::self += python::self)
+        .def(python::self * double())
+        .def(python::self / double())
        .def("__imul__", &Point3D::operator*=,
             python::return_value_policy<python::copy_non_const_reference>(),
             "Scalar multiplication")
@@ -120,6 +122,8 @@ namespace RDGeom {
        .def(python::self -= python::self)
        .def(python::self + python::self)
        .def(python::self += python::self)
+        .def(python::self * double())
+        .def(python::self / double())
        .def("__imul__", &Point2D::operator*=,
             python::return_value_policy<python::copy_non_const_reference>(),
             "Scalar multiplication")
--- a/Code/GraphMol/Atom.cpp
+++ b/Code/GraphMol/Atom.cpp
@@ -366,6 +366,25 @@ void Atom::expandQuery(Atom::QUERYATOM_QUERY *what,

 bool Atom::Match(Atom const *what) const {
  bool res = getAtomicNum() == what->getAtomicNum();
+  // special dummy--dummy match case:
+  //   X matches X, Xa, Xb, etc
+  //   Xa only matches X and Xa
+  if(res && !getAtomicNum()){
+    std::string l1;
+    if(this->hasProp("dummyLabel")){
+      this->getProp("dummyLabel",l1);
+    } else{
+      l1="X";
+    }
+    if(l1!="X"){
+      std::string l2;
+      if(what->hasProp("dummyLabel")) what->getProp("dummyLabel",l2);
+      else l2="X";
+      if(l2!="X" && l1!=l2){
+	res = false;
+      }
+    }
+  }
  return res;
 }
 bool Atom::Match(const Atom::ATOM_SPTR what) const {
--- a/Code/GraphMol/ChemTransforms/ChemTransforms.cpp
+++ b/Code/GraphMol/ChemTransforms/ChemTransforms.cpp
@@ -0,0 +1,183 @@
+// $Id$
+//
+//  Copyright (C) 2006 Greg Landrum
+//
+//   @@ All Rights Reserved  @@
+//
+#include <RDGeneral/utils.h>
+#include <RDGeneral/Invariant.h>
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/Substruct/SubstructMatch.h>
+
+#include <vector>
+#include <algorithm>
+
+namespace RDKit{
+
+  ROMol *deleteSubstructs(const ROMol &mol, const ROMol &query,
+                          bool onlyFrags) {
+    RWMol *res = static_cast<RWMol*>(new ROMol(mol,false));
+    std::vector<MatchVectType> fgpMatches;
+    std::vector<MatchVectType>::const_iterator mati;
+    std::pair<int, int> amat;
+    VECT_INT_VECT matches; // all matches onto the molecule - list of list of atom ids
+    MatchVectType::const_iterator mi;
+    // do the substructure matching and get the atoms that match the query
+    SubstructMatch(*res, query, fgpMatches);
+
+    // if didn't find any matches nothing to be done here
+    // simply return a copy of the molecule
+    if (fgpMatches.size() == 0) {
+      return res;
+    }
+
+    for (mati = fgpMatches.begin(); mati != fgpMatches.end(); mati++) {
+      INT_VECT match; // each match onto the molecule - list of atoms ids
+      for (mi = mati->begin(); mi != mati->end(); mi++) {
+        match.push_back(mi->second);
+      }
+      matches.push_back(match);
+    }
+
+    // now loop over the list of matches and check if we can delete any of them
+    INT_VECT delList;
+    
+    VECT_INT_VECT_I mxi, fi;
+    if (onlyFrags) {
+      VECT_INT_VECT frags;
+      
+      unsigned int nfrags = MolOps::getMolFrags(*res, frags);
+      for (fi = frags.begin(); fi != frags.end(); fi++) {
+        std::sort(fi->begin(), fi->end());
+        for (mxi = matches.begin(); mxi != matches.end(); mxi++) {
+          std::sort(mxi->begin(), mxi->end());
+          if ((*fi) == (*mxi) ) {
+            INT_VECT tmp; 
+            Union((*mxi), delList, tmp);
+            delList = tmp;
+            break;
+          } // end of if we found a matching fragment
+        } // endof loop over matches
+      } // end of loop over fragments
+    } // end of if onlyFrags
+    else {
+      // in this case we want to delete any matches we find
+      // simply loop over the matches and collect the atoms that need to 
+      // be removed
+      for (mxi = matches.begin(); mxi != matches.end(); mxi++) {
+        INT_VECT tmp; 
+        Union((*mxi), delList, tmp);
+        delList = tmp;
+      }
+    }
+
+    // now loop over the union list and delete the atoms
+    // Will do this in the decreasing order of the atomIds
+    // this is so that the AtomIds ids in the "delList" are
+    // not invalidated by a previous removal (removing atom number i changes 
+    // the atom indices only atoms with indices >i )
+    std::sort(delList.begin(), delList.end());
+
+    INT_VECT_RI dri;
+    for (dri = delList.rbegin(); dri != delList.rend(); dri++) {
+      res->removeAtom(*dri);
+    }
+    // if we removed any atoms, clear the computed properties:
+    if(delList.size()){
+      res->clearComputedProps(true);
+      // update our properties, but allow unhappiness:
+      res->updatePropertyCache(false);
+    }
+    return res;
+  }
+
+  std::vector<ROMOL_SPTR>
+  replaceSubstructs(const ROMol &mol, const ROMol &query,const ROMol &replacement,
+                    bool replaceAll) {
+    std::vector<ROMOL_SPTR> res;
+    std::vector<MatchVectType> fgpMatches;
+
+    // do the substructure matching and get the atoms that match the query
+    SubstructMatch(mol, query, fgpMatches);
+
+    // if we didn't find any matches, there's nothing to be done here
+    // simply return a list with a copy of the starting molecule
+    if (fgpMatches.size() == 0) {
+      res.push_back(ROMOL_SPTR(new ROMol(mol,false)));
+      return res;
+    }
+
+    INT_VECT delList;
+
+    // now loop over the list of matches and replace them:
+    for (std::vector<MatchVectType>::const_iterator mati = fgpMatches.begin();
+         mati != fgpMatches.end(); mati++) {
+      INT_VECT match; // each match onto the molecule - list of atoms ids
+      for (MatchVectType::const_iterator mi = mati->begin();
+           mi != mati->end(); mi++) {
+        match.push_back(mi->second);
+      }
+      INT_VECT sortMatch = match;
+      std::sort(sortMatch.begin(),sortMatch.end());
+
+      if( !replaceAll || !res.size() ) {
+        res.push_back(ROMOL_SPTR(new ROMol(mol,false)));
+      }
+      RWMol *newMol = static_cast<RWMol *>(res.rbegin()->get());
+
+      // we need a tab to the orig number of atoms because the
+      // new molecule will start numbered above this:
+      int numOrigAtoms=newMol->getNumAtoms();
+      
+      // Add the atoms and bonds from the replacement:
+      newMol->insertMol(replacement);
+
+      // loop over the central atom's (the first atom in match) bonds
+      // and duplicate any that connect to the remainder of the molecule:
+      Atom *origAtom=newMol->getAtomWithIdx(match[0]);
+      ROMol::ADJ_ITER nbrIdx,endNbrs;
+      boost::tie(nbrIdx,endNbrs) = newMol->getAtomNeighbors(origAtom);
+      while(nbrIdx!=endNbrs){
+        // we don't want to duplicate any "intra-match" bonds:
+        if(!std::binary_search(sortMatch.begin(),sortMatch.end(),int(*nbrIdx))){
+          Bond *oBond=newMol->getBondBetweenAtoms(match[0],*nbrIdx);
+          CHECK_INVARIANT(oBond,"required bond not found");
+          newMol->addBond(numOrigAtoms,*nbrIdx,oBond->getBondType());
+        }
+        nbrIdx++;
+      }
+      
+      if(replaceAll){
+        // we'll accumulate  a list of atoms to be removed:
+        INT_VECT tmp; 
+        Union(sortMatch, delList, tmp);
+        delList = tmp;
+      } else {
+        // just delete the atoms now:
+        for (INT_VECT_RI dri = sortMatch.rbegin(); dri != sortMatch.rend(); dri++) {
+          newMol->removeAtom(*dri);
+        }
+      }
+    }
+
+    if(replaceAll){
+      // remove the atoms from the delList:
+      std::sort(delList.begin(),delList.end());
+      RWMol *newMol = static_cast<RWMol *>(res[0].get());
+      for (INT_VECT_RI dri = delList.rbegin(); dri != delList.rend(); dri++) {
+        newMol->removeAtom(*dri);
+      }
+    }
+
+    // clear computed props and do basic updates on the
+    // the resulting molecules, but allow unhappiness:
+    for(std::vector<ROMOL_SPTR>::iterator resI=res.begin();
+        resI!=res.end();resI++){
+      (*resI)->clearComputedProps(true);
+      (*resI)->updatePropertyCache(false);
+    }
+
+    return res;
+  }
+
+}
--- a/Code/GraphMol/ChemTransforms/ChemTransforms.h
+++ b/Code/GraphMol/ChemTransforms/ChemTransforms.h
@@ -0,0 +1,72 @@
+//
+//  Copyright (C) 2006 Greg Landrum
+//
+//   @@ All Rights Reserved  @@
+//
+#ifndef _RD_CHEMTRANSFORMS_H__
+#define _RD_CHEMTRANSFORMS_H__
+
+#include <boost/smart_ptr.hpp>
+#include <vector>
+
+namespace RDKit{
+  class ROMol;
+  typedef boost::shared_ptr<ROMol>    ROMOL_SPTR;
+
+  //! \brief Returns a copy of an ROMol with the atoms and bonds that 
+  //!      match a pattern removed.
+  /*!
+      \param mol       the ROMol of interest
+      \param query     the query ROMol
+      \param onlyFrags if this is set, only matches that correspond to an
+                       entire fragment will be removed.  This is useful for
+		       salt removal
+
+      \return a copy of \c mol with the matching atoms and bonds (if any)
+              removed.		       
+  */
+  ROMol *deleteSubstructs(const ROMol &mol, const ROMol &query,
+			  bool replaceAll=false);
+
+  //! \brief Returns a list of copies of an ROMol with the atoms and bonds that 
+  //!      match a pattern replaced with the atoms contained in another molecule.
+  /*!
+     Bonds are created between the joining atom in the existing molecule
+     and the atoms in the new molecule. So, using SMILES instead of molecules:
+            replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]') ->
+	          ['[X]NCCNC(=O)O','OC(=O)NCCN[X]']
+            replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]',true) ->
+	          ['[X]NCCN[X]']
+     Chains should be handled "correctly":
+            replaceSubstructs('CC(=O)C','C(=O)','[X]') ->
+	          ['C[X]C']
+     As should rings:
+            replaceSubstructs('C1C(=O)C1','C(=O)','[X]') ->
+	          ['C1[X]C1']
+     And higher order branches:
+            replaceSubstructs('CC(=O)(C)C','C(=O)','[X]') ->
+	          ['C[X](C)C']
+     Note that the client is responsible for making sure that the
+       resulting molecule actually makes sense - this function does not
+       perform sanitization.
+
+      \param mol         the ROMol of interest
+      \param query       the query ROMol
+      \param replacement the ROMol to be inserted
+      \param replaceAll  if this is true, only a single result, with all occurances
+                         of the substructure replaced, will be returned.
+
+      \return a vector of pointers to copies of \c mol with the matching atoms
+          and bonds (if any) replaced
+
+  */
+  std::vector<ROMOL_SPTR> replaceSubstructs(const ROMol &mol, const ROMol &query,
+					    const ROMol &replacement,
+					    bool replaceAll=false);
+}
+
+#endif
+
+
+
+
--- a/Code/GraphMol/ChemTransforms/ChemTransforms.vcproj
+++ b/Code/GraphMol/ChemTransforms/ChemTransforms.vcproj
@@ -0,0 +1,143 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="libChemTransforms"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="4"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(BOOSTHOME)\include\$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_LIB"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				UsePrecompiledHeader="2"
+				PrecompiledHeaderFile=".\Debug/ChemTransforms.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\Debug\ChemTransforms.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="4"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(BOOSTHOME)\include\$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				RuntimeTypeInfo="TRUE"
+				UsePrecompiledHeader="2"
+				PrecompiledHeaderFile=".\Release/ChemTransforms.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\Release\ChemTransforms.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\ChemTransforms.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="ChemTransforms.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>
--- a/Code/GraphMol/ChemTransforms/testChemTransforms.cpp
+++ b/Code/GraphMol/ChemTransforms/testChemTransforms.cpp
@@ -0,0 +1,194 @@
+// $Id$
+//
+//  Copyright (C) 2006 Greg Landrum
+//
+//   @@ All Rights Reserved  @@
+//
+#include <RDGeneral/RDLog.h>
+#include <GraphMol/RDKitBase.h>
+#include <string>
+#include <iostream>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/ChemTransforms/ChemTransforms.h>
+
+using namespace RDKit;
+
+void testDeleteSubstruct() 
+{
+  int i = 0;
+  ROMol *mol1=0,*mol2=0,*matcher1=0,*matcher2=0,*matcher3=0;
+  std::string smi,sma;
+  
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "Testing deleteSubstruct" << std::endl;
+
+  // a lot of the seemingly repetitive stuff is here for Issue96
+  smi = "CCC(=O).C=O";
+  mol1 = SmilesToMol(smi);
+  TEST_ASSERT(mol1);
+  TEST_ASSERT(mol1->getNumAtoms()==6)
+  sma = "C=O";
+  matcher1 = SmartsToMol(sma);
+  TEST_ASSERT(matcher1);
+
+  
+  mol2 = deleteSubstructs(*mol1,*matcher1,0);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==2)
+  mol2 = deleteSubstructs(*mol2,*matcher1,0);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==2)
+  
+  delete matcher1;
+  sma = "[Cl;H1&X1,-]";
+  matcher1 = SmartsToMol(sma);
+  sma = "[Na+]";
+  matcher2 = SmartsToMol(sma);
+  sma = "[O;H2,H1&-,X0&-2]";
+  matcher3 = SmartsToMol(sma);
+  delete mol1;
+  mol1 = SmilesToMol("CCO.Cl");
+  TEST_ASSERT(mol1);
+  TEST_ASSERT(mol1->getNumAtoms()==4);
+
+  delete mol2;
+  mol2 = deleteSubstructs(*mol1,*matcher1,true);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==3);
+  mol2 = deleteSubstructs(*mol2,*matcher2,true);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==3);
+  mol2 = deleteSubstructs(*mol2,*matcher3,true);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==3);
+
+  delete mol1;
+  mol1 = SmilesToMol("CC(=O)[O-].[Na+]");
+  TEST_ASSERT(mol1);
+  TEST_ASSERT(mol1->getNumAtoms()==5);
+
+  delete matcher1;
+  matcher1 = SmartsToMol("[Cl;H1&X1,-]");
+  delete matcher2;
+  matcher2 = SmartsToMol("[Na+]");
+
+  mol2 = deleteSubstructs(*mol1,*matcher1,true);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==5);
+
+  mol2 = deleteSubstructs(*mol2,*matcher2,true);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==4);
+
+  mol2 = deleteSubstructs(*mol2,*matcher1,true);
+  TEST_ASSERT(mol2);
+  TEST_ASSERT(mol2->getNumAtoms()==4);
+
+  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
+}
+
+void testReplaceSubstructs() 
+{
+  int i = 0;
+  ROMol *mol1=0,*mol2=0,*matcher1=0,*frag=0;
+  std::string smi,sma;
+  std::vector<ROMOL_SPTR> vect;
+
+  
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "Testing replaceSubstruct" << std::endl;
+
+  smi = "CCCC";
+  mol1 = SmilesToMol(smi);
+  TEST_ASSERT(mol1);
+
+  sma = "C(=O)O";
+  matcher1 = SmartsToMol(sma);
+  TEST_ASSERT(matcher1);
+
+  smi = "N";
+  frag = SmilesToMol(smi);
+  TEST_ASSERT(frag);
+
+  vect = replaceSubstructs(*mol1,*matcher1,*frag);
+  TEST_ASSERT(vect.size()==1);
+  TEST_ASSERT(mol1->getNumAtoms()==4);
+  TEST_ASSERT(vect[0]->getNumAtoms()==4);
+  
+
+  delete mol1;
+  smi = "CCCC(=O)O";
+  mol1 = SmilesToMol(smi);
+  TEST_ASSERT(mol1);
+  vect = replaceSubstructs(*mol1,*matcher1,*frag);
+  TEST_ASSERT(vect.size()==1);
+  TEST_ASSERT(mol1->getNumAtoms()==6);
+  TEST_ASSERT(vect[0]->getNumAtoms()==4);
+  
+  vect = replaceSubstructs(*mol1,*matcher1,*frag,true);
+  TEST_ASSERT(vect.size()==1);
+  TEST_ASSERT(mol1->getNumAtoms()==6);
+  TEST_ASSERT(vect[0]->getNumAtoms()==4);
+  
+  delete mol1;
+  smi = "OC(=O)CCCC(=O)O";
+  mol1 = SmilesToMol(smi);
+  TEST_ASSERT(mol1);
+  vect = replaceSubstructs(*mol1,*matcher1,*frag);
+  TEST_ASSERT(vect.size()==2);
+  TEST_ASSERT(mol1->getNumAtoms()==9);
+  TEST_ASSERT(vect[0]->getNumAtoms()==7);
+  TEST_ASSERT(vect[1]->getNumAtoms()==7);
+
+  // use replaceAll when a single replacement is available:
+  vect = replaceSubstructs(*mol1,*matcher1,*frag,true);
+  TEST_ASSERT(vect.size()==1);
+  TEST_ASSERT(mol1->getNumAtoms()==9);
+  TEST_ASSERT(vect[0]->getNumAtoms()==5);
+  
+  delete matcher1;
+  sma = "C=O";
+  matcher1 = SmartsToMol(sma);
+  TEST_ASSERT(matcher1);
+
+  delete mol1;
+  smi = "CC(=O)C";
+  mol1 = SmilesToMol(smi);
+  TEST_ASSERT(mol1);
+  vect = replaceSubstructs(*mol1,*matcher1,*frag);
+  TEST_ASSERT(vect.size()==1);
+  TEST_ASSERT(mol1->getNumAtoms()==4);
+  TEST_ASSERT(vect[0]->getNumAtoms()==3);
+
+  delete mol1;
+  smi = "C1C(=O)C1";
+  mol1 = SmilesToMol(smi);
+  TEST_ASSERT(mol1);
+  vect = replaceSubstructs(*mol1,*matcher1,*frag);
+  TEST_ASSERT(vect.size()==1);
+  TEST_ASSERT(mol1->getNumAtoms()==4);
+  TEST_ASSERT(vect[0]->getNumAtoms()==3);
+  TEST_ASSERT(vect[0]->getNumBonds()==3);
+
+  
+  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
+}
+
+
+
+
+int main() { 
+  RDLog::InitLogs();
+    
+  BOOST_LOG(rdInfoLog) << "********************************************************\n";
+  BOOST_LOG(rdInfoLog) << "Testing Chemical Transforms \n";
+
+#if 1
+  testDeleteSubstruct();
+  testReplaceSubstructs();
+#endif
+
+  BOOST_LOG(rdInfoLog) << "*******************************************************\n";
+  return(0);
+}
+
--- a/Code/GraphMol/ChemTransforms/testChemTransforms.vcproj
+++ b/Code/GraphMol/ChemTransforms/testChemTransforms.vcproj
@@ -0,0 +1,156 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="testChemTransforms"
+	ProjectGUID="{5408B0E6-0B50-4E12-921A-8F1B3E483716}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\testExecs"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(BOOSTHOME)/include/$(BOOSTBASE),$(RDBASE)/Code"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				PrecompiledHeaderFile=".\Debug/testChemTransforms.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib"
+				OutputFile="./testExecs/main.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(BOOSTHOME)\lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\Debug/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Debug/testChemTransforms.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(BOOSTHOME)/include/$(BOOSTBASE),$(RDBASE)/Code"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/testChemTransforms.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib"
+				OutputFile="./testExecs/main.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(BOOSTHOME)\lib"
+				ProgramDatabaseFile=".\Release/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/testChemTransforms.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\testChemTransforms.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>
--- a/Code/GraphMol/ChemTransforms/test_list.py
+++ b/Code/GraphMol/ChemTransforms/test_list.py
@@ -0,0 +1,14 @@
+import sys
+
+tests=[
+  ("testExecs/main.exe","",{}),
+  ]
+
+longTests=[
+  ]
+
+if __name__=='__main__':
+  import sys
+  import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))
--- a/Code/GraphMol/FileParsers/MolFileParser.cpp
+++ b/Code/GraphMol/FileParsers/MolFileParser.cpp
@@ -197,7 +197,8 @@ namespace RDKit{
    //double pX,pY,pZ;
    std::string symb;
    int massDiff,chg,hCount;
-    //int rxnComponentType,rxnComponentNumber,atomMapNumber,inversionFlag,exactChangeFlag;
+    int stereoCare,totValence;
+    int atomMapNumber,inversionFlag,exactChangeFlag;
    
    try {
      pos.x = stripSpacesAndCast<double>(text.substr(0,10));
@@ -250,6 +251,18 @@ namespace RDKit{
    if(symb=="L" || symb=="A" || symb=="Q" || symb=="*" || symb=="LP"
       || (symb>="R0" && symb<="R9") ){
      res->setAtomicNum(0);
+      if(symb=="*") res->setProp("dummyLabel",std::string("X"));
+      else if(symb=="R0") res->setProp("dummyLabel",std::string("Xa"));
+      else if(symb=="R1") res->setProp("dummyLabel",std::string("Xb"));
+      else if(symb=="R2") res->setProp("dummyLabel",std::string("Xc"));
+      else if(symb=="R3") res->setProp("dummyLabel",std::string("Xd"));
+      else if(symb=="R4") res->setProp("dummyLabel",std::string("Xe"));
+      else if(symb=="R5") res->setProp("dummyLabel",std::string("Xf"));
+      else if(symb=="R6") res->setProp("dummyLabel",std::string("Xg"));
+      else if(symb=="R7") res->setProp("dummyLabel",std::string("Xh"));
+      else if(symb=="R8") res->setProp("dummyLabel",std::string("Xi"));
+      else if(symb=="R9") res->setProp("dummyLabel",std::string("Xj"));
+      else res->setProp("dummyLabel",symb);
    } else {
      res->setAtomicNum(PeriodicTable::getTable()->getAtomicNumber(symb));
      res->setMass(PeriodicTable::getTable()->getAtomicWeight(res->getAtomicNum()));
@@ -264,7 +277,7 @@ namespace RDKit{
      res->setMass(res->getMass()+massDiff);
    }
    
-#if 0
+#if 1
    stereoCare=0;
    if(text.size()>=48){
      try {
@@ -287,28 +300,6 @@ namespace RDKit{
 	throw FileParseException(errout.str()) ;
      }
    }
-    rxnComponentType=0;
-    if(text.size()>=57){
-      try {
-	rxnComponentType= stripSpacesAndCast<int>(text.substr(54,3));
-      }
-      catch (boost::bad_lexical_cast &) {
-	std::ostringstream errout;
-	errout << "Cannot convert " << text.substr(54,3) << " to int";
-	throw FileParseException(errout.str()) ;
-      }
-    }
-    rxnComponentNumber=0;
-    if(text.size()>=60){
-      try {
-	rxnComponentNumber= stripSpacesAndCast<int>(text.substr(57,3));
-      }
-      catch (boost::bad_lexical_cast &) {
-	std::ostringstream errout;
-	errout << "Cannot convert " << text.substr(57,3) << " to int";
-	throw FileParseException(errout.str()) ;
-      }
-    }
    atomMapNumber=0;
    if(text.size()>=63){
      try {
@@ -345,13 +336,11 @@ namespace RDKit{
    

    // save it for later
-    res->setProp("stereoCare",stereoCare);
-    res->setProp("totValence",totValence);
-    res->setProp("rxnComponentType",rxnComponentType);
-    res->setProp("rxnComponentNumber",rxnComponentNumber);
-    res->setProp("atomMapNumber",atomMapNumber);
-    res->setProp("inversionFlag",inversionFlag);
-    res->setProp("exactChangeFlag",exactChangeFlag);
+    res->setProp("molStereoCare",stereoCare);
+    res->setProp("molTotValence",totValence);
+    res->setProp("molAtomMapNumber",atomMapNumber);
+    res->setProp("molInversionFlag",inversionFlag);
+    res->setProp("molExactChangeFlag",exactChangeFlag);
 #endif    
    return res;
  };
@@ -442,19 +431,19 @@ namespace RDKit{
      } catch (boost::bad_lexical_cast) {
 	;
      }
-#if 0
+#if 1
    if( text.size() >= 18 )
      try {
-	topology = stripSpacesAndCast<int>(text.substr(15,3));
-	res->setProp("topology",topology);
+	int topology = stripSpacesAndCast<int>(text.substr(15,3));
+	res->setProp("molTopology",topology);
      } catch (boost::bad_lexical_cast) {
 	;
      }
    
    if( text.size() >= 21 )
      try {
-	reactStatus = stripSpacesAndCast<int>(text.substr(18,3));
-	res->setProp("reactStatus",reactStatus);
+	int reactStatus = stripSpacesAndCast<int>(text.substr(18,3));
+	res->setProp("molReactStatus",reactStatus);
      } catch (boost::bad_lexical_cast) {
 	;
      }
--- a/Code/GraphMol/QueryOps.cpp
+++ b/Code/GraphMol/QueryOps.cpp
@@ -509,7 +509,8 @@ ATOM_EQUALS_QUERY *makeAtomInRingQuery(){
 }

 ATOM_EQUALS_QUERY *makeAtomInNRingsQuery(int what){
-  ATOM_EQUALS_QUERY *res= makeAtomSimpleQuery(what,queryIsAtomInNRings);
+  ATOM_EQUALS_QUERY *res;
+  res = makeAtomSimpleQuery(what,queryIsAtomInNRings);
  res->setDescription("AtomInNRings");
  return res;
 }
--- a/Code/GraphMol/QueryOps.h
+++ b/Code/GraphMol/QueryOps.h
@@ -79,7 +79,53 @@ namespace RDKit{
  //! returns a Query for matching any atom
  ATOM_NULL_QUERY *makeAtomNullQuery();

+  static int queryAtomRingMembership(Atom const *at) {
+    return static_cast<int>(at->getOwningMol().getRingInfo()->numAtomRings(at->getIdx()));
+  }

+  // I'm pretty sure that this typedef shouldn't be necessary,
+  // but VC++ generates a warning about const Atom const * in
+  // the definition of Match, then complains about an override
+  // that differs only by const/volatile (c4301), then generates
+  // incorrect code if we don't do this... so let's do it.
+  typedef Atom const *ConstAtomPtr;
+  class InRingQuery : public Queries::EqualityQuery<int, ConstAtomPtr,true> {
+  public:
+    InRingQuery() : Queries::EqualityQuery<int,ConstAtomPtr,true>(-1) {
+      this->setDescription("AtomInNRings");
+      this->setDataFunc(queryAtomRingMembership);
+    };
+    explicit InRingQuery(int v) : Queries::EqualityQuery<int,ConstAtomPtr,true>(v) {
+      this->setDescription("AtomInNRings");
+      this->setDataFunc(queryAtomRingMembership);
+    };
+
+    virtual bool Match(const ConstAtomPtr what) const {
+      int v = this->TypeConvert(what,Queries::Int2Type<true>());
+      bool res;
+      if(this->d_val<0){
+	res = v!=0;
+      } else {
+	res=!Queries::queryCmp(v,this->d_val,this->d_tol);
+      }
+      if(this->getNegation()){
+	res=!res;
+      }
+      return res;
+    }
+
+    //! returns a copy of this query
+    Queries::Query<int,ConstAtomPtr,true> *
+    copy() const {
+      InRingQuery *res =
+	new InRingQuery(this->d_val);
+      res->setNegation(getNegation());
+      res->setTol(this->getTol());
+      res->d_description = this->d_description;
+      return res;
+    }
+  };
+  
  //! allows use of recursive structure queries (e.g. recursive SMARTS)
  class RecursiveStructureQuery : public Queries::SetQuery<int,Atom const *,true> {
  public:
--- a/Code/GraphMol/ROMol.h
+++ b/Code/GraphMol/ROMol.h
@@ -294,7 +294,7 @@ namespace RDKit{
        ... atomPtr is a const Atom * ...
        ROMol::OEDGE_ITER beg,end;
        ROMol::GRAPH_MOL_BOND_PMAP::const_type pMap = molPtr->getBondPMap();
-	boost::tie(beg,end) = molPtr->getAtomNeighbors(atomPtr);
+	boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
 	while(beg!=end){
 	  const Bond *bond=pMap[*beg];
 	  ... do something with the Bond ...
@@ -307,7 +307,7 @@ namespace RDKit{
        ... atomPtr is a const Atom * ...
        ROMol::OEDGE_ITER beg,end;
        ROMol::GRAPH_MOL_BOND_PMAP::type pMap = molPtr->getBondPMap();
-	boost::tie(beg,end) = molPtr->getAtomNeighbors(atomPtr);
+	boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
 	while(beg!=end){
 	  Bond *bond=pMap[*beg];
 	  ... do something with the Bond ...
--- a/Code/GraphMol/SmilesParse/SmartsWrite.cpp
+++ b/Code/GraphMol/SmilesParse/SmartsWrite.cpp
@@ -150,7 +150,10 @@ namespace RDKit {
 	needParen = true;
      }
      else if (descrip == "AtomInNRings") {
-	res << "R" << query->getVal();
+	res << "R";
+ 	if(query->getVal()>=0){
+	  res << query->getVal();
+	}
 	needParen = true;
      }
      else if (descrip == "AtomFormalCharge") {
--- a/Code/GraphMol/SmilesParse/SmilesParseOps.cpp
+++ b/Code/GraphMol/SmilesParse/SmilesParseOps.cpp
@@ -5,6 +5,7 @@
 //   @@ All Rights Reserved  @@
 //
 #include <GraphMol/RDKitBase.h>
+#include <GraphMol/RDKitQueries.h>
 #include "SmilesParse.h"
 #include "SmilesParseOps.h"
 #include <list>
@@ -28,7 +29,7 @@ namespace SmilesParseOps{
  //  between the fragment and the molecule
  //
  void AddFragToMol(RWMol *mol,RWMol *frag,Bond::BondType bondOrder,
-		    Bond::BondDir bondDir,bool closeRings ){
+		    Bond::BondDir bondDir,bool closeRings,bool doingQuery ){
    RWMol::GRAPH_NODE_TYPE lastAt = mol->getActiveAtom();
    int nOrigAtoms = mol->getNumAtoms();
    int nOrigBonds = mol->getNumBonds();
@@ -84,28 +85,56 @@ namespace SmilesParseOps{
 	leadingBond->setEndAtomIdx(atomIdx1);
 	mol->addBond(leadingBond,true);
      } else {
-	if(bondOrder == Bond::UNSPECIFIED){
-	  // no bond order provided, figure it out ourselves
-	  if(lastAt->getIsAromatic() && firstAt->getIsAromatic() ){
-	    bo = Bond::AROMATIC;
+	if(!doingQuery){
+	  if(bondOrder == Bond::UNSPECIFIED){
+	    // no bond order provided, figure it out ourselves
+	    if(lastAt->getIsAromatic() && firstAt->getIsAromatic() ){
+	      bo = Bond::AROMATIC;
+	    }
+	    else{
+	      bo = Bond::SINGLE;
+	    }
 	  }
 	  else{
-	    bo = Bond::SINGLE;
+	    bo = bondOrder;
+	  }
+	  if(bo==Bond::DATIVEL){
+	    int tmp=atomIdx2;
+	    atomIdx2 = atomIdx1;
+	    atomIdx1 = tmp;
+	    bo = Bond::DATIVE;
+	  } else if(bo == Bond::DATIVER){
+	    bo = Bond::DATIVE;
+	  }
+	  int idx = mol->addBond(atomIdx2,atomIdx1,bo)-1;
+	  mol->getBondWithIdx(idx)->setBondDir(bondDir);
+	} else {
+	  // semantics are different in SMARTS, unspecified bonds can be single or aromatic:
+	  if(bondOrder == Bond::UNSPECIFIED){
+	    QueryBond *newB=new QueryBond(Bond::SINGLE);
+	    newB->expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),
+			      Queries::COMPOSITE_OR,
+			      true);
+	    newB->setOwningMol(mol);
+	    newB->setBeginAtomIdx(atomIdx1);
+	    newB->setEndAtomIdx(atomIdx2);
+	    mol->addBond(newB);
+	    delete newB;
+	  }
+	  else{
+	    bo=bondOrder;
+	    if(bo==Bond::DATIVEL){
+	      int tmp=atomIdx2;
+	      atomIdx2 = atomIdx1;
+	      atomIdx1 = tmp;
+	      bo = Bond::DATIVE;
+	    } else if(bo == Bond::DATIVER){
+	      bo = Bond::DATIVE;
+	    }
+	    int idx = mol->addBond(atomIdx2,atomIdx1,bo)-1;
+	    mol->getBondWithIdx(idx)->setBondDir(bondDir);
 	  }
 	}
-	else{
-	  bo = bondOrder;
-	}
-	if(bo==Bond::DATIVEL){
-	  int tmp=atomIdx2;
-	  atomIdx2 = atomIdx1;
-	  atomIdx1 = tmp;
-	  bo = Bond::DATIVE;
-	} else if(bo == Bond::DATIVER){
-	  bo = Bond::DATIVE;
-	}
-	int idx = mol->addBond(atomIdx2,atomIdx1,bo)-1;
-	mol->getBondWithIdx(idx)->setBondDir(bondDir);
      }
    }

--- a/Code/GraphMol/SmilesParse/SmilesParseOps.h
+++ b/Code/GraphMol/SmilesParse/SmilesParseOps.h
@@ -16,7 +16,7 @@ namespace SmilesParseOps {
  void AddFragToMol(RDKit::RWMol *mol,RDKit::RWMol *frag,
 		    RDKit::Bond::BondType bondOrder=RDKit::Bond::UNSPECIFIED,
 		    RDKit::Bond::BondDir bondDir=RDKit::Bond::NONE,
-		    bool closeRings=false);
+		    bool closeRings=false,bool doingQuery=false);
  RDKit::Bond::BondType GetUnspecifiedBondType(const RDKit::RWMol *mol,
 					       const RDKit::Atom *atom1,
 					       const RDKit::Atom *atom2);
--- a/Code/GraphMol/SmilesParse/SmilesWrite.cpp
+++ b/Code/GraphMol/SmilesParse/SmilesWrite.cpp
@@ -300,7 +300,9 @@ namespace RDKit{
  // decisions and I'm gonna want to smack myself for doing this,
  // but we'll try anyway.
  std::string MolToSmiles(ROMol &mol,bool doIsomericSmiles,
-			  bool doKekule){
+			  bool doKekule,int rootedAtAtom){
+    PRECONDITION(rootedAtAtom<0||static_cast<unsigned int>(rootedAtAtom)<mol.getNumAtoms(),
+		 "rootedAtomAtom must be less than the number of atoms");
    if(doIsomericSmiles){
      mol.setProp("_doIsoSmiles",1);
    } else if(mol.hasProp("_doIsoSmiles")){
@@ -315,18 +317,17 @@ namespace RDKit{
 #endif  
    std::string res;

-    int nAtoms=mol.getNumAtoms();
-    for(ROMol::AtomIterator atIt=mol.beginAtoms();atIt!=mol.endAtoms();atIt++)
+    for(ROMol::AtomIterator atIt=mol.beginAtoms();atIt!=mol.endAtoms();atIt++){
      (*atIt)->updatePropertyCache();
+    }

-    INT_VECT ranks;
-    ranks.resize(nAtoms);
+    unsigned int nAtoms=mol.getNumAtoms();
+    INT_VECT ranks(nAtoms,-1);

    // clean up the chirality on any atom that is marked as chiral,
    // but that should not be:
    if(doIsomericSmiles){
      MolOps::assignAtomChiralCodes(mol,true);
-      //MolOps::assignBondStereoCodes(mol,true);
      MolOps::rankAtoms(mol,ranks,ComprehensiveInvariants,
 			true,0,true);
    } else {
@@ -343,14 +344,20 @@ namespace RDKit{
    colorIt = colors.begin();
    // loop to deal with the possibility that there might be disconnected fragments
    while(colorIt != colors.end()){
-      int i,nextAtomIdx,nextRank;
+      int nextAtomIdx;
      std::string subSmi;
+
      // find the next atom for a traverse
-      nextRank = nAtoms+1;
-      for(i=0;i<nAtoms;i++){
-	if( colors[i] == Canon::WHITE_NODE && ranks[i] < nextRank ){
-	  nextRank = ranks[i];
-	  nextAtomIdx = i;
+      if(rootedAtAtom>=0){
+	nextAtomIdx=rootedAtAtom;
+	rootedAtAtom=-1;
+      } else {
+	int nextRank = nAtoms+1;
+	for(unsigned int i=0;i<nAtoms;i++){
+	  if( colors[i] == Canon::WHITE_NODE && ranks[i] < nextRank ){
+	    nextRank = ranks[i];
+	    nextAtomIdx = i;
+	  }
 	}
      }

--- a/Code/GraphMol/SmilesParse/SmilesWrite.h
+++ b/Code/GraphMol/SmilesParse/SmilesWrite.h
@@ -17,6 +17,6 @@ namespace SmilesWrite {

 namespace RDKit{
  std::string MolToSmiles(ROMol &mol,bool doIsomericSmiles=false,
-			  bool doKekule=false);
+			  bool doKekule=false,int rootedAtAtom=-1);
 }
 #endif
--- a/Code/GraphMol/SmilesParse/smarts.flex
+++ b/Code/GraphMol/SmilesParse/smarts.flex
@@ -160,14 +160,12 @@ using namespace RDKit;
 }
 <IN_ATOM_STATE>R {
 	yysmarts_lval.atom = new QueryAtom();
-	// FIX: this doesn't default properly
-	yysmarts_lval.atom->setQuery(makeAtomInNRingsQuery(1));
+	yysmarts_lval.atom->setQuery(new InRingQuery(-1));
 	return COMPLEX_ATOM_QUERY_TOKEN;
 }
 <IN_ATOM_STATE>r {
 	yysmarts_lval.atom = new QueryAtom();
-	// FIX: this doesn't default properly
-	yysmarts_lval.atom->setQuery(makeAtomInRingOfSizeQuery(3));
+	yysmarts_lval.atom->setQuery(makeAtomInRingQuery());
 	return RINGSIZE_ATOM_QUERY_TOKEN;
 }

--- a/Code/GraphMol/SmilesParse/smarts.y
+++ b/Code/GraphMol/SmilesParse/smarts.y
@@ -61,7 +61,7 @@ static RWMol * curMol_gps = 0;
 %left SEMI_TOKEN
 %left OR_TOKEN
 %left AND_TOKEN
-%nonassoc NOT_TOKEN
+%right NOT_TOKEN

 %%

@@ -190,7 +190,7 @@ mol: atomd {
 | mol branch {
  RWMol *m1_p = molList_g[$$],*m2_p=molList_g[$2];
  // FIX: handle generic bonds here
-  SmilesParseOps::AddFragToMol(m1_p,m2_p,Bond::UNSPECIFIED,Bond::NONE,false);
+  SmilesParseOps::AddFragToMol(m1_p,m2_p,Bond::UNSPECIFIED,Bond::NONE,false,true);
  delete m2_p;
  int sz = molList_g.size();
  if ( sz==$2+1) {
--- a/Code/GraphMol/SmilesParse/smatest.cpp
+++ b/Code/GraphMol/SmilesParse/smatest.cpp
@@ -133,6 +133,8 @@ std::vector< MatchVectType > _checkMatches(std::string smarts, std::string smile

  matcher = SmartsToMol(smarts);
  CHECK_INVARIANT(matcher,smarts);
+
+  //std::cerr << "\tSMA: " << smarts << " -> " << MolToSmarts(*matcher) << std::endl;;
  
  mol = SmilesToMol(smiles);
  CHECK_INVARIANT(mol,smiles);
@@ -240,17 +242,45 @@ void testMatches3(){

  _checkMatches("[CH3][CH]", "C(C)(C)CC(=O)[O-]", 2, 2);

-  _checkMatches("[!C;R]", "c1ccccc1", 6, 1);
-
-  _checkMatches("[!C;R]", "C1COC1", 1, 1);
-
  _checkMatches("[c;H]", "c1ccccc1", 6, 1);
  _checkNoMatches("[c;H]", "C1CCCCC1");

+  _checkMatches("[#6]([#7])[#6]", "c1ncccc1", 2, 3);
+
  _checkMatches("[c;H]", "c1c[c-]ccc1", 5, 1);

  _checkMatches("C~O", "C(=O)[O-]", 2, 2);

+
+  // -----
+  // This block is connected to SF-Issue 1538280
+  //   http://sourceforge.net/tracker/index.php?func=detail&aid=1538280&group_id=160139&atid=814650
+  _checkMatches("[R]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[r]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[R;!O]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[c]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[R;c]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[c;#6]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[R;R]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[#6;R]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[c;R]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[!O;R]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[!C;R]", "c1ccccc1", 6, 1);
+
+  _checkMatches("[!C;R]", "C1COC1", 1, 1);
+
+
+  
  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
 }

@@ -613,77 +643,6 @@ void testSmartsWrite() {
 }


-void testDeleteSubstruct() 
-{
-  int i = 0;
-  ROMol *mol1=0,*mol2=0,*matcher1=0,*matcher2=0,*matcher3=0;
-  std::string smi,sma;
-  
-  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
-  BOOST_LOG(rdInfoLog) << "Testing deleteSubstruct" << std::endl;
-
-  // a lot of the seemingly repetitive stuff is here for Issue96
-  smi = "CCC(=O).C=O";
-  mol1 = SmilesToMol(smi);
-  TEST_ASSERT(mol1);
-  sma = "C=O";
-  matcher1 = SmartsToMol(sma);
-  TEST_ASSERT(matcher1);
-  
-  mol2 = deleteSubstructs(*mol1,*matcher1,0);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms(4))
-  mol2 = deleteSubstructs(*mol2,*matcher1,0);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms(4))
-  
-  delete matcher1;
-  sma = "[Cl;H1&X1,-]";
-  matcher1 = SmartsToMol(sma);
-  sma = "[Na+]";
-  matcher2 = SmartsToMol(sma);
-  sma = "[O;H2,H1&-,X0&-2]";
-  matcher3 = SmartsToMol(sma);
-  delete mol1;
-  mol1 = SmilesToMol("CCO.Cl");
-  TEST_ASSERT(mol1);
-  TEST_ASSERT(mol1->getNumAtoms()==4);
-
-  delete mol2;
-  mol2 = deleteSubstructs(*mol1,*matcher1,true);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms()==3);
-  mol2 = deleteSubstructs(*mol2,*matcher2,true);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms()==3);
-  mol2 = deleteSubstructs(*mol2,*matcher3,true);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms()==3);
-
-  delete mol1;
-  mol1 = SmilesToMol("CC(=O)[O-].[Na+]");
-  TEST_ASSERT(mol1);
-  TEST_ASSERT(mol1->getNumAtoms()==5);
-
-  delete matcher1;
-  matcher1 = SmartsToMol("[Cl;H1&X1,-]");
-  delete matcher2;
-  matcher2 = SmartsToMol("[Na+]");
-
-  mol2 = deleteSubstructs(*mol1,*matcher1,true);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms()==5);
-
-  mol2 = deleteSubstructs(*mol2,*matcher2,true);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms()==4);
-
-  mol2 = deleteSubstructs(*mol2,*matcher1,true);
-  TEST_ASSERT(mol2);
-  TEST_ASSERT(mol2->getNumAtoms()==4);
-
-  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
-}

 void testIssue196() 
 {
@@ -864,7 +823,7 @@ int
 main(int argc, char *argv[])
 {
  RDLog::InitLogs();
-#if LOCAL_TEST_ALL
+#if 1
  testPass();
  testFail();
  testMatches();
@@ -876,12 +835,12 @@ main(int argc, char *argv[])
  testSmartsWrite();
  testFrags();
  testProblems();
-  testDeleteSubstruct();
  testIssue196();
  testIssue254();
  testIssue255();
  testIssue330();
-#endif
  testIssue351();
+#endif
+
  return 0;
 }
--- a/Code/GraphMol/SmilesParse/test.cpp
+++ b/Code/GraphMol/SmilesParse/test.cpp
@@ -1231,6 +1231,28 @@ void testIssue266(){
  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
 }

+void testRootedAt(){
+  RWMol *mol;
+  std::string smi;
+  int numE=0;
+
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "Testing rootedAtAtom functionality" << std::endl;
+
+  smi ="CN(C)C";
+  mol = SmilesToMol(smi);
+  TEST_ASSERT(mol);
+  smi = MolToSmiles(*mol,false,false,-1);
+  TEST_ASSERT(smi=="CN(C)C");
+  smi = MolToSmiles(*mol,false,false,1);
+  TEST_ASSERT(smi=="N(C)(C)C");
+  smi = MolToSmiles(*mol,false,false,2);
+  TEST_ASSERT(smi=="CN(C)C");
+
+  
+  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
+}
+

 int
 main(int argc, char *argv[])
@@ -1257,6 +1279,7 @@ main(int argc, char *argv[])
  testIssue184();
  testIssue191();
  testIssue256();
-#endif
  testIssue266();
+#endif
+  testRootedAt();
 }
--- a/Code/RDCode.sln
+++ b/Code/RDCode.sln
@@ -82,6 +82,7 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testQuery", "Query\QueryTes
 EndProject
 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testSmartsParse", "GraphMol\SmilesParse\SmartsParseTest.vcproj", "{1F0176D6-8882-4399-B8AF-E75B8287A591}"
 	ProjectSection(ProjectDependencies) = postProject
+		{676E091A-4E6E-429B-91EE-0399C46060C6} = {676E091A-4E6E-429B-91EE-0399C46060C6}
 		{DDF70921-1F56-4EBF-BE90-0E3A0C8BFACB} = {DDF70921-1F56-4EBF-BE90-0E3A0C8BFACB}
 		{08AF0B31-BA0F-4C46-A889-4411ADB81D68} = {08AF0B31-BA0F-4C46-A889-4411ADB81D68}
 		{2E8DFE39-3377-45C0-81D6-D32A2C192F34} = {2E8DFE39-3377-45C0-81D6-D32A2C192F34}
@@ -97,6 +98,7 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libSmilesParse", "GraphMol\
 EndProject
 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testSmilesParse", "GraphMol\SmilesParse\SmilesParseTest.vcproj", "{20AFEDA7-3046-41F0-9BEF-425D0398362A}"
 	ProjectSection(ProjectDependencies) = postProject
+		{676E091A-4E6E-429B-91EE-0399C46060C6} = {676E091A-4E6E-429B-91EE-0399C46060C6}
 		{DDF70921-1F56-4EBF-BE90-0E3A0C8BFACB} = {DDF70921-1F56-4EBF-BE90-0E3A0C8BFACB}
 		{08AF0B31-BA0F-4C46-A889-4411ADB81D68} = {08AF0B31-BA0F-4C46-A889-4411ADB81D68}
 		{2E8DFE39-3377-45C0-81D6-D32A2C192F34} = {2E8DFE39-3377-45C0-81D6-D32A2C192F34}
@@ -185,6 +187,7 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "wrapGraphMol", "GraphMol\Wr
 		{33BB4E07-B13A-44EB-931F-E748D22A548D} = {33BB4E07-B13A-44EB-931F-E748D22A548D}
 		{58DBEB0A-76E7-4029-83DC-0B2AC5AAFA5F} = {58DBEB0A-76E7-4029-83DC-0B2AC5AAFA5F}
 		{0B51D40C-2E72-42AF-97EE-C7D188E717C0} = {0B51D40C-2E72-42AF-97EE-C7D188E717C0}
+		{676E091A-4E6E-429B-91EE-0399C46060C6} = {676E091A-4E6E-429B-91EE-0399C46060C6}
 		{08AF0B31-BA0F-4C46-A889-4411ADB81D68} = {08AF0B31-BA0F-4C46-A889-4411ADB81D68}
 		{2E8DFE39-3377-45C0-81D6-D32A2C192F34} = {2E8DFE39-3377-45C0-81D6-D32A2C192F34}
 		{1D9A3F4A-DAFD-498E-9C56-59FAE69194C8} = {1D9A3F4A-DAFD-498E-9C56-59FAE69194C8}
@@ -222,6 +225,7 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "wrapMolOps", "GraphMol\Wrap
 		{33BB4E07-B13A-44EB-931F-E748D22A548D} = {33BB4E07-B13A-44EB-931F-E748D22A548D}
 		{58DBEB0A-76E7-4029-83DC-0B2AC5AAFA5F} = {58DBEB0A-76E7-4029-83DC-0B2AC5AAFA5F}
 		{0B51D40C-2E72-42AF-97EE-C7D188E717C0} = {0B51D40C-2E72-42AF-97EE-C7D188E717C0}
+		{676E091A-4E6E-429B-91EE-0399C46060C6} = {676E091A-4E6E-429B-91EE-0399C46060C6}
 		{2E8DFE39-3377-45C0-81D6-D32A2C192F34} = {2E8DFE39-3377-45C0-81D6-D32A2C192F34}
 		{1D9A3F4A-DAFD-498E-9C56-59FAE69194C8} = {1D9A3F4A-DAFD-498E-9C56-59FAE69194C8}
 		{8DA7765B-EF8E-45D4-B192-2C950C5C79F5} = {8DA7765B-EF8E-45D4-B192-2C950C5C79F5}
@@ -458,6 +462,7 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ZZZGraphMolRegrs", "GraphMo
 		{C6555EDD-5666-4CF7-8AE2-1CF49A262636} = {C6555EDD-5666-4CF7-8AE2-1CF49A262636}
 		{55973DDE-14F0-47A9-9F85-5B387884F136} = {55973DDE-14F0-47A9-9F85-5B387884F136}
 		{B873A5E6-B25D-425C-8527-C52FB524F607} = {B873A5E6-B25D-425C-8527-C52FB524F607}
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716} = {5408B0E6-0B50-4E12-921A-8F1B3E483716}
 		{4D9A72F3-BF82-4B1D-BF0C-580DF04E7429} = {4D9A72F3-BF82-4B1D-BF0C-580DF04E7429}
 		{BB2B6CF7-385A-4478-8D03-F7BA96F5ABD4} = {BB2B6CF7-385A-4478-8D03-F7BA96F5ABD4}
 	EndProjectSection
@@ -949,6 +954,22 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testDistGeom", "DistGeom\te
 		{DD564ACC-9799-4A4F-AA43-C42565165EFD} = {DD564ACC-9799-4A4F-AA43-C42565165EFD}
 	EndProjectSection
 EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libChemTransforms", "GraphMol\ChemTransforms\ChemTransforms.vcproj", "{676E091A-4E6E-429B-91EE-0399C46060C6}"
+	ProjectSection(ProjectDependencies) = postProject
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testChemTransforms", "GraphMol\ChemTransforms\testChemTransforms.vcproj", "{5408B0E6-0B50-4E12-921A-8F1B3E483716}"
+	ProjectSection(ProjectDependencies) = postProject
+		{676E091A-4E6E-429B-91EE-0399C46060C6} = {676E091A-4E6E-429B-91EE-0399C46060C6}
+		{DDF70921-1F56-4EBF-BE90-0E3A0C8BFACB} = {DDF70921-1F56-4EBF-BE90-0E3A0C8BFACB}
+		{08AF0B31-BA0F-4C46-A889-4411ADB81D68} = {08AF0B31-BA0F-4C46-A889-4411ADB81D68}
+		{2E8DFE39-3377-45C0-81D6-D32A2C192F34} = {2E8DFE39-3377-45C0-81D6-D32A2C192F34}
+		{8DA7765B-EF8E-45D4-B192-2C950C5C79F5} = {8DA7765B-EF8E-45D4-B192-2C950C5C79F5}
+		{41B2DB92-DBB1-4C73-916C-BD7372F46FD4} = {41B2DB92-DBB1-4C73-916C-BD7372F46FD4}
+		{8A443D9F-4C81-455C-82AB-AA26C9F9EE1C} = {8A443D9F-4C81-455C-82AB-AA26C9F9EE1C}
+		{A6FD01DB-2F79-4317-85F8-BA361B8EA095} = {A6FD01DB-2F79-4317-85F8-BA361B8EA095}
+	EndProjectSection
+EndProject
 Global
 	GlobalSection(SolutionConfiguration) = preSolution
 		Debug = Debug
@@ -1616,6 +1637,18 @@ Global
 		{91158915-015A-434B-AE89-CE55709440DC}.DebugPython.Build.0 = Debug|Win32
 		{91158915-015A-434B-AE89-CE55709440DC}.Release.ActiveCfg = Release|Win32
 		{91158915-015A-434B-AE89-CE55709440DC}.Release.Build.0 = Release|Win32
+		{676E091A-4E6E-429B-91EE-0399C46060C6}.Debug.ActiveCfg = Debug|Win32
+		{676E091A-4E6E-429B-91EE-0399C46060C6}.Debug.Build.0 = Debug|Win32
+		{676E091A-4E6E-429B-91EE-0399C46060C6}.DebugPython.ActiveCfg = Debug|Win32
+		{676E091A-4E6E-429B-91EE-0399C46060C6}.DebugPython.Build.0 = Debug|Win32
+		{676E091A-4E6E-429B-91EE-0399C46060C6}.Release.ActiveCfg = Release|Win32
+		{676E091A-4E6E-429B-91EE-0399C46060C6}.Release.Build.0 = Release|Win32
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716}.Debug.ActiveCfg = Debug|Win32
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716}.Debug.Build.0 = Debug|Win32
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716}.DebugPython.ActiveCfg = Debug|Win32
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716}.DebugPython.Build.0 = Debug|Win32
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716}.Release.ActiveCfg = Release|Win32
+		{5408B0E6-0B50-4E12-921A-8F1B3E483716}.Release.Build.0 = Release|Win32
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 	EndGlobalSection