cdxml parser (#5273)

Code/JavaWrappers/ChemReactions.i

@@ -42,6 +42,10 @@
 #include <GraphMol/ChemReactions/ReactionPickler.h>
 %}
 
+%ignore RDKit::CDXMLToChemicalReactions;  //(const std::string &);
+%ignore RDKit::CDXMLFileToChemicalReactions; //(const std::string &);
+%ignore RDKit::CDXMLDataStreamToChemicalReactions; //(std::istream &);
+
 %include <GraphMol/ChemReactions/Reaction.h>
 %include <GraphMol/ChemReactions/ReactionParser.h>
 %ignore RDKit::ChemicalReaction::validate(unsigned int &,unsigned int &,bool);
@@ -51,6 +55,7 @@
 %ignore RDKit::isMoleculeProductOfReaction(const ChemicalReaction &r,const ROMol &,
                                             unsigned int &);
 
+
 %newobject ReactionFromSmarts;
 %newobject ReactionFromRxnBlock;
 %newobject ReactionFromRxnFile;
@@ -140,4 +145,24 @@ static RDKit::ChemicalReaction *RxnFromBinary(std::vector<int> pkl){
     return res;
   };
 
+static std::vector<std::shared_ptr<ChemicalReaction>> CDXMLToChemicalReactions(
+  const std::string &block, bool sanitize=false, bool removeHs=false) {
+  auto reactions = RDKit::CDXMLToChemicalReactions(block, sanitize, removeHs);
+  std::vector<std::shared_ptr<RDKit::ChemicalReaction>> result;
+  for(auto &rxn : reactions) {
+    result.emplace_back(rxn.release());
+  }
+  return result;
+}
+
+static std::vector<std::shared_ptr<ChemicalReaction>> CDXMLFileToChemicalReactions(
+  const std::string &filename, bool sanitize=false, bool removeHs=false) {
+  auto reactions = RDKit::CDXMLFileToChemicalReactions(filename, sanitize, removeHs);
+  std::vector<std::shared_ptr<RDKit::ChemicalReaction>> result;
+  for(auto &rxn : reactions) {
+    result.emplace_back(rxn.release());
+  }
+  return result;
+}
+
 }

Code/JavaWrappers/RWMol.i

@@ -41,6 +41,8 @@
 #include <GraphMol/FileParsers/MolFileStereochem.h>
 %}
 
+%template(RWMol_Vect) std::vector< boost::shared_ptr<RDKit::RWMol> >;
+
 // ignore the methods that allow the molecule to take ownership of atoms/Bonds
 // (instead of copying them). This just leads to memory problems with Java
 %ignore RDKit::RWMol::addAtom(Atom *atom,bool updateLabel,bool takeOwnership);
@@ -128,6 +130,27 @@ static RDKit::RWMOL_SPTR MolFromHELM(std::string text,
   return RDKit::RWMOL_SPTR(mol);
 }
 
+static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(std::string text,
+						     bool sanitize=true){
+  auto res = RDKit::CDXMLToMols(text, sanitize);
+  std::vector<RDKit::RWMOL_SPTR> mols;
+  for(auto &mol: res) {
+    mols.emplace_back(mol.release());
+  }
+  return mols;
+
+}
+
+static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXMLFile(std::string text,
+							 bool sanitize=true){
+  auto res = RDKit::CDXMLFileToMols(text, sanitize);
+  std::vector<RDKit::RWMOL_SPTR> mols;
+  for(auto &mol: res) {
+    mols.emplace_back(mol.release());
+  }
+  return mols;
+}
+
 
   /* Methods from MolFileStereoChem.h */
   void DetectAtomStereoChemistry(const RDKit::Conformer *conf) {

Code/JavaWrappers/gmwrapper/src-test/org/RDKit/WrapperTests.java

@@ -33,7 +33,7 @@
 package org.RDKit;
 
 import static org.junit.Assert.*;
-
+import java.io.*;
 import java.io.File;
 import java.util.ArrayList;
 
@@ -327,6 +327,26 @@ public class WrapperTests extends GraphMolTest {
         uInt_Vect.delete();
         e.delete();
     }
+
+    @Test
+    public void cdxmlReader() {
+	String rdpath = System.getenv("RDBASE");
+	if (rdpath == null)
+	    org.junit.Assert.fail("No definition for RDBASE");
+	File base = new File(rdpath);
+	File testFile = new File(base, "Code" + File.separator + "GraphMol"
+				 + File.separator + "test_data" + File.separator +
+				 "CDXML" + File.separator + "beta-cypermethrin.cdxml");
+	String fn = testFile.getAbsolutePath();
+	RWMol_Vect prods = RWMol.MolsFromCDXMLFile(fn);
+	assertEquals(prods.size(), 1);
+	for(int idx = 0; idx < prods.size(); idx++) {
+	    if(idx == 0) {
+		assertEquals(prods.get(idx).MolToSmiles(true), "CC1(C)[C@H](C=C(Cl)Cl)[C@H]1C(=O)O[C@@H](C#N)c1cccc(Oc2ccccc2)c1");
+	    }
+	}
+
+    }
     
     public static void main(String args[]) {
       org.junit.runner.JUnitCore.main("org.RDKit.WrapperTests");