test_class.file: src/com/genentech/oechem/tools/OEToolsTest.java
test_class.identifier: OEToolsTest
test_case.body: @Test()
     public static void TestNeutralize()
     {  OEGraphMol mol = new OEGraphMol();
  
        OETools.smiToMol(mol,"CC(=O)[O-]");
        OETools.neutralize(mol);
        String s = OETools.molToCanSmi(mol, true);
        assert "CC(=O)O".equals(s) : "neutralize CC(=O)[O-]: " + s;
           
        OETools.smiToMol(mol,"CC[N+H3]");
        OETools.neutralize(mol);
        s = OETools.molToCanSmi(mol, true);
        assert "CCN".equals(s) : "neutralize CC[N+H3]: " + s;
           
        OETools.smiToMol(mol,"CC[N+](C)(C)[H]");
        OETools.neutralize(mol);
        s = OETools.molToCanSmi(mol, true);
        assert "CCN(C)C".equals(s) : "neutralize CC[N+](C)(C)[H]: " + s;
           
        OETools.smiToMol(mol,"CC[N+](C)(C)C");
        OETools.neutralize(mol);
        s = OETools.molToCanSmi(mol, true);
        assert "CC[N+](C)(C)C".equals(s) : "neutralize CC[N+](C)(C)C: " + s;
           
        OETools.smiToMol(mol,"CC[N+](=O)[O-]");
        OETools.neutralize(mol);
        s = OETools.molToCanSmi(mol, true);
        assert "CC[N+](=O)[O-]".equals(s) : "neutralize CC[N+](=O)[O-]: " + s;      
        
        mol.delete();
     }
test_case.class_method_signature: OEToolsTest.TestNeutralize()
test_case.full_signature: @Test() public static void TestNeutralize()
test_case.identifier: TestNeutralize
test_case.invocations: smiToMol neutralize molToCanSmi equals smiToMol neutralize molToCanSmi equals smiToMol neutralize molToCanSmi equals smiToMol neutralize molToCanSmi equals smiToMol neutralize molToCanSmi equals delete
test_case.modifiers: @Test() public static
test_case.parameters: ()
test_case.return: void
test_case.signature: void TestNeutralize()
focal_class.declarator: HASChargeFunctor = new AtomHasChargeFunctor()
focal_class.modifier: private static final
focal_class.original_string: private static final AtomHasChargeFunctor HASChargeFunctor = new AtomHasChargeFunctor();
focal_class.type: AtomHasChargeFunctor
focal_class.var_name: HASChargeFunctor
focal_class.file: src/com/genentech/oechem/tools/OETools.java
focal_class.identifier: OETools
focal_class.class_method_signature: OETools.molToString(OEMolBase mol)
focal_class.full_signature: public static String molToString(OEMolBase mol)
focal_class.identifier: molToString
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol)
focal_class.return: String
focal_class.signature: String molToString(OEMolBase mol)
focal_class.class_method_signature: OETools.molToSDF(OEMolBase mol)
focal_class.full_signature: public static String molToSDF(OEMolBase mol)
focal_class.identifier: molToSDF
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol)
focal_class.return: String
focal_class.signature: String molToSDF(OEMolBase mol)
focal_class.class_method_signature: OETools.molToString(OEMolBase mol, int type)
focal_class.full_signature: private static String molToString(OEMolBase mol, int type)
focal_class.identifier: molToString
focal_class.modifiers: private static
focal_class.parameters: (OEMolBase mol, int type)
focal_class.return: String
focal_class.signature: String molToString(OEMolBase mol, int type)
focal_class.class_method_signature: OETools.smiToMol(OEMolBase mol, String smi)
focal_class.full_signature: public static OEMolBase smiToMol(OEMolBase mol, String smi)
focal_class.identifier: smiToMol
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol, String smi)
focal_class.return: OEMolBase
focal_class.signature: OEMolBase smiToMol(OEMolBase mol, String smi)
focal_class.class_method_signature: OETools.stringToMol(OEMolBase mol, String molStr)
focal_class.full_signature: public static OEMolBase stringToMol(OEMolBase mol, String molStr)
focal_class.identifier: stringToMol
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol, String molStr)
focal_class.return: OEMolBase
focal_class.signature: OEMolBase stringToMol(OEMolBase mol, String molStr)
focal_class.class_method_signature: OETools.molToCanSmi(OEMolBase mol, boolean iso)
focal_class.full_signature: public static String molToCanSmi(OEMolBase mol, boolean iso)
focal_class.identifier: molToCanSmi
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol, boolean iso)
focal_class.return: String
focal_class.signature: String molToCanSmi(OEMolBase mol, boolean iso)
focal_class.class_method_signature: OETools.getAverageBondLength(OEMolBase in)
focal_class.full_signature: public static double getAverageBondLength(OEMolBase in)
focal_class.identifier: getAverageBondLength
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase in)
focal_class.return: double
focal_class.signature: double getAverageBondLength(OEMolBase in)
focal_class.class_method_signature: OETools.combineStructures(OEMolBase base, OEMolBase toAdd)
focal_class.full_signature: public static OEMolBase combineStructures(OEMolBase base, OEMolBase toAdd)
focal_class.identifier: combineStructures
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase base, OEMolBase toAdd)
focal_class.return: OEMolBase
focal_class.signature: OEMolBase combineStructures(OEMolBase base, OEMolBase toAdd)
focal_class.class_method_signature: OETools.combineStructures(OEMolBase base, OEMolBase toAdd,
              int count)
focal_class.full_signature: public static OEMolBase combineStructures(OEMolBase base, OEMolBase toAdd,
              int count)
focal_class.identifier: combineStructures
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase base, OEMolBase toAdd,
              int count)
focal_class.return: OEMolBase
focal_class.signature: OEMolBase combineStructures(OEMolBase base, OEMolBase toAdd,
              int count)
focal_class.class_method_signature: OETools.getMinCoor(OEMolBase toAdd, int axis)
focal_class.full_signature: public static double getMinCoor(OEMolBase toAdd, int axis)
focal_class.identifier: getMinCoor
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase toAdd, int axis)
focal_class.return: double
focal_class.signature: double getMinCoor(OEMolBase toAdd, int axis)
focal_class.class_method_signature: OETools.getMaxCoor(OEMolBase toAdd, int axis)
focal_class.full_signature: public static double getMaxCoor(OEMolBase toAdd, int axis)
focal_class.identifier: getMaxCoor
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase toAdd, int axis)
focal_class.return: double
focal_class.signature: double getMaxCoor(OEMolBase toAdd, int axis)
focal_class.class_method_signature: OETools.getIsotpictWeight(OEMolBase mol)
focal_class.full_signature: public static double getIsotpictWeight(OEMolBase mol)
focal_class.identifier: getIsotpictWeight
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol)
focal_class.return: double
focal_class.signature: double getIsotpictWeight(OEMolBase mol)
focal_class.class_method_signature: OETools.getCharge(OEMolBase mol)
focal_class.full_signature: public static int getCharge(OEMolBase mol)
focal_class.identifier: getCharge
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol)
focal_class.return: int
focal_class.signature: int getCharge(OEMolBase mol)
focal_class.class_method_signature: OETools.countAtoms(OEMolBase mol, OEUnaryAtomPred pred)
focal_class.full_signature: public static int countAtoms(OEMolBase mol, OEUnaryAtomPred pred)
focal_class.identifier: countAtoms
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol, OEUnaryAtomPred pred)
focal_class.return: int
focal_class.signature: int countAtoms(OEMolBase mol, OEUnaryAtomPred pred)
focal_class.class_method_signature: OETools.neutralize(OEMolBase mol)
focal_class.full_signature: public static void neutralize(OEMolBase mol)
focal_class.identifier: neutralize
focal_class.modifiers: public static
focal_class.parameters: (OEMolBase mol)
focal_class.return: void
focal_class.signature: void neutralize(OEMolBase mol)
focal_class.class_method_signature: OETools.neutralizeNegative(OEAtomBase at)
focal_class.full_signature: private static void neutralizeNegative(OEAtomBase at)
focal_class.identifier: neutralizeNegative
focal_class.modifiers: private static
focal_class.parameters: (OEAtomBase at)
focal_class.return: void
focal_class.signature: void neutralizeNegative(OEAtomBase at)
focal_class.class_method_signature: OETools.neutralizePositive(OEAtomBase at)
focal_class.full_signature: private static void neutralizePositive(OEAtomBase at)
focal_class.identifier: neutralizePositive
focal_class.modifiers: private static
focal_class.parameters: (OEAtomBase at)
focal_class.return: void
focal_class.signature: void neutralizePositive(OEAtomBase at)
focal_class.class_method_signature: OETools.main(String... args)
focal_class.full_signature: public static void main(String... args)
focal_class.identifier: main
focal_class.modifiers: public static
focal_class.parameters: (String... args)
focal_class.return: void
focal_class.signature: void main(String... args)
focal_class.class_method_signature: OETools.main2(String... args)
focal_class.full_signature: public static void main2(String... args)
focal_class.identifier: main2
focal_class.modifiers: public static
focal_class.parameters: (String... args)
focal_class.return: void
focal_class.signature: void main2(String... args)
focal_method.body: public static void neutralize(OEMolBase mol)
     {  OEAtomBaseIter atIt = mol.GetAtoms(HASChargeFunctor);
        while(atIt.hasNext())
        {  OEAtomBase at = atIt.next();
           if( at.GetFormalCharge() < 0 )
           {  neutralizeNegative(at);
  
           } else if( at.GetFormalCharge() > 0 )
           {  neutralizePositive(at);
           }
        }
        atIt.delete();
     }
focal_method.class_method_signature: OETools.neutralize(OEMolBase mol)
focal_method.full_signature: public static void neutralize(OEMolBase mol)
focal_method.identifier: neutralize
focal_method.invocations: GetAtoms hasNext next GetFormalCharge neutralizeNegative GetFormalCharge neutralizePositive delete
focal_method.modifiers: public static
focal_method.parameters: (OEMolBase mol)
focal_method.return: void
focal_method.signature: void neutralize(OEMolBase mol)