Fields may be final

cdk · Feb 10, 2022 · ef24841 · ef24841
1 parent 3470a79
commit ef24841
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diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java b/app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java
@@ -213,7 +213,7 @@ public final class DepictionGenerator {
     /**
      * Object that should be highlighted
      */
-    private Map<IChemObject, Color> highlight = new HashMap<>();
+    private final Map<IChemObject, Color> highlight = new HashMap<>();
 
     /**
      * Create a depiction generator using the standard sans-serif

diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/SvgDrawVisitor.java b/app/depict/src/main/java/org/openscience/cdk/depict/SvgDrawVisitor.java
@@ -71,7 +71,7 @@ final class SvgDrawVisitor implements IDrawVisitor {
     private int             indentLvl     = 0;
     private AffineTransform transform     = null;
     private RendererModel   model         = null;
-    private NumberFormat    decimalFormat = new DecimalFormat(".##", new DecimalFormatSymbols(Locale.ROOT));
+    private final NumberFormat    decimalFormat = new DecimalFormat(".##", new DecimalFormatSymbols(Locale.ROOT));
 
     private boolean defaultsWritten    = false;
     private Color   defaultStroke      = null;

diff --git a/app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java b/app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java
@@ -40,7 +40,7 @@
 
 public class AbbreviationsTest {
 
-    private static SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+    private static final SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
 
     static IAtomContainer smi(String smi) throws Exception {
         return smipar.parseSmiles(smi);

diff --git a/base/atomtype/src/main/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java b/base/atomtype/src/main/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
@@ -50,11 +50,11 @@ public class SybylAtomTypeMatcher implements IAtomTypeMatcher {
     private final static String                                  SYBYL_ATOM_TYPE_LIST = "org/openscience/cdk/dict/data/sybyl-atom-types.owl";
     private final static String                                  CDK_TO_SYBYL_MAP     = "org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl";
 
-    private AtomTypeFactory                                      factory;
-    private CDKAtomTypeMatcher                                   cdkMatcher;
-    private AtomTypeMapper                                       mapper;
+    private final AtomTypeFactory                                      factory;
+    private final CDKAtomTypeMatcher                                   cdkMatcher;
+    private final AtomTypeMapper                                       mapper;
 
-    private static Map<IChemObjectBuilder, SybylAtomTypeMatcher> factories            = new Hashtable<>(
+    private static final Map<IChemObjectBuilder, SybylAtomTypeMatcher> factories            = new Hashtable<>(
             1);
 
     private SybylAtomTypeMatcher(IChemObjectBuilder builder) {

diff --git a/base/atomtype/src/main/java/org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java b/base/atomtype/src/main/java/org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java
@@ -35,11 +35,11 @@
  */
 public class AtomTypeMapper {
 
-    private static Map<String, AtomTypeMapper> mappers = new HashMap<>();
+    private static final Map<String, AtomTypeMapper> mappers = new HashMap<>();
 
-    private String                             mappingFile;
+    private final String                             mappingFile;
 
-    private Map<String, String>                mappings;
+    private final Map<String, String>                mappings;
 
     private AtomTypeMapper(String mappingFile) {
         this.mappingFile = mappingFile;

diff --git a/...atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java b/...atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java
@@ -46,8 +46,8 @@
 public class OWLAtomTypeMappingReader {
 
     private XMLReader           parser;
-    private Reader              input;
-    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(OWLAtomTypeReader.class);
+    private final Reader              input;
+    private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(OWLAtomTypeReader.class);
 
     /**
      * Instantiates the XML based AtomTypeReader.

diff --git a/base/core/src/main/java/org/openscience/cdk/CDK.java b/base/core/src/main/java/org/openscience/cdk/CDK.java
@@ -37,7 +37,7 @@
  */
 public class CDK {
 
-    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(CDK.class);
+    private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(CDK.class);
     private static final String RESOURCE_LOCATION = "/build.props";
     private static volatile String version;
 

diff --git a/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -60,12 +60,12 @@ public class CDKAtomTypeMatcher implements IAtomTypeMatcher {
     public final static int                                                  REQUIRE_NOTHING            = 1;
     public final static int                                                  REQUIRE_EXPLICIT_HYDROGENS = 2;
 
-    private AtomTypeFactory                                                  factory;
-    private int                                                              mode;
+    private final AtomTypeFactory                                                  factory;
+    private final int                                                              mode;
 
     private final static Object                                              LOCK                       = new Object();
 
-    private static Map<Integer, Map<IChemObjectBuilder, CDKAtomTypeMatcher>> factories                  = new ConcurrentHashMap<>(5);
+    private static final Map<Integer, Map<IChemObjectBuilder, CDKAtomTypeMatcher>> factories                  = new ConcurrentHashMap<>(5);
 
     private CDKAtomTypeMatcher(IChemObjectBuilder builder, int mode) {
         factory = AtomTypeFactory.getInstance("org/openscience/cdk/dict/data/cdk-atom-types.owl", builder);

diff --git a/base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java b/base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java
@@ -92,7 +92,7 @@ public class AtomTypeFactory {
     private final static String                 XML_EXTENSION         = "xml";
     private final static String                 OWL_EXTENSION         = "owl";
 
-    private static ILoggingTool                 logger                = LoggingToolFactory
+    private static final ILoggingTool                 logger                = LoggingToolFactory
                                                                               .createLoggingTool(AtomTypeFactory.class);
     private static Map<String, AtomTypeFactory> tables                = null;
     private Map<String,IAtomType>               atomTypes             = null;

diff --git a/base/core/src/main/java/org/openscience/cdk/config/BODRIsotope.java b/base/core/src/main/java/org/openscience/cdk/config/BODRIsotope.java
@@ -40,11 +40,11 @@
  */
 final class BODRIsotope implements IIsotope {
 
-    private String  element;
-    private Integer atomicNumber;
-    private Double  naturalAbundance;
-    private Double  exactMass;
-    private Integer massNumber;
+    private final String  element;
+    private final Integer atomicNumber;
+    private final Double  naturalAbundance;
+    private final Double  exactMass;
+    private final Integer massNumber;
 
     protected BODRIsotope(String element, Integer atomicNumber, Integer massNumber, Double exactMass,
             Double naturalAbundance) {

diff --git a/base/core/src/main/java/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java b/base/core/src/main/java/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java
@@ -39,10 +39,10 @@
  */
 public class CDKBasedAtomTypeConfigurator implements IAtomTypeConfigurator {
 
-    private String              configFile = "org.openscience.cdk.config.data.structgen_atomtypes.xml";
+    private final String              configFile = "org.openscience.cdk.config.data.structgen_atomtypes.xml";
     private InputStream         ins        = null;
 
-    private static ILoggingTool logger     = LoggingToolFactory.createLoggingTool(CDKBasedAtomTypeConfigurator.class);
+    private static final ILoggingTool logger     = LoggingToolFactory.createLoggingTool(CDKBasedAtomTypeConfigurator.class);
 
     public CDKBasedAtomTypeConfigurator() {}
 

diff --git a/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java b/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java
@@ -44,9 +44,9 @@ public abstract class IsotopeFactory {
 
     public static final IIsotope[] EMPTY_ISOTOPE_ARRAY = new IIsotope[0];
     @SuppressWarnings("unchecked")
-    private List<IIsotope>[] isotopes = new List[256];
+    private final List<IIsotope>[] isotopes = new List[256];
     @SuppressWarnings("unchecked")
-    private IIsotope[] majorIsotope = new IIsotope[256];
+    private final IIsotope[] majorIsotope = new IIsotope[256];
     protected static ILoggingTool  logger        = LoggingToolFactory.createLoggingTool(IsotopeFactory.class);
 
     /**

diff --git a/base/core/src/main/java/org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java b/base/core/src/main/java/org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java
@@ -38,7 +38,7 @@
 public class OWLBasedAtomTypeConfigurator implements IAtomTypeConfigurator {
 
     private InputStream         ins    = null;
-    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(OWLBasedAtomTypeConfigurator.class);
+    private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(OWLBasedAtomTypeConfigurator.class);
 
     public OWLBasedAtomTypeConfigurator() {}
 

diff --git a/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java b/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
@@ -44,7 +44,7 @@
  */
 public class TXTBasedAtomTypeConfigurator implements IAtomTypeConfigurator {
 
-    private String      configFile = "org/openscience/cdk/config/data/jmol_atomtypes.txt";
+    private final String      configFile = "org/openscience/cdk/config/data/jmol_atomtypes.txt";
     private InputStream ins        = null;
 
     public TXTBasedAtomTypeConfigurator() {}

diff --git a/base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeHandler.java b/base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeHandler.java
@@ -57,7 +57,7 @@ public class AtomTypeHandler extends DefaultHandler {
     private final int                 SCALAR_PIBONDCOUNT           = 13;
     private final int                 SCALAR_LONEPAIRCOUNT         = 14;
 
-    private static ILoggingTool       logger                       = LoggingToolFactory
+    private static final ILoggingTool       logger                       = LoggingToolFactory
                                                                            .createLoggingTool(AtomTypeHandler.class);
     private String                    currentChars;
     private List<IAtomType>           atomTypes;

diff --git a/base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeReader.java b/base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeReader.java
@@ -50,8 +50,8 @@
 public class AtomTypeReader {
 
     private XMLReader           parser;
-    private Reader              input;
-    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(AtomTypeReader.class);
+    private final Reader              input;
+    private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(AtomTypeReader.class);
 
     /**
      * Instantiates the XML based AtomTypeReader.

diff --git a/base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java b/base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
@@ -41,7 +41,7 @@ public class OWLAtomTypeHandler extends DefaultHandler {
 
     private final String              NS_ATOMTYPE = "http://cdk.sf.net/ontologies/atomtypes#";
 
-    private static ILoggingTool       logger      = LoggingToolFactory.createLoggingTool(OWLAtomTypeHandler.class);
+    private static final ILoggingTool       logger      = LoggingToolFactory.createLoggingTool(OWLAtomTypeHandler.class);
     private String                    currentChars;
     private List<IAtomType>           atomTypes;
     private IAtomType                 currentAtomType;

diff --git a/base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java b/base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
@@ -48,8 +48,8 @@
 public class OWLAtomTypeReader {
 
     private XMLReader           parser;
-    private Reader              input;
-    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(OWLAtomTypeReader.class);
+    private final Reader              input;
+    private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(OWLAtomTypeReader.class);
 
     /**
      * Instantiates the XML based AtomTypeReader.

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java b/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
@@ -1198,7 +1198,8 @@ private int[][] findInFused(int[][] g, int length) throws Intractable {
      */
     private static final class Fallback implements CycleFinder {
 
-        private CycleFinder primary, auxiliary;
+        private final CycleFinder primary;
+        private final CycleFinder auxiliary;
 
         /**
          * Create a fallback for two cycle finders.
@@ -1240,7 +1241,7 @@ public Cycles find(IAtomContainer molecule, int[][] graph, int length) throws In
      */
     private static final class Unchorded implements CycleFinder {
 
-        private CycleFinder primary;
+        private final CycleFinder primary;
 
         /**
          * Filter any cycles produced by the {@code primary} cycle finder and

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java
@@ -490,7 +490,7 @@ static InitialCycles ofBiconnectedComponent(int[][] graph, int limit) {
      */
     static abstract class Cycle implements Comparable<Cycle> {
 
-        private int[] path;
+        private final int[] path;
         ShortestPaths paths;
         BitSet        edgeVector;
 

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java
@@ -493,7 +493,7 @@ private static int[][] copy(final int[][] g) {
     private static class Path implements Comparable<Path> {
 
         /** Path of vertices. */
-        private int[] vertices;
+        private final int[] vertices;
 
         /**
          * Create a new path from the given vertices.

diff --git a/base/core/src/main/java/org/openscience/cdk/io/ChemObjectIO.java b/base/core/src/main/java/org/openscience/cdk/io/ChemObjectIO.java
@@ -50,8 +50,8 @@ public abstract class ChemObjectIO implements IChemObjectIO {
     /**
      * Holder of reader event listeners.
      */
-    private List<IChemObjectIOListener> listeners = new ArrayList<>(2);
-    private SettingManager<IOSetting>   settings  = new SettingManager<>();
+    private final List<IChemObjectIOListener> listeners = new ArrayList<>(2);
+    private final SettingManager<IOSetting>   settings  = new SettingManager<>();
 
     /**
      *{@inheritDoc}

diff --git a/...core/src/main/java/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java b/...core/src/main/java/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java
@@ -42,7 +42,7 @@ public abstract class DefaultRandomAccessChemObjectReader implements IRandomAcce
     /**
      * Holder of reader event listeners.
      */
-    private List<IChemObjectIOListener> listenerList = new ArrayList<>();
+    private final List<IChemObjectIOListener> listenerList = new ArrayList<>();
 
     public void addChemObjectIOListener(IChemObjectIOListener listener) {
         listenerList.add(listener);

diff --git a/base/core/src/main/java/org/openscience/cdk/io/setting/OptionIOSetting.java b/base/core/src/main/java/org/openscience/cdk/io/setting/OptionIOSetting.java
@@ -33,7 +33,7 @@
  */
 public class OptionIOSetting extends IOSetting {
 
-    private List<String> settings;
+    private final List<String> settings;
 
     /**
      * OptionIOSetting is IOSetting for which the value must be

diff --git a/base/core/src/main/java/org/openscience/cdk/io/setting/SettingManager.java b/base/core/src/main/java/org/openscience/cdk/io/setting/SettingManager.java
@@ -81,7 +81,7 @@ public class SettingManager<T extends ISetting> {
     /**
      * Settings are stored in a map of name -> instance.
      */
-    private Map<String, T>       settings    = new HashMap<>(3);
+    private final Map<String, T>       settings    = new HashMap<>(3);
 
     /**
      * Generate a simple key for the given name. This method normalises the name by

diff --git a/base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java b/base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java
@@ -42,10 +42,10 @@ class JumboCyclicVertexSearch implements CyclicVertexSearch {
     private final BitSet  cyclic;
 
     /* cycle systems as they are discovered */
-    private List<BitSet>  cycles = new ArrayList<>(1);
+    private final List<BitSet>  cycles = new ArrayList<>(1);
 
     /* indicates if the 'cycle' at 'i' in 'cycles' is fused */
-    private List<Boolean> fused  = new ArrayList<>(1);
+    private final List<Boolean> fused  = new ArrayList<>(1);
 
     /* set of visited vertices */
     private BitSet        visited;

diff --git a/base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java b/base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java
@@ -42,10 +42,10 @@ class RegularCyclicVertexSearch implements CyclicVertexSearch {
     private long           cyclic;
 
     /* cycle systems as they are discovered */
-    private List<Long>     cycles = new ArrayList<>(1);
+    private final List<Long>     cycles = new ArrayList<>(1);
 
     /* indicates if the 'cycle' at 'i' in 'cycles' is fused */
-    private List<Boolean>  fused  = new ArrayList<>(1);
+    private final List<Boolean>  fused  = new ArrayList<>(1);
 
     /* set of visited vertices */
     private long           visited;

diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java b/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java
@@ -39,8 +39,8 @@ abstract class AbstractStereo<F extends IChemObject, C extends IChemObject>
     implements IStereoElement<F, C> {
 
     private int     value;
-    private F       focus;
-    private List<C> carriers;
+    private final F       focus;
+    private final List<C> carriers;
     private IChemObjectBuilder builder;
 
     protected static int numCarriers(int cfg) {

diff --git a/base/core/src/main/java/org/openscience/cdk/tools/SystemOutLoggingTool.java b/base/core/src/main/java/org/openscience/cdk/tools/SystemOutLoggingTool.java
@@ -37,7 +37,7 @@ public class SystemOutLoggingTool implements ILoggingTool {
     private int level = ILoggingTool.WARN;
 
     /** Name of the class for which this {@link ILoggingTool} is reporting. */
-    private String              classname;
+    private final String              classname;
 
     /** Length of the stack to print for reported {@link Exception}s. */
     private int                 stackLength;

diff --git a/base/data/src/main/java/org/openscience/cdk/BioPolymer.java b/base/data/src/main/java/org/openscience/cdk/BioPolymer.java
@@ -57,7 +57,7 @@ public class BioPolymer extends Polymer implements java.io.Serializable, IBioPol
      */
     private static final long    serialVersionUID = -5001873073769634393L;
 
-    private Map<String, IStrand> strands;                                 // the list of all the contained Strands.
+    private final Map<String, IStrand> strands;                                 // the list of all the contained Strands.
 
     /**
      * Constructs a new Polymer to store the Strands.

diff --git a/base/data/src/main/java/org/openscience/cdk/ConformerContainer.java b/base/data/src/main/java/org/openscience/cdk/ConformerContainer.java
@@ -61,7 +61,7 @@ public class ConformerContainer implements List<IAtomContainer> {
 
     private IAtomContainer  atomContainer = null;
     private String          title         = null;
-    private List<Point3d[]> coordinates;
+    private final List<Point3d[]> coordinates;
 
     private Point3d[] getCoordinateList(IAtomContainer atomContainer) {
 

diff --git a/base/data/src/main/java/org/openscience/cdk/ReactionScheme.java b/base/data/src/main/java/org/openscience/cdk/ReactionScheme.java
@@ -40,7 +40,7 @@
 public class ReactionScheme extends ReactionSet implements IReactionScheme {
 
     /** A List of reaction schemes*/
-    private List<IReactionScheme> reactionScheme;
+    private final List<IReactionScheme> reactionScheme;
     /**
      * Determines if a de-serialized object is compatible with this class.
      *

diff --git a/base/data/src/main/java/org/openscience/cdk/Strand.java b/base/data/src/main/java/org/openscience/cdk/Strand.java
@@ -54,7 +54,7 @@ public class Strand extends AtomContainer implements java.io.Serializable, IStra
     private static final long     serialVersionUID = 4200943086350928356L;
 
     /** The list of all Monomers in the Strand.*/
-    private Map<String, IMonomer> monomers;
+    private final Map<String, IMonomer> monomers;
     /** The name of this strand (e.g. A, B). */
     private String                strandName;
     /** The type of this strand (e.g. PEPTIDE, DNA, RNA). */

diff --git a/base/data/src/main/java/org/openscience/cdk/formula/AdductFormula.java b/base/data/src/main/java/org/openscience/cdk/formula/AdductFormula.java
@@ -58,7 +58,7 @@ public class AdductFormula implements Iterable<IMolecularFormula>, IAdductFormul
     private static final long       serialVersionUID = -811384981700039389L;
 
     /**  Internal List of IMolecularFormula. */
-    private List<IMolecularFormula> components;
+    private final List<IMolecularFormula> components;
 
     /**
      *  Constructs an empty AdductFormula.

diff --git a/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java b/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java
@@ -55,7 +55,7 @@ public class MolecularFormula implements IMolecularFormula {
      */
     private static final long      serialVersionUID = -2011407700837295287L;
 
-    private Map<IIsotope, Integer> isotopes;
+    private final Map<IIsotope, Integer> isotopes;
     /**
      *  The partial charge of the molecularFormula. The default value is Double.NaN.
      */

diff --git a/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormulaSet.java b/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormulaSet.java
@@ -50,7 +50,7 @@ public class MolecularFormulaSet implements Iterable<IMolecularFormula>, IMolecu
     private static final long       serialVersionUID = -2043178712150212550L;
 
     /**  Internal List of IMolecularFormula. */
-    private List<IMolecularFormula> components;
+    private final List<IMolecularFormula> components;
 
     /**
      *  Constructs an empty MolecularFormulaSet.

diff --git a/base/data/src/main/java/org/openscience/cdk/templates/TestMoleculeFactory.java b/base/data/src/main/java/org/openscience/cdk/templates/TestMoleculeFactory.java
@@ -44,7 +44,7 @@
  */
 public class TestMoleculeFactory {
 
-    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(TestMoleculeFactory.class);
+    private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(TestMoleculeFactory.class);
 
     private static IAtomContainer newAtomContainer() {
         return DefaultChemObjectBuilder.getInstance().newAtomContainer();