Package org.jmol.adapter.readers.xml

Class XmlCmlReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xml.XmlReader
org.jmol.adapter.readers.xml.XmlCmlReader
All Implemented Interfaces:
GenericLineReader
Direct Known Subclasses:
XmlMOReader, XmlNmrmlReader
public class XmlCmlReader extends XmlReader
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection. If passed a JSObject (from LiveConnect) we treat it as a JS DOM tree, and walk the tree, (using the same processing as the SAX parser) to construct the AtomSetCollection. symmetry added by Bob Hanson: setSpaceGroupName() setUnitCellItem() setFractionalCoordinates() setAtomCoord() applySymmetryAndSetTrajectory() "isotope" added 4/6/2009 Bob Hanson

  • Field Details

    • tokens

      protected String[] tokens

    • processing

      protected boolean processing

    • state

      protected int state

    • moleculeID

      protected String moleculeID

    • htModelAtomMap

      protected Map<String,Object> htModelAtomMap

    • START

      protected static final int START
      state constants
      See Also:

    • CML

      protected static final int CML
      state constants
      See Also:

    • CRYSTAL

      protected static final int CRYSTAL
      state constants
      See Also:

    • CRYSTAL_SCALAR

      protected static final int CRYSTAL_SCALAR
      state constants
      See Also:

    • CRYSTAL_SYMMETRY

      protected static final int CRYSTAL_SYMMETRY
      state constants
      See Also:

    • CRYSTAL_SYMMETRY_TRANSFORM3

      protected static final int CRYSTAL_SYMMETRY_TRANSFORM3
      state constants
      See Also:

    • MOLECULE

      protected static final int MOLECULE
      state constants
      See Also:

    • MOLECULE_ATOM_ARRAY

      protected static final int MOLECULE_ATOM_ARRAY
      state constants
      See Also:

    • MOLECULE_ATOM

      protected static final int MOLECULE_ATOM
      state constants
      See Also:

    • MOLECULE_ATOM_SCALAR

      protected static final int MOLECULE_ATOM_SCALAR
      state constants
      See Also:

    • MOLECULE_BOND_ARRAY

      protected static final int MOLECULE_BOND_ARRAY
      state constants
      See Also:

    • MOLECULE_BOND

      protected static final int MOLECULE_BOND
      state constants
      See Also:

    • MOLECULE_BOND_STEREO

      protected static final int MOLECULE_BOND_STEREO
      state constants
      See Also:

    • MOLECULE_FORMULA

      protected static final int MOLECULE_FORMULA
      state constants
      See Also:

    • MOLECULE_ATOM_BUILTIN

      protected static final int MOLECULE_ATOM_BUILTIN
      state constants
      See Also:

    • MOLECULE_BOND_BUILTIN

      protected static final int MOLECULE_BOND_BUILTIN
      state constants
      See Also:

    • MODULE

      protected static final int MODULE
      state constants
      See Also:

    • SYMMETRY

      protected static final int SYMMETRY
      state constants
      See Also:

    • LATTICE_VECTOR

      protected static final int LATTICE_VECTOR
      state constants
      See Also:

    • ASSOCIATION

      protected static final int ASSOCIATION
      state constants
      See Also:

  • Constructor Details

    • XmlCmlReader

      public XmlCmlReader()

  • Method Details