Package org.jmol.adapter.readers.xml

Class XmlCmlReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader
    Direct Known Subclasses:
    XmlMOReader
    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 Detail

      • scalarDictRef

        private java.lang.String scalarDictRef

      • scalarDictValue

        private java.lang.String scalarDictValue

      • scalarTitle

        private java.lang.String scalarTitle

      • cellParameterType

        private java.lang.String cellParameterType

      • checkedSerial

        private boolean checkedSerial

      • isSerial

        private boolean isSerial

      • moleculeNesting

        private int moleculeNesting

      • latticeVectorPtr

        private int latticeVectorPtr

      • embeddedCrystal

        private boolean embeddedCrystal

      • atomIdNames

        private java.util.Properties atomIdNames

      • tokens

        protected java.lang.String[] tokens

      • aaLen

        private int aaLen

      • atomArray

        private Atom[] atomArray

      • bondCount

        private int bondCount

      • bondArray

        private Bond[] bondArray

      • tokenCount

        private int tokenCount

      • moduleNestingLevel

        private int moduleNestingLevel

      • haveMolecule

        private boolean haveMolecule

      • localSpaceGroupName

        private java.lang.String localSpaceGroupName

      • processing

        protected boolean processing

      • state

        protected int state

      • atomIndex0

        private int atomIndex0

      • joinList

        private javajs.util.Lst<java.lang.String[]> joinList

      • mapRtoA

        private java.util.Map<Atom,​java.lang.String> mapRtoA

      • deleteAtoms

        private BS deleteAtoms

      • moleculeID

        protected java.lang.String moleculeID

      • htModelAtomMap

        protected java.util.Map<java.lang.String,​java.lang.Object> htModelAtomMap

      • is2d

        private boolean is2d

      • CRYSTAL_SCALAR

        protected static final int CRYSTAL_SCALAR
        state constants
        See Also:
        Constant Field Values

      • CRYSTAL_SYMMETRY

        protected static final int CRYSTAL_SYMMETRY
        state constants
        See Also:
        Constant Field Values

      • CRYSTAL_SYMMETRY_TRANSFORM3

        protected static final int CRYSTAL_SYMMETRY_TRANSFORM3
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_ATOM_ARRAY

        protected static final int MOLECULE_ATOM_ARRAY
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_ATOM

        protected static final int MOLECULE_ATOM
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_ATOM_SCALAR

        protected static final int MOLECULE_ATOM_SCALAR
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_BOND_ARRAY

        protected static final int MOLECULE_BOND_ARRAY
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_BOND

        protected static final int MOLECULE_BOND
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_FORMULA

        protected static final int MOLECULE_FORMULA
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_ATOM_BUILTIN

        protected static final int MOLECULE_ATOM_BUILTIN
        state constants
        See Also:
        Constant Field Values

      • MOLECULE_BOND_BUILTIN

        protected static final int MOLECULE_BOND_BUILTIN
        state constants
        See Also:
        Constant Field Values

      • LATTICE_VECTOR

        protected static final int LATTICE_VECTOR
        state constants
        See Also:
        Constant Field Values

      • unitCellParamTags

        private static final java.lang.String[] unitCellParamTags

    • Constructor Detail

      • XmlCmlReader

        public XmlCmlReader()

    • Method Detail

      • processXml

        protected void processXml​(XmlReader parent,
                          java.lang.Object saxReader)
                   throws java.lang.Exception
        the current state
        Overrides:
        processXml in class XmlReader
        Throws:
        java.lang.Exception

      • processStartElement

        public void processStartElement​(java.lang.String name,
                                java.lang.String nodeName)
        Overrides:
        processStartElement in class XmlReader
        nodeName - TODO

      • processStart2

        protected void processStart2​(java.lang.String name)

      • getAtomIndex

        private int getAtomIndex​(java.lang.String label)

      • processEnd2

        public void processEnd2​(java.lang.String name)

      • addBond

        private void addBond​(Bond bond)

      • checkBondToR

        private boolean checkBondToR​(java.lang.String a1name,
                             java.lang.String a2name)
        Checks to see if we have a bond to R and, if so, adds this R atom as a key to its attached atom
        Parameters:
        a1name -
        a2name -
        Returns:
        true if handled so no need to add a bond

      • setAtomNames

        private void setAtomNames()

      • addNewBond

        private void addNewBond​(java.lang.String a1,
                        java.lang.String a2,
                        int order)

      • fixSerialName

        private java.lang.String fixSerialName​(java.lang.String a)

      • getDictRefValue

        private void getDictRefValue()

      • checkUnitCellItem

        private void checkUnitCellItem​(java.lang.String[] tags,
                               java.lang.String value)

      • addAtom

        private void addAtom​(Atom atom)

      • parseBondToken

        private int parseBondToken​(java.lang.String str)

      • breakOutTokens

        private void breakOutTokens​(java.lang.String str)

      • breakOutAtomTokens

        void breakOutAtomTokens​(java.lang.String str)

      • checkAtomArrayLength

        void checkAtomArrayLength​(int newAtomCount)

      • breakOutBondTokens

        void breakOutBondTokens​(java.lang.String str)

      • checkBondArrayLength

        void checkBondArrayLength​(int newBondCount)

      • createNewAtomSet

        private void createNewAtomSet()