Class CDXMLWriter

java.lang.Object
org.jmol.adapter.writers.CMLWriter
org.jmol.adapter.writers.CDXMLWriter
All Implemented Interfaces:
JmolWriter

public class CDXMLWriter extends CMLWriter
Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the basic necessities for XmlCDXReader.
  • Field Details

    • doc

      private javajs.api.GenericBinaryDocument doc
    • objects

      private Stack<String> objects
    • sb

      private javajs.util.SB sb
    • sbpt

      private int sbpt
    • kCDXProp_ChemicalWarning

      private static final int kCDXProp_ChemicalWarning
      See Also:
    • kCDXProp_2DPosition

      private static final int kCDXProp_2DPosition
      See Also:
    • kCDXProp_Node_Type

      private static final int kCDXProp_Node_Type
      See Also:
    • kCDXProp_Node_Element

      private static final int kCDXProp_Node_Element
      See Also:
    • kCDXProp_Atom_Isotope

      private static final int kCDXProp_Atom_Isotope
      See Also:
    • kCDXProp_Atom_Charge

      private static final int kCDXProp_Atom_Charge
      See Also:
    • kCDXProp_Node_Attachments

      private static final int kCDXProp_Node_Attachments
      See Also:
    • kCDXProp_Atom_GenericNickname

      private static final int kCDXProp_Atom_GenericNickname
      See Also:
    • kCDXProp_Bond_Order

      private static final int kCDXProp_Bond_Order
      See Also:
    • kCDXProp_Bond_Display

      private static final int kCDXProp_Bond_Display
      See Also:
    • kCDXProp_Bond_Display2

      private static final int kCDXProp_Bond_Display2
      See Also:
    • kCDXProp_Bond_Begin

      private static final int kCDXProp_Bond_Begin
      See Also:
    • kCDXProp_Bond_End

      private static final int kCDXProp_Bond_End
      See Also:
    • kCDXProp_Bond_BeginAttach

      private static final int kCDXProp_Bond_BeginAttach
      See Also:
    • kCDXProp_Bond_EndAttach

      private static final int kCDXProp_Bond_EndAttach
      See Also:
    • kCDXProp_Text

      private static final int kCDXProp_Text
      See Also:
    • kCDXObj_Document

      private static final int kCDXObj_Document
      See Also:
    • kCDXObj_Page

      private static final int kCDXObj_Page
      See Also:
    • kCDXObj_Group

      private static final int kCDXObj_Group
      See Also:
    • kCDXObj_Fragment

      private static final int kCDXObj_Fragment
      See Also:
    • kCDXObj_Node

      private static final int kCDXObj_Node
      See Also:
    • kCDXObj_Bond

      private static final int kCDXObj_Bond
      See Also:
    • kCDXObj_Text

      private static final int kCDXObj_Text
      See Also:
    • kCDXNodeType_Unspecified

      private static final int kCDXNodeType_Unspecified
      See Also:
    • kCDXNodeType_Element

      private static final int kCDXNodeType_Element
      See Also:
    • kCDXNodeType_ElementList

      private static final int kCDXNodeType_ElementList
      See Also:
    • kCDXNodeType_ElementListNickname

      private static final int kCDXNodeType_ElementListNickname
      See Also:
    • kCDXNodeType_Nickname

      private static final int kCDXNodeType_Nickname
      See Also:
    • kCDXNodeType_Fragment

      private static final int kCDXNodeType_Fragment
      See Also:
    • kCDXNodeType_Formula

      private static final int kCDXNodeType_Formula
      See Also:
    • kCDXNodeType_GenericNickname

      private static final int kCDXNodeType_GenericNickname
      See Also:
    • kCDXNodeType_AnonymousAlternativeGroup

      private static final int kCDXNodeType_AnonymousAlternativeGroup
      See Also:
    • kCDXNodeType_NamedAlternativeGroup

      private static final int kCDXNodeType_NamedAlternativeGroup
      See Also:
    • kCDXNodeType_MultiAttachment

      private static final int kCDXNodeType_MultiAttachment
      See Also:
    • kCDXNodeType_VariableAttachment

      private static final int kCDXNodeType_VariableAttachment
      See Also:
    • kCDXNodeType_ExternalConnectionPoint

      private static final int kCDXNodeType_ExternalConnectionPoint
      See Also:
    • kCDXNodeType_LinkNode

      private static final int kCDXNodeType_LinkNode
      See Also:
    • kCDXBondOrder_Single

      private static final int kCDXBondOrder_Single
      See Also:
    • kCDXBondOrder_Double

      private static final int kCDXBondOrder_Double
      See Also:
    • kCDXBondOrder_Triple

      private static final int kCDXBondOrder_Triple
      See Also:
    • kCDXBondOrder_Quadruple

      private static final int kCDXBondOrder_Quadruple
      See Also:
    • kCDXBondOrder_Quintuple

      private static final int kCDXBondOrder_Quintuple
      See Also:
    • kCDXBondOrder_Sextuple

      private static final int kCDXBondOrder_Sextuple
      See Also:
    • kCDXBondOrder_Half

      private static final int kCDXBondOrder_Half
      See Also:
    • kCDXBondOrder_OneHalf

      private static final int kCDXBondOrder_OneHalf
      See Also:
    • kCDXBondOrder_TwoHalf

      private static final int kCDXBondOrder_TwoHalf
      See Also:
    • kCDXBondOrder_ThreeHalf

      private static final int kCDXBondOrder_ThreeHalf
      See Also:
    • kCDXBondOrder_FourHalf

      private static final int kCDXBondOrder_FourHalf
      See Also:
    • kCDXBondOrder_FiveHalf

      private static final int kCDXBondOrder_FiveHalf
      See Also:
    • kCDXBondOrder_Dative

      private static final int kCDXBondOrder_Dative
      See Also:
    • kCDXBondOrder_Ionic

      private static final int kCDXBondOrder_Ionic
      See Also:
    • kCDXBondOrder_Hydrogen

      private static final int kCDXBondOrder_Hydrogen
      See Also:
    • kCDXBondOrder_ThreeCenter

      private static final int kCDXBondOrder_ThreeCenter
      See Also:
    • kCDXBondDisplay_Solid

      private static final int kCDXBondDisplay_Solid
      See Also:
    • kCDXBondDisplay_Dash

      private static final int kCDXBondDisplay_Dash
      See Also:
    • kCDXBondDisplay_Hash

      private static final int kCDXBondDisplay_Hash
      See Also:
    • kCDXBondDisplay_WedgedHashBegin

      private static final int kCDXBondDisplay_WedgedHashBegin
      See Also:
    • kCDXBondDisplay_WedgedHashEnd

      private static final int kCDXBondDisplay_WedgedHashEnd
      See Also:
    • kCDXBondDisplay_Bold

      private static final int kCDXBondDisplay_Bold
      See Also:
    • kCDXBondDisplay_WedgeBegin

      private static final int kCDXBondDisplay_WedgeBegin
      See Also:
    • kCDXBondDisplay_WedgeEnd

      private static final int kCDXBondDisplay_WedgeEnd
      See Also:
    • kCDXBondDisplay_Wavy

      private static final int kCDXBondDisplay_Wavy
      See Also:
    • kCDXBondDisplay_HollowWedgeBegin

      private static final int kCDXBondDisplay_HollowWedgeBegin
      See Also:
    • kCDXBondDisplay_HollowWedgeEnd

      private static final int kCDXBondDisplay_HollowWedgeEnd
      See Also:
    • kCDXBondDisplay_WavyWedgeBegin

      private static final int kCDXBondDisplay_WavyWedgeBegin
      See Also:
    • kCDXBondDisplay_WavyWedgeEnd

      private static final int kCDXBondDisplay_WavyWedgeEnd
      See Also:
    • kCDXBondDisplay_Dot

      private static final int kCDXBondDisplay_Dot
      See Also:
    • kCDXBondDisplay_DashDot

      private static final int kCDXBondDisplay_DashDot
      See Also:
  • Constructor Details

    • CDXMLWriter

      public CDXMLWriter()
  • Method Details

    • set

      public void set(Viewer viewer, javajs.util.OC out, Object[] data)
      Specified by:
      set in interface JmolWriter
      Overrides:
      set in class CMLWriter
    • write

      public String write(javajs.util.BS bs)
      Specified by:
      write in interface JmolWriter
      Overrides:
      write in class CMLWriter
    • fromCDX

      public static String fromCDX(javajs.api.GenericBinaryDocument binaryDoc) throws Exception
      Throws:
      Exception
    • cdxToCdxml

      private String cdxToCdxml(javajs.api.GenericBinaryDocument doc) throws Exception
      Throws:
      Exception
    • processObject

      private void processObject(int type) throws Exception
      Throws:
      Exception
    • writeNodeProperties

      private void writeNodeProperties(int prop, int len) throws Exception
      Throws:
      Exception
    • writeBondProperties

      private void writeBondProperties(int prop, int len) throws Exception
      Throws:
      Exception
    • writeTextProperty

      private void writeTextProperty(int prop, int len) throws Exception
      Throws:
      Exception
    • wrapCData

      public static String wrapCData(String s)
      wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
      Parameters:
      s -
      Returns:
      wrapped text
    • getNodeType

      private static String getNodeType(int n)
    • getBondDisplay

      private static String getBondDisplay(int i)
    • getBondOrder

      private static String getBondOrder(int i)
    • removeObject

      private void removeObject()
    • skip

      private void skip(int len)
    • readInt

      private int readInt(int len) throws Exception
      Throws:
      Exception
    • readString

      private String readString(int len) throws Exception
      Throws:
      Exception
    • readArray

      private String readArray() throws Exception
      Throws:
      Exception
    • readLength

      private int readLength() throws Exception
      Throws:
      Exception
    • toPoint

      private static double toPoint(int i)
    • main

      public static void main(String[] args)