Package org.jmol.adapter.writers
Class CDXMLWriter
java.lang.Object
org.jmol.adapter.writers.CMLWriter
org.jmol.adapter.writers.CDXMLWriter
- All Implemented Interfaces:
JmolWriter
Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the
basic necessities for XmlCDXReader.
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.api.GenericBinaryDocument
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private javajs.util.SB
private int
Fields inherited from class org.jmol.adapter.writers.CMLWriter
addBonds, allTrajectories, atomsMax, doTransform, oc, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate String
cdxToCdxml
(javajs.api.GenericBinaryDocument doc) static String
fromCDX
(javajs.api.GenericBinaryDocument binaryDoc) private static String
getBondDisplay
(int i) private static String
getBondOrder
(int i) private static String
getNodeType
(int n) static void
private void
processObject
(int type) private String
private int
readInt
(int len) private int
private String
readString
(int len) private void
void
private void
skip
(int len) private static double
toPoint
(int i) static String
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA terminationwrite
(javajs.util.BS bs) private void
writeBondProperties
(int prop, int len) private void
writeNodeProperties
(int prop, int len) private void
writeTextProperty
(int prop, int len) Methods inherited from class org.jmol.adapter.writers.CMLWriter
addAttribute, addAttributes, appendEmptyTag, closeTag, openDocument, openTag, startOpenTag, terminateEmptyTag, terminateTag, toString
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Field Details
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doc
private javajs.api.GenericBinaryDocument doc -
objects
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sb
private javajs.util.SB sb -
sbpt
private int sbpt -
kCDXProp_ChemicalWarning
private static final int kCDXProp_ChemicalWarning- See Also:
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kCDXProp_2DPosition
private static final int kCDXProp_2DPosition- See Also:
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kCDXProp_Node_Type
private static final int kCDXProp_Node_Type- See Also:
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kCDXProp_Node_Element
private static final int kCDXProp_Node_Element- See Also:
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kCDXProp_Atom_Isotope
private static final int kCDXProp_Atom_Isotope- See Also:
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kCDXProp_Atom_Charge
private static final int kCDXProp_Atom_Charge- See Also:
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kCDXProp_Node_Attachments
private static final int kCDXProp_Node_Attachments- See Also:
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kCDXProp_Atom_GenericNickname
private static final int kCDXProp_Atom_GenericNickname- See Also:
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kCDXProp_Bond_Order
private static final int kCDXProp_Bond_Order- See Also:
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kCDXProp_Bond_Display
private static final int kCDXProp_Bond_Display- See Also:
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kCDXProp_Bond_Display2
private static final int kCDXProp_Bond_Display2- See Also:
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kCDXProp_Bond_Begin
private static final int kCDXProp_Bond_Begin- See Also:
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kCDXProp_Bond_End
private static final int kCDXProp_Bond_End- See Also:
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kCDXProp_Bond_BeginAttach
private static final int kCDXProp_Bond_BeginAttach- See Also:
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kCDXProp_Bond_EndAttach
private static final int kCDXProp_Bond_EndAttach- See Also:
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kCDXProp_Text
private static final int kCDXProp_Text- See Also:
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kCDXObj_Document
private static final int kCDXObj_Document- See Also:
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kCDXObj_Page
private static final int kCDXObj_Page- See Also:
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kCDXObj_Group
private static final int kCDXObj_Group- See Also:
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kCDXObj_Fragment
private static final int kCDXObj_Fragment- See Also:
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kCDXObj_Node
private static final int kCDXObj_Node- See Also:
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kCDXObj_Bond
private static final int kCDXObj_Bond- See Also:
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kCDXObj_Text
private static final int kCDXObj_Text- See Also:
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kCDXNodeType_Unspecified
private static final int kCDXNodeType_Unspecified- See Also:
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kCDXNodeType_Element
private static final int kCDXNodeType_Element- See Also:
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kCDXNodeType_ElementList
private static final int kCDXNodeType_ElementList- See Also:
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kCDXNodeType_ElementListNickname
private static final int kCDXNodeType_ElementListNickname- See Also:
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kCDXNodeType_Nickname
private static final int kCDXNodeType_Nickname- See Also:
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kCDXNodeType_Fragment
private static final int kCDXNodeType_Fragment- See Also:
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kCDXNodeType_Formula
private static final int kCDXNodeType_Formula- See Also:
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kCDXNodeType_GenericNickname
private static final int kCDXNodeType_GenericNickname- See Also:
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kCDXNodeType_AnonymousAlternativeGroup
private static final int kCDXNodeType_AnonymousAlternativeGroup- See Also:
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kCDXNodeType_NamedAlternativeGroup
private static final int kCDXNodeType_NamedAlternativeGroup- See Also:
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kCDXNodeType_MultiAttachment
private static final int kCDXNodeType_MultiAttachment- See Also:
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kCDXNodeType_VariableAttachment
private static final int kCDXNodeType_VariableAttachment- See Also:
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kCDXNodeType_ExternalConnectionPoint
private static final int kCDXNodeType_ExternalConnectionPoint- See Also:
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kCDXNodeType_LinkNode
private static final int kCDXNodeType_LinkNode- See Also:
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kCDXBondOrder_Single
private static final int kCDXBondOrder_Single- See Also:
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kCDXBondOrder_Double
private static final int kCDXBondOrder_Double- See Also:
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kCDXBondOrder_Triple
private static final int kCDXBondOrder_Triple- See Also:
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kCDXBondOrder_Quadruple
private static final int kCDXBondOrder_Quadruple- See Also:
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kCDXBondOrder_Quintuple
private static final int kCDXBondOrder_Quintuple- See Also:
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kCDXBondOrder_Sextuple
private static final int kCDXBondOrder_Sextuple- See Also:
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kCDXBondOrder_Half
private static final int kCDXBondOrder_Half- See Also:
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kCDXBondOrder_OneHalf
private static final int kCDXBondOrder_OneHalf- See Also:
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kCDXBondOrder_TwoHalf
private static final int kCDXBondOrder_TwoHalf- See Also:
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kCDXBondOrder_ThreeHalf
private static final int kCDXBondOrder_ThreeHalf- See Also:
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kCDXBondOrder_FourHalf
private static final int kCDXBondOrder_FourHalf- See Also:
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kCDXBondOrder_FiveHalf
private static final int kCDXBondOrder_FiveHalf- See Also:
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kCDXBondOrder_Dative
private static final int kCDXBondOrder_Dative- See Also:
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kCDXBondOrder_Ionic
private static final int kCDXBondOrder_Ionic- See Also:
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kCDXBondOrder_Hydrogen
private static final int kCDXBondOrder_Hydrogen- See Also:
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kCDXBondOrder_ThreeCenter
private static final int kCDXBondOrder_ThreeCenter- See Also:
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kCDXBondDisplay_Solid
private static final int kCDXBondDisplay_Solid- See Also:
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kCDXBondDisplay_Dash
private static final int kCDXBondDisplay_Dash- See Also:
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kCDXBondDisplay_Hash
private static final int kCDXBondDisplay_Hash- See Also:
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kCDXBondDisplay_WedgedHashBegin
private static final int kCDXBondDisplay_WedgedHashBegin- See Also:
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kCDXBondDisplay_WedgedHashEnd
private static final int kCDXBondDisplay_WedgedHashEnd- See Also:
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kCDXBondDisplay_Bold
private static final int kCDXBondDisplay_Bold- See Also:
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kCDXBondDisplay_WedgeBegin
private static final int kCDXBondDisplay_WedgeBegin- See Also:
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kCDXBondDisplay_WedgeEnd
private static final int kCDXBondDisplay_WedgeEnd- See Also:
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kCDXBondDisplay_Wavy
private static final int kCDXBondDisplay_Wavy- See Also:
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kCDXBondDisplay_HollowWedgeBegin
private static final int kCDXBondDisplay_HollowWedgeBegin- See Also:
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kCDXBondDisplay_HollowWedgeEnd
private static final int kCDXBondDisplay_HollowWedgeEnd- See Also:
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kCDXBondDisplay_WavyWedgeBegin
private static final int kCDXBondDisplay_WavyWedgeBegin- See Also:
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kCDXBondDisplay_WavyWedgeEnd
private static final int kCDXBondDisplay_WavyWedgeEnd- See Also:
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kCDXBondDisplay_Dot
private static final int kCDXBondDisplay_Dot- See Also:
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kCDXBondDisplay_DashDot
private static final int kCDXBondDisplay_DashDot- See Also:
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Constructor Details
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CDXMLWriter
public CDXMLWriter()
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Method Details
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set
- Specified by:
set
in interfaceJmolWriter
- Overrides:
set
in classCMLWriter
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write
- Specified by:
write
in interfaceJmolWriter
- Overrides:
write
in classCMLWriter
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fromCDX
- Throws:
Exception
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cdxToCdxml
- Throws:
Exception
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processObject
- Throws:
Exception
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writeNodeProperties
- Throws:
Exception
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writeBondProperties
- Throws:
Exception
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writeTextProperty
- Throws:
Exception
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wrapCData
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination- Parameters:
s
-- Returns:
- wrapped text
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getNodeType
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getBondDisplay
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getBondOrder
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removeObject
private void removeObject() -
skip
private void skip(int len) -
readInt
- Throws:
Exception
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readString
- Throws:
Exception
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readArray
- Throws:
Exception
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readLength
- Throws:
Exception
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toPoint
private static double toPoint(int i) -
main
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