ChemoJunAtomConnection

ChemoJun050 (2006/08/08) Copyright 2002-2006 National Institute of Informatics, Research Organization of Information and Systems.

category:

• ChemoJun-Basic-Objects

inheritance:

• Object
  • ChemoJunAtomConnection

instance variables:

• attributeTable
• bondType
• fromAtom
• stereoType
• toAtom

class instance variables:

class variables:

pool variables:

instance methods:

1. attributeTable [attribute accessing]
   

   	attributeTable isNil ifTrue: [attributeTable := JunAttributeTable new].
   	^attributeTable

2. bondType [accessing]
   

   	bondType isNil ifTrue: [bondType := self defaultBondType].
   	^bondType

3. bondType: aNumber [accessing]
   

    
   	aNumber isNil 
   		ifTrue: [bondType := self defaultBondType]
   		ifFalse: [bondType := aNumber]

4. bondTypeSymbol [accessing]
   

   	self bondType = 1 ifTrue: [^#single].
   	self bondType = 2 ifTrue: [^#double].
   	self bondType = 3 ifTrue: [^#triple].
   	self bondType = 4 ifTrue: [^#aromatic].
   	self bondType = 5 ifTrue: [^#single].
   	self bondType = 6 ifTrue: [^#single].
   	self bondType = 7 ifTrue: [^#single].
   	self bondType = 8 ifTrue: [^#none].
   	^#unknown

5. connectionColor [attribute accessing]
   

   	^self attributeTable at: #connectionColor
   		ifAbsent: [self defaultConnectionColor]

6. connectionColor: colorValue [attribute accessing]
   

    
   	colorValue ifNil: [self attributeTable removeKey: #connectionColor]
   		ifNotNil: [:it | self attributeTable at: #connectionColor put: it]

7. defaultBondType [defaults]
   

   	^1

8. defaultConnectionColor [defaults]
   

   	^ColorValue veryDarkGray

9. defaultFromAtom [defaults]
   

   	^self class defaultAtomObjectClass new

10. defaultStereoType [defaults]
    

    	^0

11. defaultToAtom [defaults]
    

    	^self class defaultAtomObjectClass new

12. fromAtom [accessing]
    

    	fromAtom isNil ifTrue: [fromAtom := self defaultFromAtom].
    	^fromAtom

13. fromAtom: atomObject [accessing]
    

     
    	atomObject isNil
    		ifTrue: [fromAtom := self defaultFromAtom]
    		ifFalse: [fromAtom := atomObject]

14. hasConnectionColor [testing]
    

    	^self attributeTable includesKey: #connectionColor

15. initialize [initialize-release]
    

    	super initialize.
    	fromAtom := nil.
    	toAtom := nil.
    	bondType := nil.
    	stereoType := nil.
    	attributeTable := nil

16. isAromatic [testing]
    

    	^self bondType = 4

17. isDouble [testing]
    

    	^self bondType = 2

18. isSingle [testing]
    

    	^self bondType = 1

19. isTriple [testing]
    

    	^self bondType = 3

20. postCopy [copying]
    

    	super postCopy.
    	attributeTable := attributeTable copy
    
    	"You must copy fromAtom and toAtom."

21. printOn: aStream [printing]
    

     
    	aStream nextPutAll: '('.
    	aStream nextPutAll: self fromAtom printString.
    	aStream space.
    	aStream nextPutAll: self toAtom printString.
    	aStream space.
    	aStream nextPutAll: self bondTypeSymbol printString.
    	aStream space.
    	aStream nextPutAll: self stereoTypeSymbol printString.
    	aStream nextPutAll: ')'

22. stereoType [accessing]
    

    	stereoType isNil ifTrue: [stereoType := self defaultStereoType].
    	^stereoType

23. stereoType: aNumber [accessing]
    

     
    	aNumber isNil 
    		ifTrue: [stereoType := self defaultBondType]
    		ifFalse: [stereoType := aNumber]

24. stereoTypeSymbol [accessing]
    

    	self stereoType = 0 ifTrue: [^#none].
    	self stereoType = 1 ifTrue: [^#up].
    	self stereoType = 4 ifTrue: [^#either].
    	self stereoType = 6 ifTrue: [^#down].
    	^#unknown

25. toAtom [accessing]
    

    	toAtom isNil ifTrue: [toAtom := self defaultToAtom].
    	^toAtom

26. toAtom: atomObject [accessing]
    

     
    	atomObject isNil
    		ifTrue: [toAtom := self defaultToAtom]
    		ifFalse: [toAtom := atomObject]

class methods:

1. copyright [copyright]
   

   	^'ChemoJun050 (2006/08/08) Copyright 2002-2006 National Institute of Informatics, Research Organization of Information and Systems.'

2. defaultAtomObjectClass [defaults]
   

   	^self defaultMoleculeObjectClass defaultAtomObjectClass

3. defaultMoleculeObjectClass [defaults]
   

   	^ChemoJunMoleculeObject

4. example1 [examples]
   

   	"ChemoJunAtomConnection example1."
   
   	| atomConnection |
   	atomConnection := ChemoJunAtomConnection new.
   	^atomConnection

5. fromAtom: fromAtomObject toAtom: toAtomObject [instance creation]
   

    
   	| atomConnection |
   	atomConnection := self new.
   	atomConnection fromAtom: fromAtomObject.
   	atomConnection toAtom: toAtomObject.
   	^atomConnection

6. fromAtom: fromAtomObject toAtom: toAtomObject bondType: bondType [instance creation]
   

    
   	| atomConnection |
   	atomConnection := self new.
   	atomConnection fromAtom: fromAtomObject.
   	atomConnection toAtom: toAtomObject.
   	atomConnection bondType: bondType.
   	^atomConnection

7. fromAtom: fromAtomObject toAtom: toAtomObject bondType: bondType stereoType: stereoType [instance creation]
   

    
   	| atomConnection |
   	atomConnection := self new.
   	atomConnection fromAtom: fromAtomObject.
   	atomConnection toAtom: toAtomObject.
   	atomConnection bondType: bondType.
   	atomConnection stereoType: stereoType.
   	^atomConnection

8. system [copyright]
   

   	^'ChemoJun'

9. version [copyright]
   

   	^'050'