index

ChemoJunMoleculeObject

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

superclass:

instance variables:

class instance variables:

class variabels:

pool variabels:

instance methods:

  1. arrayOfPolylinesForAromaticBondAsPlane: atomConnection [3d aux]
  2. arrayOfPolylinesForDoubleBondAsPlane: atomConnection [3d aux]
  3. arrayOfPolylinesForSingleBondAsPlane: atomConnection [3d aux]
  4. arrayOfPolylinesForTripleBondAsPlane: atomConnection [3d aux]
  5. asGraph [converting]
  6. asGrapher [converting]
  7. atomConnection: atomObject with: anotherAtomObject [accessing connection]
  8. atomConnections [accessing connection]
  9. atomConnections: atomConnectionCollection [accessing connection]
  10. atomConnectionsDo: aBlock [enumerating]
  11. atomObjectAt: serialNumber [accessing atom]
  12. atomObjects [accessing atom]
  13. atomObjects: atomObjectCollection [accessing atom]
  14. atomObjectsAndIndexesDo: aBlock [enumerating]
  15. atomObjectsDo: aBlock [enumerating]
  16. atomResolution [accessing]
  17. atomResolution: aSymbol [accessing]
  18. atomTable [accessing]
  19. attributeTable [attribute accessing]
  20. changeColor: colorValue serialNumberPairs: serialNumberPairs nestLevel: nestLevel [coloring]
  21. changeColor: colorValue serialNumbers: serialNumbers nestLevel: nestLevel [coloring]
  22. connectedAromaticAtomsAround: atomConnection [accessing atom]
  23. connectedAtomsAndConnectionsWith: atomObject [accessing atom]
  24. connectedAtomsAround: atomConnection [accessing atom]
  25. connectedAtomsWith: atomObject [accessing atom]
  26. connectedConnectionsAround: atomConnection [accessing connection]
  27. connectionsWith: atomObject [accessing connection]
  28. connectionTable [accessing connection]
  29. cylinderFrom: fromPoint to: toPoint width: widthValue by: divisionNumber [3d aux]
  30. default2dMolfilePatterns [defaults]
  31. defaultAtomConnectionClass [defaults]
  32. defaultAtomObjectClass [defaults]
  33. defaultBallDivisionNumberHigh [defaults]
  34. defaultBallDivisionNumberLow [defaults]
  35. defaultBallDivisionNumberMedium [defaults]
  36. defaultBondThickness [defaults]
  37. defaultFrontierMinimumDistance [defaults]
  38. defaultFrontierRevisedCoeffcient [defaults]
  39. defaultGraphClass [defaults]
  40. defaultGrapherClass [defaults]
  41. defaultHalftoneValue [defaults]
  42. defaultMinimumTriangleArea [defaults]
  43. defaultMolFileReaderClass [defaults]
  44. defaultSpaceFillDivisionNumber [defaults]
  45. defaultSpaceFillDivisionNumberHigh [defaults]
  46. defaultSpaceFillDivisionNumberLow [defaults]
  47. defaultSpaceFillDivisionNumberMedium [defaults]
  48. defaultTubeDivisionNumber [defaults]
  49. defaultTubeDivisionNumberHigh [defaults]
  50. defaultTubeDivisionNumberLow [defaults]
  51. defaultTubeDivisionNumberMedium [defaults]
  52. distancesFrom: aPoint [functions]
  53. exceptHydrogen [accessing]
  54. exceptHydrogen: aBoolean [accessing]
  55. frontierPoint: aLine rejectedBy: aBall [frontier]
  56. frontierPolygons: aPolygon of: atomObject offset: offsetValue [frontier]
  57. frontierTriangles: aTriangle rejectedBy: aBall [frontier]
  58. hasHydroxyl: atomObject [testing]

    *-OH
    ^
  59. informationString [accessing]
  60. initialize [initialize-release]
  61. is2d [testing]
  62. is3d [testing]
  63. isAldehyde: atomObject [testing]

    -CHO
    ^
  64. isAmino: atomObject [testing]

    -NH2 or -NH
    ^ ^
  65. isCarbonyl: atomObject [testing]

    -C=O
    ^
  66. isCarboxyl: atomObject [testing]

    -COOH
    ^
  67. isHydroxyl: atomObject [testing]

    -OH
    ^
  68. isMethyl: atomObject [testing]

    -CH3
    ^
  69. isSulfanyl: atomObject [testing]

    -SH
    ^
  70. modifierAssociation: atomObject normalPresentation: aBoolean [private]
  71. moleculeAsBallAndStick [3d accessing]
  72. moleculeAsBallAndStick: divisionNumber [3d accessing]
  73. moleculeAsPlane [3d accessing]
  74. moleculeAsSpaceFill [3d accessing]
  75. moleculeAsSpaceFill: divisionNumber [3d accessing]
  76. moleculeAsSpaceFill: divisionNumber offsetValue: offsetValue [3d accessing]
  77. moleculeAsSpaceFill: divisionNumber offsetValue: offsetValue smoothShading: aBoolean [3d accessing]
  78. moleculeAsStick [3d accessing]
  79. moleculeAsStick: divisionNumber [3d accessing]
  80. moleculeAsStickAndSpaceFill [3d accessing]
  81. molfileHeaderBlock [attribute accessing]
  82. molfileHeaderBlock: aCollection [attribute accessing]
  83. numberOfAtoms [accessing atom]
  84. numberOfConnections [accessing connection]
  85. numberOfHydrogens: atomObject [accessing]
  86. numberOfHydrogensTable: atomObject [private]
  87. numberOfNitrogens: atomObject [accessing]
  88. numberOfOxygens: atomObject [accessing]
  89. postCopy [copying]
  90. surfaceInformationString [accessing]
  91. translationOffsetOf: atomConnection [3d aux]

class methods:

  1. copyright [copyright]
  2. defaultAtomConnectionClass [defaults]
  3. defaultAtomObjectClass [defaults]
  4. defaultExceptHydrogen [defaults]
  5. defaultGraphClass [defaults]
  6. defaultGrapherClass [defaults]
  7. defaultMolFileReaderClass [defaults]
  8. example1 [examples]
    ChemoJunMoleculeObject example1.
  9. example2 [examples]
    ChemoJunMoleculeObject example2.
  10. example3 [examples]
    ChemoJunMoleculeObject example3.
  11. example4 [examples]
    ChemoJunMoleculeObject example4.
  12. example5 [examples]
    ChemoJunMoleculeObject example5.
  13. example6 [examples]
    ChemoJunMoleculeObject example6.
  14. example7 [examples]
    ChemoJunMoleculeObject example7.
  15. example8 [examples]
    ChemoJunMoleculeObject example8.
  16. example9 [examples]
    ChemoJunMoleculeObject example9.
  17. exampleA [examples]
    ChemoJunMoleculeObject exampleA.
  18. exampleB [examples]
    ChemoJunMoleculeObject exampleB.
  19. fileName: aFilename [instance creation]
  20. fromReader: aReader [instance creation]
  21. moleculeObjectFromReader: aReader [private]
  22. request [utilities]
    ChemoJunMoleculeObject request.
  23. system [copyright]
  24. version [copyright]
index