Package chemaxon.marvin.alignment

Class AlignmentMolecule

java.lang.Object
chemaxon.marvin.alignment.AlignmentMolecule
@PublicAPI public class AlignmentMolecule extends Object

  • Field Details

    • nodes

      public chemaxon.marvin.alignment.NodeSum nodes

    • molID

      protected int molID

  • Method Details

    • setMolID

      public void setMolID(int molID)

    • getNodes

      public chemaxon.marvin.alignment.NodeSum getNodes()

    • initVariables

      public void initVariables(boolean enableTranslateAndRotate)

    • getColoringScheme

      public AlignmentProperties.ColoringScheme getColoringScheme()

    • getColors

      public chemaxon.marvin.alignment.NodeColor getColors()

    • getVisualizable

      public chemaxon.marvin.alignment.Visualizable getVisualizable()

    • getRotBondCount

      public int getRotBondCount()

    • create

      @Deprecated public static AlignmentMolecule create(byte[] bytes)
      Deprecated.
      Deserializes an AlignmentMolecule from a byte array.
      Parameters:
      bytes - ShapeData object in a serialized form created by ShapeData.toData() method.
      Returns:
      the AlignmentMolecule created with AlignmentMoleculeFactory.create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType) with DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE
      Throws:
      IOException

    • cloneMolecule

      public AlignmentMolecule cloneMolecule()

    • toData

      @Deprecated public byte[] toData()
      Deprecated.
      use ShapeData.toData() instead.
      Serializes the current object to a byte array
      Returns:
      the serialized array

    • distanceRangeStore

      public chemaxon.marvin.alignment.DistanceRangeStore distanceRangeStore()

    • getVolume

      public double getVolume()
      Returns:
      the volume of the molecule in A^3

    • getAtomCount

      public int getAtomCount()

    • crdSafeRefresh

      public void crdSafeRefresh()

    • crdMolRefresh

      public void crdMolRefresh()

    • getMolID

      public int getMolID()

    • getNodeCount

      public int getNodeCount()

    • getMolCrd

      public double[][] getMolCrd()

    • getMoleculeOrig

      public Molecule getMoleculeOrig()
      Gets back a clone of the unmodified input structure.
      Returns:
      clone of the unmodified input structure

    • setAssigned

      public void setAssigned(int i, boolean b)

    • clearAssigned

      public void clearAssigned()

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • isEnableTranslateAndRotate

      public boolean isEnableTranslateAndRotate()

    • setEnableTranslateAndRotate

      public void setEnableTranslateAndRotate(boolean enableTranslateAndRotate) throws chemaxon.marvin.alignment.AlignmentException
      Throws:
      chemaxon.marvin.alignment.AlignmentException

    • showSelectedNodes

      public Molecule showSelectedNodes()

    • ownOverlap

      public double ownOverlap(AlignmentAccuracyMode mode)