Package chemaxon.marvin.alignment

Class MMPAlignmentProperties

java.lang.Object
chemaxon.marvin.alignment.MMPAlignmentProperties
@PublicApi public final class MMPAlignmentProperties extends Object
Input property settings for MMPAlignment.

  • Constructor Details

    • MMPAlignmentProperties

      public MMPAlignmentProperties()
      Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3

    • MMPAlignmentProperties

      public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit)
      Constructs a MMPAlignmentProperties object.
      Parameters:
      flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.
      mode - Determines the shape representation accuracy for molecules.
      mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.

    • MMPAlignmentProperties

      public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, int confTryCountLimit)
      Constructs a MMPAlignmentProperties object.
      Parameters:
      flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.
      mode - Determines the shape representation accuracy for molecules.
      mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.
      confTryCountLimit - number of starting conformations for the non-MCS part to start the optimization for maximizing the shape overlay.

    • MMPAlignmentProperties

      public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, boolean fastMode)
      Constructs a MMPAlignmentProperties object.
      Parameters:
      flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.
      mode - Determines the shape representation accuracy for molecules.
      mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.
      fastMode - do fast mode Alignment

    • MMPAlignmentProperties

      public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, boolean fastMode, int confTryCountLimit)
      Constructs a MMPAlignmentProperties object.
      Parameters:
      flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.
      mode - Determines the shape representation accuracy for molecules.
      mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.
      fastMode - do fast mode Alignment
      confTryCountLimit - number of starting conformations for the non-MCS part to start the optimization for maximizing the shape overlay.

  • Method Details

    • getAccuracyMode

      public AlignmentAccuracyMode getAccuracyMode()

    • getFlexibilityMode

      public AlignmentProperties.FlexibilityMode getFlexibilityMode()
      Returns:
      the selected conformational flexibility treatment mode during the alignment.

    • getMcsSimilarityLimit

      public double getMcsSimilarityLimit()
      Returns:
      the mcs Tanimoto similarity limit.

    • getConfTryCountLimit

      public int getConfTryCountLimit()
      Returns:
      the confTryCountLimit