Class MMPAlignmentProperties


  • @PublicAPI
    public final class MMPAlignmentProperties
    extends Object
    Input property settings for MMPAlignment.
    • Constructor Detail

      • 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 Detail

      • getMcsSimilarityLimit

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

        public int getConfTryCountLimit()
        Returns:
        the confTryCountLimit