Class SubunitClustererParameters

    • Constructor Summary

      Constructors 
      Constructor Description
      SubunitClustererParameters()
      Initialize with "local" metrics by default.
      SubunitClustererParameters​(boolean useGlobalMetrics)
      "Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getAbsoluteMinimumSequenceLength()
      If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
      SubunitClustererMethod getClustererMethod()
      Method to cluster subunits.
      int getMinimumSequenceLength()
      Get the minimum number of residues of a subunits to be considered in the clusters.
      double getMinimumSequenceLengthFraction()
      If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
      double getRMSDThreshold()
      Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
      double getSequenceCoverageThreshold()
      The minimum coverage of the sequence alignment between two subunits to be clustered together.
      double getSequenceIdentityThreshold()
      Sequence identity threshold to consider for the subunits clustering.
      double getStructureCoverageThreshold()
      The minimum coverage of the structure alignment between two subunits to be clustered together.
      String getSuperpositionAlgorithm()
      Method to superpose subunits (i.e., structural aligner).
      double getTMThreshold()
      Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
      boolean isHighConfidenceScores​(double sequenceIdentity, double sequenceCoverage)
      Whether the subunits can be considered "identical" by sequence alignment.
      boolean isInternalSymmetry()
      The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.
      boolean isOptimizeAlignment()
      Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
      boolean isUseEntityIdForSeqIdentityDetermination()
      Whether to use the entity id of subunits to infer that sequences are identical.
      boolean isUseGlobalMetrics()
      Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
      boolean isUseRMSD()
      Use RMSD for evaluating structure similarity
      boolean isUseSequenceCoverage()
      Use sequence coverage for evaluating sequence similarity
      boolean isUseStructureCoverage()
      Use structure coverage for evaluating sequence similarity
      boolean isUseTMScore()
      Use TMScore for evaluating structure similarity
      void setAbsoluteMinimumSequenceLength​(int absoluteMinimumSequenceLength)
      If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
      void setClustererMethod​(SubunitClustererMethod method)
      Method to cluster subunits.
      void setInternalSymmetry​(boolean internalSymmetry)
      The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.
      void setMinimumSequenceLength​(int minimumSequenceLength)
      Set the minimum number of residues of a subunits to be considered in the clusters.
      void setMinimumSequenceLengthFraction​(double minimumSequenceLengthFraction)
      If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
      void setOptimizeAlignment​(boolean optimizeAlignment)
      Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
      void setRMSDThreshold​(double rmsdThreshold)
      Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
      void setSequenceCoverageThreshold​(double sequenceCoverageThreshold)
      The minimum coverage of the sequence alignment between two subunits to be clustered together.
      void setSequenceIdentityThreshold​(double sequenceIdentityThreshold)
      Sequence identity threshold to consider for the sequence subunit clustering.
      void setStructureCoverageThreshold​(double structureCoverageThreshold)
      The minimum coverage of the structure alignment between two subunits to be clustered together.
      void setSuperpositionAlgorithm​(String superpositionAlgorithm)
      Method to cluster subunits.
      void setTMThreshold​(double tmThreshold)
      Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
      void setUseEntityIdForSeqIdentityDetermination​(boolean useEntityIdForSeqIdentityDetermination)
      Whether to use the entity id of subunits to infer that sequences are identical.
      void setUseGlobalMetrics​(boolean useGlobalMetrics)
      Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
      void setUseRMSD​(boolean useRMSD)
      Use RMSD for evaluating structure similarity
      void setUseSequenceCoverage​(boolean useSequenceCoverage)
      Use sequence coverage for evaluating sequence similarity
      void setUseStructureCoverage​(boolean useStructureCoverage)
      Use structure coverage for evaluating sequence similarity
      void setUseTMScore​(boolean useTMScore)
      Use TMScore for evaluating structure similarity
      String toString()  
    • Constructor Detail

      • SubunitClustererParameters

        public SubunitClustererParameters​(boolean useGlobalMetrics)
        "Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required. "Global" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a global alignment (normalised by the length of the alignment) SubunitClustererMethod.STRUCTURE: TMScore of the aligned structures (normalised by the length of the larger structure) One threshold for each method is required.
    • Method Detail

      • getMinimumSequenceLength

        public int getMinimumSequenceLength()
        Get the minimum number of residues of a subunits to be considered in the clusters.
        Returns:
        minimumSequenceLength
      • setMinimumSequenceLength

        public void setMinimumSequenceLength​(int minimumSequenceLength)
        Set the minimum number of residues of a subunits to be considered in the clusters.
        Parameters:
        minimumSequenceLength -
      • getAbsoluteMinimumSequenceLength

        public int getAbsoluteMinimumSequenceLength()
        If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

        This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)

        Returns:
        the absoluteMinimumSequenceLength
      • setAbsoluteMinimumSequenceLength

        public void setAbsoluteMinimumSequenceLength​(int absoluteMinimumSequenceLength)
        If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

        This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)

        Parameters:
        absoluteMinimumSequenceLength -
      • getMinimumSequenceLengthFraction

        public double getMinimumSequenceLengthFraction()
        If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

        This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)

        Returns:
        the minimumSequenceLengthFraction
      • setMinimumSequenceLengthFraction

        public void setMinimumSequenceLengthFraction​(double minimumSequenceLengthFraction)
        If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

        This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)

        Parameters:
        minimumSequenceLengthFraction -
      • getSequenceIdentityThreshold

        public double getSequenceIdentityThreshold()
        Sequence identity threshold to consider for the subunits clustering.

        Two subunits with sequence identity equal or higher than the threshold will be clustered together.

        Returns:
        sequenceIdentityThreshold
      • setSequenceIdentityThreshold

        public void setSequenceIdentityThreshold​(double sequenceIdentityThreshold)
        Sequence identity threshold to consider for the sequence subunit clustering.

        Two subunits with sequence identity equal or higher than the threshold will be clustered together.

        Parameters:
        sequenceIdentityThreshold -
      • getSequenceCoverageThreshold

        public double getSequenceCoverageThreshold()
        The minimum coverage of the sequence alignment between two subunits to be clustered together.
        Returns:
        sequenceCoverageThreshold
      • setSequenceCoverageThreshold

        public void setSequenceCoverageThreshold​(double sequenceCoverageThreshold)
        The minimum coverage of the sequence alignment between two subunits to be clustered together.
        Parameters:
        sequenceCoverageThreshold -
      • getRMSDThreshold

        public double getRMSDThreshold()
        Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
        Returns:
        rmsdThreshold
      • setRMSDThreshold

        public void setRMSDThreshold​(double rmsdThreshold)
        Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
        Parameters:
        rmsdThreshold -
      • getTMThreshold

        public double getTMThreshold()
        Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
        Returns:
        tmThreshold
      • setTMThreshold

        public void setTMThreshold​(double tmThreshold)
        Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
        Parameters:
        tmThreshold -
      • getStructureCoverageThreshold

        public double getStructureCoverageThreshold()
        The minimum coverage of the structure alignment between two subunits to be clustered together.
        Returns:
        structureCoverageThreshold
      • setStructureCoverageThreshold

        public void setStructureCoverageThreshold​(double structureCoverageThreshold)
        The minimum coverage of the structure alignment between two subunits to be clustered together.
        Parameters:
        structureCoverageThreshold -
      • isInternalSymmetry

        public boolean isInternalSymmetry()
        The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.

        The SubunitClustererMethod.STRUCTURE must be chosen to consider internal symmetry, otherwise this parameter will be ignored.

        Returns:
        true if internal symmetry is considered, false otherwise
      • setInternalSymmetry

        public void setInternalSymmetry​(boolean internalSymmetry)
        The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.

        The SubunitClustererMethod.STRUCTURE must be chosen to consider internal symmetry, otherwise this parameter will be ignored.

        Parameters:
        internalSymmetry - true if internal symmetry is considered, false otherwise
      • getSuperpositionAlgorithm

        public String getSuperpositionAlgorithm()
        Method to superpose subunits (i.e., structural aligner).
        Returns:
        superpositionAlgorithm
      • setSuperpositionAlgorithm

        public void setSuperpositionAlgorithm​(String superpositionAlgorithm)
        Method to cluster subunits.
        Parameters:
        superpositionAlgorithm -
      • isOptimizeAlignment

        public boolean isOptimizeAlignment()
        Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. Effect depends on implementation of the specific algorithm's method. *
        Returns:
        optimizeAlignment
      • setOptimizeAlignment

        public void setOptimizeAlignment​(boolean optimizeAlignment)
        Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. Effect depends on implementation of the specific algorithm's method. *
        Parameters:
        optimizeAlignment -
      • isUseRMSD

        public boolean isUseRMSD()
        Use RMSD for evaluating structure similarity
        Returns:
        useRMSD
      • setUseRMSD

        public void setUseRMSD​(boolean useRMSD)
        Use RMSD for evaluating structure similarity
        Parameters:
        useRMSD -
      • isUseTMScore

        public boolean isUseTMScore()
        Use TMScore for evaluating structure similarity
        Returns:
        useTMScore
      • setUseTMScore

        public void setUseTMScore​(boolean useTMScore)
        Use TMScore for evaluating structure similarity
        Parameters:
        useTMScore -
      • isUseSequenceCoverage

        public boolean isUseSequenceCoverage()
        Use sequence coverage for evaluating sequence similarity
        Returns:
        useSequenceCoverage
      • setUseSequenceCoverage

        public void setUseSequenceCoverage​(boolean useSequenceCoverage)
        Use sequence coverage for evaluating sequence similarity
        Parameters:
        useSequenceCoverage -
      • isUseStructureCoverage

        public boolean isUseStructureCoverage()
        Use structure coverage for evaluating sequence similarity
        Returns:
        useStructureCoverage
      • setUseStructureCoverage

        public void setUseStructureCoverage​(boolean useStructureCoverage)
        Use structure coverage for evaluating sequence similarity
        Parameters:
        useStructureCoverage -
      • isUseGlobalMetrics

        public boolean isUseGlobalMetrics()
        Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
        Returns:
        useGlobalMetrics
      • setUseGlobalMetrics

        public void setUseGlobalMetrics​(boolean useGlobalMetrics)
        Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
        Parameters:
        useGlobalMetrics -
      • isHighConfidenceScores

        public boolean isHighConfidenceScores​(double sequenceIdentity,
                                              double sequenceCoverage)
        Whether the subunits can be considered "identical" by sequence alignment. For local sequence alignment (normalized by the number of aligned pairs) this means 0.95 or higher identity and 0.75 or higher coverage. For global sequence alignment (normalised by the alignment length) this means 0.85 or higher sequence identity.
        Parameters:
        sequenceIdentity -
        sequenceCoverage -
        Returns:
        true if the sequence alignment scores are equal to or better than the "high confidence" scores, false otherwise.