Class QuatSymmetryDetector


  • public class QuatSymmetryDetector
    extends java.lang.Object
    Detects the symmetry (global, pseudo, internal and local) of protein structures.

    The SubunitClustererParameters determine the subunit definition and clustering, while the QuatSymmetryParameters determine the calculated symmetry results (point group and axes).

    Author:
    Peter Rose, Aleix Lafita
    • Method Detail

      • calcGlobalSymmetry

        public static QuatSymmetryResults calcGlobalSymmetry​(Structure structure,
                                                             QuatSymmetryParameters symmParams,
                                                             SubunitClustererParameters clusterParams)
        Calculate GLOBAL symmetry results. This means that all Subunit are included in the symmetry.
        Parameters:
        structure - protein chains will be extracted as Subunit
        symmParams - quaternary symmetry parameters
        clusterParams - subunit clustering parameters
        Returns:
        GLOBAL quaternary structure symmetry results
      • calcGlobalSymmetry

        public static QuatSymmetryResults calcGlobalSymmetry​(java.util.List<Subunit> subunits,
                                                             QuatSymmetryParameters symmParams,
                                                             SubunitClustererParameters clusterParams)
        Calculate GLOBAL symmetry results. This means that all Subunit are included in the symmetry.
        Parameters:
        subunits - list of Subunit
        symmParams - quaternary symmetry parameters
        clusterParams - subunit clustering parameters
        Returns:
        GLOBAL quaternary structure symmetry results
      • calcGlobalSymmetry

        public static QuatSymmetryResults calcGlobalSymmetry​(Stoichiometry composition,
                                                             QuatSymmetryParameters symmParams)
        Calculate GLOBAL symmetry results. This means that all Subunit are included in the symmetry.
        Parameters:
        composition - Stoichiometry object that contains clustering results
        symmParams - quaternary symmetry parameters
        Returns:
        GLOBAL quaternary structure symmetry results
      • calcLocalSymmetries

        public static java.util.List<QuatSymmetryResults> calcLocalSymmetries​(Structure structure,
                                                                              QuatSymmetryParameters symmParams,
                                                                              SubunitClustererParameters clusterParams)
        Returns a List of LOCAL symmetry results. This means that a subset of the SubunitCluster is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.

        Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)

        Parameters:
        structure - protein chains will be extracted as Subunit
        symmParams - quaternary symmetry parameters
        clusterParams - subunit clustering parameters
        Returns:
        List of LOCAL quaternary structure symmetry results. Empty if none.
      • calcLocalSymmetries

        public static java.util.List<QuatSymmetryResults> calcLocalSymmetries​(java.util.List<Subunit> subunits,
                                                                              QuatSymmetryParameters symmParams,
                                                                              SubunitClustererParameters clusterParams)
        Returns a List of LOCAL symmetry results. This means that a subset of the SubunitCluster is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.

        Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)

        Parameters:
        subunits - list of Subunit
        symmParams - quaternary symmetry parameters
        clusterParams - subunit clustering parameters
        Returns:
        List of LOCAL quaternary structure symmetry results. Empty if none.
      • calcLocalSymmetries

        public static java.util.List<QuatSymmetryResults> calcLocalSymmetries​(Stoichiometry globalComposition,
                                                                              QuatSymmetryParameters symmParams)
        Returns a List of LOCAL symmetry results. This means that a subset of the SubunitCluster is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.

        Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)

        Parameters:
        globalComposition - Stoichiometry object that contains global clustering results
        symmParams - quaternary symmetry parameters
        Returns:
        List of LOCAL quaternary structure symmetry results. Empty if none.