Class BioAssemblyTools


  • public class BioAssemblyTools
    extends java.lang.Object
    Author:
    Peter Rose
    • Constructor Detail

      • BioAssemblyTools

        public BioAssemblyTools()
    • Method Detail

      • isUnaryExpression

        public static boolean isUnaryExpression​(java.lang.String expression)
        Checks if the passed in expression is a unary operator expression Example: (1,2,3) or (1-60) are unary operator expressions (1-60)(61-88) is a binary operator expression, representing a cartesian product of the two parenthesised lists
        Parameters:
        expression -
        Returns:
        true if expression is a unary operator expression
      • parseUnaryOperatorExpression

        public static java.util.List<java.lang.String> parseUnaryOperatorExpression​(java.lang.String operatorExpression)
                                                                             throws java.lang.IllegalArgumentException
        Throws:
        java.lang.IllegalArgumentException
      • parseBinaryOperatorExpression

        public static java.util.List<OrderedPair<java.lang.String>> parseBinaryOperatorExpression​(java.lang.String expression)
                                                                                           throws java.lang.IllegalArgumentException
        Throws:
        java.lang.IllegalArgumentException
      • getAtomCoordinateBounds

        public static double[][] getAtomCoordinateBounds​(Structure s)
      • getMaximumExtend

        public static double getMaximumExtend​(Structure structure)
        Returns the maximum extend of the structure in the x, y, or z direction.
        Parameters:
        structure -
        Returns:
        maximum extend
      • getBiologicalMoleculeMaximumExtend

        public static double getBiologicalMoleculeMaximumExtend​(Structure structure,
                                                                java.util.List<BiologicalAssemblyTransformation> transformations)
        Returns the maximum extend of the biological molecule in the x, y, or z direction.
        Parameters:
        structure -
        Returns:
        maximum extend
      • getBiologicalMoleculeCentroid

        public static double[] getBiologicalMoleculeCentroid​(Structure asymUnit,
                                                             java.util.List<BiologicalAssemblyTransformation> transformations)
                                                      throws java.lang.IllegalArgumentException
        Returns the centroid of the biological molecule.
        Parameters:
        structure -
        Returns:
        centroid
        Throws:
        java.lang.IllegalArgumentException - if structure is null
      • getReducedCAStructure

        @Deprecated
        public static Structure getReducedCAStructure​(Structure orig)
        Deprecated.
        Use the more generic getReducedStructure(Structure)
        reduce a structure to a Calpha representation only
        Parameters:
        orig -
        Returns:
      • getReducedStructure

        public static Structure getReducedStructure​(Structure orig)
        reduce a structure to a single-atom representation (e.g. CA atoms
        Parameters:
        orig -
        Returns:
        Since:
        Biojava 4.1.0