Package org.biojava.nbio.structure.quaternary

Class OperatorResolver

  • public class OperatorResolver
extends Object
    A class to resolve the operators for transformations
    Author:
    Peter Rose

    • Method Detail

      • parseOperatorExpressionString

        public void parseOperatorExpressionString​(String operatorExpression)
                                   throws IllegalArgumentException
        Parses the operator expression and save the operators as a list of unary or binary operators (i.e. matrix multiplication, see below). Operation expressions are given in a compact notation and specify matrices from the operations list. An operation expression can be a comma-separated list 1, 5, 9, a dash-delimited range 1-60 or a matrix multiplication involving two or more lists or ranges. For instance, (X0)(1-20) specifies the portion of the X174 procapsid crystal asymmetric unit belonging to the first independent virus particle and corresponds to the 20 transformations [X0][1], [X0][2], ... , [X0][20]. See C. Lawson, Acta Cryst., D64, 874-882, 2008.
        Parameters:
        operatorExpression - the operator expression to be parsed
        Throws:
        IllegalArgumentException

      • getUnaryOperators

        public List<String> getUnaryOperators()
        Returns a list of operators for this assembly. The operators refer to the transformations that should be applied to the asym ids to generate this macromolecular assembly.
        Returns:
        the unary operators for this assembly

      • getBinaryOperators

        public List<OrderedPair<String>> getBinaryOperators()
        Returns a list of operators for this assembly. The operators refer to the transformations that should be applied to the asym ids to generate this macromolecular assembly. Each ordered pair refers to the multiplication of the two transformation matrices in the pdbx_structure_oper_list category.
        Returns:
        the binary operators for this assembly