Class BioAssemblyTools

Method Details

• isUnaryExpression

  public static boolean isUnaryExpression(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 List<String> parseUnaryOperatorExpression(String operatorExpression) throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• parseBinaryOperatorExpression

  public static List<OrderedPair<String>> parseBinaryOperatorExpression(String expression) throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• getBiologicalMoleculeBounds

  public static double[][] getBiologicalMoleculeBounds(Structure asymStructure, List<BiologicalAssemblyTransformation> transformations)

• 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, 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, List<BiologicalAssemblyTransformation> transformations) throws IllegalArgumentException

  Returns the centroid of the biological molecule.

  Parameters:

  structure -

  Returns:

  centroid

  Throws:

  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