Class BioAssemblyTools
- java.lang.Object
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- org.biojava.nbio.structure.quaternary.BioAssemblyTools
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public class BioAssemblyTools extends java.lang.Object
- Author:
- Peter Rose
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Constructor Summary
Constructors Constructor Description BioAssemblyTools()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static double[][]
getAtomCoordinateBounds(Structure s)
static double[][]
getBiologicalMoleculeBounds(Structure asymStructure, java.util.List<BiologicalAssemblyTransformation> transformations)
static double[]
getBiologicalMoleculeCentroid(Structure asymUnit, java.util.List<BiologicalAssemblyTransformation> transformations)
Returns the centroid of the biological molecule.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.static double
getMaximumExtend(Structure structure)
Returns the maximum extend of the structure in the x, y, or z direction.static Structure
getReducedStructure(Structure orig)
Reduce a structure to a single-atom representation (e.g.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 listsstatic java.util.List<OrderedPair<java.lang.String>>
parseBinaryOperatorExpression(java.lang.String expression)
static java.util.List<java.lang.String>
parseUnaryOperatorExpression(java.lang.String operatorExpression)
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Method Detail
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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
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parseUnaryOperatorExpression
public static java.util.List<java.lang.String> parseUnaryOperatorExpression(java.lang.String operatorExpression) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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parseBinaryOperatorExpression
public static java.util.List<OrderedPair<java.lang.String>> parseBinaryOperatorExpression(java.lang.String expression) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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getBiologicalMoleculeBounds
public static double[][] getBiologicalMoleculeBounds(Structure asymStructure, java.util.List<BiologicalAssemblyTransformation> transformations)
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getAtomCoordinateBounds
public static double[][] getAtomCoordinateBounds(Structure s)
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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
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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
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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
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