org.biojava.nbio.structure.quaternary

Class BioAssemblyTools

java.lang.Object

org.biojava.nbio.structure.quaternary.BioAssemblyTools

public class BioAssemblyTools
extends Object

Author:

Peter Rose

Constructor Summary

Constructors

Constructor and Description
BioAssemblyTools()

Method Summary

Modifier and Type	Method and Description
static double[][]	getAtomCoordinateBounds(Structure s)
static double[][]	getBiologicalMoleculeBounds(Structure asymStructure, List<BiologicalAssemblyTransformation> transformations)
static double[]	getBiologicalMoleculeCentroid(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) Returns the centroid of the biological molecule.
static double	getBiologicalMoleculeMaximumExtend(Structure structure, 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	getReducedCAStructure(Structure orig) Deprecated. Use the more generic getReducedStructure(Structure)
static Structure	getReducedStructure(Structure orig) reduce a structure to a single-atom representation (e.g.
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
static List<OrderedPair<String>>	parseBinaryOperatorExpression(String expression)
static List<String>	parseUnaryOperatorExpression(String operatorExpression)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioAssemblyTools

public BioAssemblyTools()

Method Detail

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