public class BioAssemblyTools
extends java.lang.Object
Constructor | Description |
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BioAssemblyTools() |
Modifier and Type | Method | Description |
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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 |
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(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
|
static java.util.List<OrderedPair<java.lang.String>> |
parseBinaryOperatorExpression(java.lang.String expression) |
|
static java.util.List<java.lang.String> |
parseUnaryOperatorExpression(java.lang.String operatorExpression) |
public static boolean isUnaryExpression(java.lang.String expression)
expression
- public static java.util.List<java.lang.String> parseUnaryOperatorExpression(java.lang.String operatorExpression) throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
public static java.util.List<OrderedPair<java.lang.String>> parseBinaryOperatorExpression(java.lang.String expression) throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
public static double[][] getBiologicalMoleculeBounds(Structure asymStructure, java.util.List<BiologicalAssemblyTransformation> transformations)
public static double[][] getAtomCoordinateBounds(Structure s)
public static double getMaximumExtend(Structure structure)
structure
- public static double getBiologicalMoleculeMaximumExtend(Structure structure, java.util.List<BiologicalAssemblyTransformation> transformations)
structure
- public static double[] getBiologicalMoleculeCentroid(Structure asymUnit, java.util.List<BiologicalAssemblyTransformation> transformations) throws java.lang.IllegalArgumentException
structure
- java.lang.IllegalArgumentException
- if structure is null@Deprecated public static Structure getReducedCAStructure(Structure orig)
getReducedStructure(Structure)
orig
-