de.bioforscher.singa.structure.model.oak

Class Structures

java.lang.Object

de.bioforscher.singa.structure.model.oak.Structures

public class Structures
extends Object

Methods to use for structures...

Method Summary

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<Atom>	calculateAtomDistanceMatrix(AtomContainer atomContainer) Returns the distance matrix of the given Atoms.
static LabeledSymmetricMatrix<Atom>	calculateAtomDistanceMatrix(List<Atom> atoms) Returns the distance matrix of the given Atoms.
static LabeledSymmetricMatrix<LeafSubstructure<?>>	calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer) Returns the distance matrix of the given LeafSubstructureContainer.
static double	calculateExtent(LeafSubstructureContainer leafSubstructureContainer) Returns the maximal extent of the given LeafSubstructureContainer.
static LabeledSymmetricMatrix<LeafSubstructure<?>>	calculateSquaredDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer) Returns the squared distance matrix of the given LeafSubstructureContainer.
static double	calculateSquaredExtent(LeafSubstructureContainer leafSubstructureContainer) Returns the maximal squared extent of the given LeafSubstructureContainer.
static List<Sphere>	convertToSpheres(AtomContainer atomContainer)
static boolean	isAlphaCarbonStructure(Structure structure) Returns true iff the given Structure consists only of alpha carbon atoms (this may include hydrogen atoms).
static boolean	isBackboneStructure(Structure structure) Returns true iff the given Structure consists only of backbone atoms (this may include beta carbon and hydrogen atoms).

Methods inherited from class java.lang.Object

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

Method Detail

calculateDistanceMatrix

public static LabeledSymmetricMatrix<LeafSubstructure<?>> calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)

Returns the distance matrix of the given LeafSubstructureContainer.

Parameters:

leafSubstructureContainer - A LeafSubstructureContainer.

Returns:

The distance matrix.

calculateSquaredDistanceMatrix

public static LabeledSymmetricMatrix<LeafSubstructure<?>> calculateSquaredDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)

Returns the squared distance matrix of the given LeafSubstructureContainer.

Parameters:

leafSubstructureContainer - A LeafSubstructureContainer.

Returns:

The squared distance matrix.

calculateExtent

public static double calculateExtent(LeafSubstructureContainer leafSubstructureContainer)

Returns the maximal extent of the given LeafSubstructureContainer.

Parameters:

leafSubstructureContainer - A LeafSubstructureContainer.

Returns:

The maximal extent.

calculateSquaredExtent

public static double calculateSquaredExtent(LeafSubstructureContainer leafSubstructureContainer)

Returns the maximal squared extent of the given LeafSubstructureContainer.

Parameters:

leafSubstructureContainer - A LeafSubstructureContainer.

Returns:

The maximal squared extent.

calculateAtomDistanceMatrix

public static LabeledSymmetricMatrix<Atom> calculateAtomDistanceMatrix(AtomContainer atomContainer)

Returns the distance matrix of the given Atoms.

Parameters:

atomContainer - A atom container with the atoms.

Returns:

The squared distance matrix.

calculateAtomDistanceMatrix

public static LabeledSymmetricMatrix<Atom> calculateAtomDistanceMatrix(List<Atom> atoms)

Returns the distance matrix of the given Atoms.

Parameters:

atoms - A atom container with the atoms.

Returns:

The squared distance matrix.

isAlphaCarbonStructure

public static boolean isAlphaCarbonStructure(Structure structure)

Returns true iff the given Structure consists only of alpha carbon atoms (this may include hydrogen atoms).

Parameters:

structure - The Structure to check.

Returns:

True iff structure contains only alpha carbon atoms.

isBackboneStructure

public static boolean isBackboneStructure(Structure structure)

Returns true iff the given Structure consists only of backbone atoms (this may include beta carbon and hydrogen atoms).

Parameters:

structure - The Structure to check.

Returns:

True iff structure contains only backbone and hydrogen atoms.

convertToSpheres

public static List<Sphere> convertToSpheres(AtomContainer atomContainer)