Represents a fragment that can be clustered based on the 3*N coordinate of atoms and attachment points, i.e., N is the sum of atoms and attachment points. More...

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Public Member Functions
	ClusterableFragment (Fragment frag)
	Constructor. More...

void	setOrderOfNodes (Collection< FragIsomorphNode > c)
	Sets the order of nodes (i.e., atoms/APs) to use for geometric comparison with other fragments, and update the vector of coordinates accordingly. More...

void	setNaturalNodeOrder ()
	Define the node order from the list of atoms and attachment points. More...

double[]	getPoint ()

List< FragIsomorphNode >	getOrderedNodes ()
	Get the ordered list of nodes representing each either an atom or an attachment point is the alignment of fragments. More...

ClusterableFragment	clone ()
	Returns a shallow copy where the vector of coordinates has a new reference. More...

Fragment	getTransformedCopy ()

Static Public Member Functions
static double[]	convertToCoordsVector (Point3d[] pts)
	Converts an array of 3-dimensional points in a vector of coordinates in 3*N-dimensional space where coordinated are ordered as [x1, y1, z1, x2, y2, z2, ...]. More...

static Point3d[]	convertToPointArray (double[] coords)
	Converts an array of 3*N-dimensional coordinates into an array of 3-dimensional points assuming coordinated are ordered as [x1, y1, z1, x2, y2, z2, ...]. More...

Protected Member Functions
void	setCoordsVector (double[] coords)
	Sets the coordinates of each atom and attachment point in this object. More...

void	setCoordsVector (Point3d[] pts)
	Sets the coordinates of each atom and attachment point in this object. More...

Fragment	getOriginalFragment ()
	The original fragment used to construct an instance of this object. More...

DefaultUndirectedGraph< FragIsomorphNode, FragIsomorphEdge >	getJGraphFragIsomorphism ()

Package Attributes
double[]	allCoords
	Ordered list of coordinated reflecting the ordered list of atoms/APs. More...

Private Attributes
Fragment	frag
	Reference to original fragment. More...

List< FragIsomorphNode >	orderedNodes
	Ordered list of nodes determined by isomorphism. More...

Detailed Description

Represents a fragment that can be clustered based on the 3*N coordinate of atoms and attachment points, i.e., N is the sum of atoms and attachment points.

Note that dummy atoms meant to break linearities (i.e., {@value DENOPTIMConstants::DUMMYATMSYMBOL} with only one connected neighbor) are not part of the pool of N points.

Definition at line 28 of file ClusterableFragment.java.

Constructor & Destructor Documentation

◆ ClusterableFragment()

denoptim.fragmenter.ClusterableFragment.ClusterableFragment ( Fragment frag )

Constructor.

Does not set the ordering of the atoms/APs. For that use setOrderOfNodes(Collection).

Parameters

frag	the fragment to wrap.

Definition at line 52 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.frag.

Referenced by denoptim.fragmenter.ClusterableFragment.clone().

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Member Function Documentation

◆ clone()

ClusterableFragment denoptim.fragmenter.ClusterableFragment.clone ( )

Returns a shallow copy where the vector of coordinates has a new reference.

Thus, changes to the clone's coordinates vector do not affect the original.

Definition at line 247 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.clone(), denoptim.fragmenter.ClusterableFragment.ClusterableFragment(), denoptim.fragmenter.ClusterableFragment.orderedNodes, and denoptim.fragmenter.ClusterableFragment.setOrderOfNodes().

Referenced by denoptim.fragmenter.DynamicCentroidCluster.addPoint(), denoptim.fragmenter.ClusterableFragment.clone(), and denoptim.fragmenter.DynamicCentroidCluster.DynamicCentroidCluster().

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◆ convertToCoordsVector()

static double[] denoptim.fragmenter.ClusterableFragment.convertToCoordsVector ( Point3d[] pts )

static

Converts an array of 3-dimensional points in a vector of coordinates in 3*N-dimensional space where coordinated are ordered as [x1, y1, z1, x2, y2, z2, ...].

Parameters

pts	points in 3-dimensional space.

Returns: vector in N-dimensional space

Definition at line 206 of file ClusterableFragment.java.

Referenced by denoptim.fragmenter.ClusterableFragment.setCoordsVector().

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◆ convertToPointArray()

static Point3d[] denoptim.fragmenter.ClusterableFragment.convertToPointArray ( double[] coords )

static

Converts an array of 3*N-dimensional coordinates into an array of 3-dimensional points assuming coordinated are ordered as [x1, y1, z1, x2, y2, z2, ...].

Parameters

coords the N-dimensional array.

Returns: the array of points in 3-dimensional space.

Definition at line 228 of file ClusterableFragment.java.

Referenced by denoptim.fragmenter.ClusterableFragment.getTransformedCopy(), denoptim.fragmenter.FragmentClusterer.mergeClusters(), and denoptim.fragmenter.FragmentClustererTest.testCluster().

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◆ getJGraphFragIsomorphism()

DefaultUndirectedGraph< FragIsomorphNode, FragIsomorphEdge > denoptim.fragmenter.ClusterableFragment.getJGraphFragIsomorphism ( )

protected

Returns: the graph representation of the original fragment used to construct an instance of this object.

Definition at line 165 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.frag, and denoptim.graph.Fragment.getJGraphFragIsomorphism().

Referenced by denoptim.fragmenter.ConformerExtractorTask.populateListOfClusterizableFragments().

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◆ getOrderedNodes()

List< FragIsomorphNode > denoptim.fragmenter.ClusterableFragment.getOrderedNodes ( )

Get the ordered list of nodes representing each either an atom or an attachment point is the alignment of fragments.

@returnthe ordered list of nodes representing each either an atom or an attachment point is the alignment of fragments.

Definition at line 192 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.orderedNodes.

Referenced by denoptim.fragmenter.ClusterableFragmentTest.testSetNaturalNodeOrder().

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◆ getOriginalFragment()

Fragment denoptim.fragmenter.ClusterableFragment.getOriginalFragment ( )

protected

The original fragment used to construct an instance of this object.

Returns

Definition at line 153 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.frag.

◆ getPoint()

double[] denoptim.fragmenter.ClusterableFragment.getPoint ( )

Returns: the vector of 3*N coordinates, if the ordering has been set by setOrderOfNodes(Collection) if the vector of coordinates has been set by setCoordsVector(double[]), or null if neither has happened.

Definition at line 179 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.allCoords.

Referenced by denoptim.fragmenter.DynamicCentroidCluster.getCentroid(), denoptim.fragmenter.DynamicCentroidCluster.getNearestToCentroid(), denoptim.fragmenter.FragmentClusterer.mergeClusters(), denoptim.fragmenter.DynamicCentroidClusterTest.testGetCentroid(), and denoptim.fragmenter.DynamicCentroidClusterTest.testGetNearestToCentroid().

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◆ getTransformedCopy()

Fragment denoptim.fragmenter.ClusterableFragment.getTransformedCopy ( )

Returns: a copy of the original fragment where the coordinates of each atom and attachment point have been transformed to reflect the content of the N-dimensional vector of coordinate of this class.

Definition at line 261 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.allCoords, denoptim.graph.Fragment.clone(), denoptim.fragmenter.ClusterableFragment.convertToPointArray(), denoptim.fragmenter.ClusterableFragment.frag, denoptim.graph.Vertex.getAP(), denoptim.graph.Fragment.getAtom(), denoptim.graph.Vertex.getIndexOfAP(), denoptim.graph.Fragment.indexOf(), and denoptim.graph.AttachmentPoint.setDirectionVector().

Referenced by denoptim.fragmenter.FragmentClusterer.getClusterCentroids(), denoptim.fragmenter.FragmentClusterer.getNearestToClusterCentroids(), and denoptim.fragmenter.ClusterableFragmentTest.testGetTransformedCopy().

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◆ setCoordsVector() [1/2]

void denoptim.fragmenter.ClusterableFragment.setCoordsVector ( double[] coords )

protected

Sets the coordinates of each atom and attachment point in this object.

Does not change the values in the original fragment used to construct an instance of this object.

Parameters

coords the 3*N-dimensional coordinates.

Definition at line 129 of file ClusterableFragment.java.

Referenced by denoptim.fragmenter.DynamicCentroidCluster.getCentroid(), and denoptim.fragmenter.ClusterableFragmentTest.testGetTransformedCopy().

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◆ setCoordsVector() [2/2]

void denoptim.fragmenter.ClusterableFragment.setCoordsVector ( Point3d[] pts )

protected

Sets the coordinates of each atom and attachment point in this object.

Does not change the values in the original fragment used to construct an instance of this object.

Parameters

pts	the N point in 3-dimensional space.

Definition at line 142 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.convertToCoordsVector().

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◆ setNaturalNodeOrder()

void denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder ( )

Define the node order from the list of atoms and attachment points.

This method is useful to bypass the finding of a consistent node order via detection of the graph isomorphism. Note that dummy atoms meant to break linearities are not included in the order. In fact, they do not have a corresponding FragIsomorphNode in the graph generated by Fragment#getJGraphFragIsomorphism()

Definition at line 91 of file ClusterableFragment.java.

References denoptim.graph.Fragment.atoms(), denoptim.fragmenter.ClusterableFragment.frag, denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.getJGraphFragIsomorphism(), and denoptim.fragmenter.ClusterableFragment.setOrderOfNodes().

Referenced by denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.fragmenter.FragmentClustererTest.testCluster2(), denoptim.fragmenter.DynamicCentroidClusterTest.testGetCentroid(), denoptim.fragmenter.DynamicCentroidClusterTest.testGetNearestToCentroid(), denoptim.fragmenter.ClusterableFragmentTest.testGetTransformedCopy(), and denoptim.fragmenter.ClusterableFragmentTest.testSetNaturalNodeOrder().

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◆ setOrderOfNodes()

void denoptim.fragmenter.ClusterableFragment.setOrderOfNodes ( Collection< FragIsomorphNode > c )

Sets the order of nodes (i.e., atoms/APs) to use for geometric comparison with other fragments, and update the vector of coordinates accordingly.

Parameters

c	the new order.

Definition at line 64 of file ClusterableFragment.java.

References denoptim.fragmenter.ClusterableFragment.allCoords, and denoptim.fragmenter.ClusterableFragment.orderedNodes.

Referenced by denoptim.fragmenter.ClusterableFragment.clone(), denoptim.fragmenter.ConformerExtractorTask.populateListOfClusterizableFragments(), and denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder().

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Member Data Documentation

◆ allCoords

double [] denoptim.fragmenter.ClusterableFragment.allCoords

package

Ordered list of coordinated reflecting the ordered list of atoms/APs.

Definition at line 43 of file ClusterableFragment.java.

Referenced by denoptim.fragmenter.ClusterableFragment.getPoint(), denoptim.fragmenter.ClusterableFragment.getTransformedCopy(), denoptim.fragmenter.ClusterableFragment.setOrderOfNodes(), and denoptim.fragmenter.FragmentClustererTest.testCluster().

◆ frag

Fragment denoptim.fragmenter.ClusterableFragment.frag

private

Reference to original fragment.

Definition at line 33 of file ClusterableFragment.java.

Referenced by denoptim.fragmenter.ClusterableFragment.ClusterableFragment(), denoptim.fragmenter.ClusterableFragment.getJGraphFragIsomorphism(), denoptim.fragmenter.ClusterableFragment.getOriginalFragment(), denoptim.fragmenter.ClusterableFragment.getTransformedCopy(), and denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder().

◆ orderedNodes

List<FragIsomorphNode> denoptim.fragmenter.ClusterableFragment.orderedNodes

private

Ordered list of nodes determined by isomorphism.

Definition at line 38 of file ClusterableFragment.java.

Referenced by denoptim.fragmenter.ClusterableFragment.clone(), denoptim.fragmenter.ClusterableFragment.getOrderedNodes(), and denoptim.fragmenter.ClusterableFragment.setOrderOfNodes().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/fragmenter/ClusterableFragment.java

Public Member Functions

Static Public Member Functions

Protected Member Functions

Package Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ClusterableFragment()

Member Function Documentation

◆ clone()

◆ convertToCoordsVector()

◆ convertToPointArray()

◆ getJGraphFragIsomorphism()

◆ getOrderedNodes()

◆ getOriginalFragment()

◆ getPoint()

◆ getTransformedCopy()

◆ setCoordsVector() [1/2]

◆ setCoordsVector() [2/2]

◆ setNaturalNodeOrder()

◆ setOrderOfNodes()

Member Data Documentation

◆ allCoords

◆ frag

◆ orderedNodes