$darkmode
DENOPTIM
Public Member Functions | Private Member Functions | Private Attributes | List of all members
denoptim.fragmenter.FragmentClustererTest Class Reference

Unit test for fragmenter's tools. More...

Collaboration diagram for denoptim.fragmenter.FragmentClustererTest:
[legend]

Public Member Functions

void testDistanceAsRMSD ()
 
void testGetRMSDStatsOfNoisyDistorsions ()
 
void testCluster () throws Exception
 
void testCluster2 () throws Exception
 

Private Member Functions

IAtomContainer getMol (Fragment frag)
 Converts the fragment into a collection of atoms where attachment points are converted into atoms that can be visualized with any molecular viewer. More...
 
Point3d getNoisyPoint (Point3d p, double noiseMagnitude)
 The noise magnitude is to be interpreted as half of the overall magnitude. More...
 

Private Attributes

IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance()
 Private builder of atom containers. More...
 
Randomizer rng = new Randomizer(1L)
 Random number generator. More...
 

Detailed Description

Unit test for fragmenter's tools.

Definition at line 38 of file FragmentClustererTest.java.

Member Function Documentation

◆ getMol()

IAtomContainer denoptim.fragmenter.FragmentClustererTest.getMol ( Fragment  frag)
private

Converts the fragment into a collection of atoms where attachment points are converted into atoms that can be visualized with any molecular viewer.

Definition at line 507 of file FragmentClustererTest.java.

References denoptim.graph.Fragment.atoms(), denoptim.fragmenter.FragmentClustererTest.builder, and denoptim.graph.Fragment.getAttachmentPoints().

Referenced by denoptim.fragmenter.FragmentClustererTest.testCluster().

Here is the call graph for this function:
Here is the caller graph for this function:

◆ getNoisyPoint()

Point3d denoptim.fragmenter.FragmentClustererTest.getNoisyPoint ( Point3d  p,
double  noiseMagnitude 
)
private

The noise magnitude is to be interpreted as half of the overall magnitude.

And the distribution of noise is uniform in [-noiseMagnitude,noiseMagnitude].

Definition at line 607 of file FragmentClustererTest.java.

References denoptim.utils.Randomizer.getNoisyPoint(), and denoptim.fragmenter.FragmentClustererTest.rng.

Referenced by denoptim.fragmenter.FragmentClustererTest.testCluster(), and denoptim.fragmenter.FragmentClustererTest.testCluster2().

Here is the call graph for this function:
Here is the caller graph for this function:

◆ testCluster()

void denoptim.fragmenter.FragmentClustererTest.testCluster ( ) throws Exception

Definition at line 188 of file FragmentClustererTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.fragmenter.ClusterableFragment.allCoords, denoptim.graph.Fragment.atoms(), denoptim.fragmenter.FragmentClustererTest.builder, denoptim.fragmenter.FragmentClusterer.cluster(), denoptim.fragmenter.ClusterableFragment.convertToPointArray(), denoptim.graph.Vertex.getAP(), denoptim.graph.Fragment.getAtom(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.fragmenter.FragmentClusterer.getClusterCentroids(), denoptim.fragmenter.FragmentClusterer.getClusters(), denoptim.graph.AttachmentPoint.getDirectionVector(), denoptim.fragmenter.FragmentClustererTest.getMol(), denoptim.fragmenter.FragmentClustererTest.getNoisyPoint(), denoptim.fragmenter.FragmentClusterer.getTransformedClusters(), denoptim.graph.APClass.make(), denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder(), denoptim.programs.RunTimeParameters.setVerbosity(), denoptim.programs.RunTimeParameters.startConsoleLogger(), denoptim.graph.Vertex.BBType.UNDEFINED, denoptim.files.FileFormat.VRTXSDF, denoptim.io.DenoptimIO.writeSDFFile(), and denoptim.io.DenoptimIO.writeVertexesToFile().

Here is the call graph for this function:

◆ testCluster2()

void denoptim.fragmenter.FragmentClustererTest.testCluster2 ( ) throws Exception

Definition at line 520 of file FragmentClustererTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.fragmenter.FragmentClustererTest.builder, denoptim.fragmenter.FragmentClusterer.cluster(), denoptim.fragmenter.FragmentClusterer.getClusters(), denoptim.fragmenter.FragmentClustererTest.getNoisyPoint(), denoptim.graph.APClass.make(), denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Here is the call graph for this function:

◆ testDistanceAsRMSD()

void denoptim.fragmenter.FragmentClustererTest.testDistanceAsRMSD ( )

Definition at line 54 of file FragmentClustererTest.java.

References denoptim.fragmenter.FragmentClusterer.DistanceAsRMSD.compute().

Here is the call graph for this function:

◆ testGetRMSDStatsOfNoisyDistorsions()

void denoptim.fragmenter.FragmentClustererTest.testGetRMSDStatsOfNoisyDistorsions ( )

Definition at line 120 of file FragmentClustererTest.java.

References denoptim.fragmenter.FragmentClusterer.getRMSDStatsOfNoisyDistorsions().

Here is the call graph for this function:

Member Data Documentation

◆ builder

IChemObjectBuilder denoptim.fragmenter.FragmentClustererTest.builder = SilentChemObjectBuilder.getInstance()
private

Private builder of atom containers.

Definition at line 44 of file FragmentClustererTest.java.

Referenced by denoptim.fragmenter.FragmentClustererTest.getMol(), denoptim.fragmenter.FragmentClustererTest.testCluster(), and denoptim.fragmenter.FragmentClustererTest.testCluster2().

◆ rng

Randomizer denoptim.fragmenter.FragmentClustererTest.rng = new Randomizer(1L)
private

Random number generator.

Definition at line 49 of file FragmentClustererTest.java.

Referenced by denoptim.fragmenter.FragmentClustererTest.getNoisyPoint().

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