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DENOPTIM
DynamicCentroidClusterTest.java
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1package denoptim.fragmenter;
2
3import static org.junit.jupiter.api.Assertions.assertTrue;
4
5import java.util.ArrayList;
6import java.util.List;
7
8import javax.vecmath.Point3d;
9
10import org.junit.jupiter.api.Test;
11import org.openscience.cdk.Atom;
12import org.openscience.cdk.interfaces.IAtomContainer;
13import org.openscience.cdk.interfaces.IBond;
14import org.openscience.cdk.interfaces.IChemObjectBuilder;
15import org.openscience.cdk.silent.SilentChemObjectBuilder;
16
17import denoptim.fragmenter.FragmentClusterer.DistanceAsRMSD;
18import denoptim.graph.APClass;
19import denoptim.graph.Fragment;
20import denoptim.graph.Vertex.BBType;
21
25public class DynamicCentroidClusterTest
26{
27
31 private IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
32
33//------------------------------------------------------------------------------
34
35 @Test
36 public void testGetCentroid() throws Exception
37 {
38 List<ClusterableFragment> sample = new ArrayList<ClusterableFragment>();
39
40 IAtomContainer mol0 = builder.newAtomContainer();
41 mol0.addAtom(new Atom("C", new Point3d(0,0,0)));
42 mol0.addAtom(new Atom("H", new Point3d(2,0,0)));
43 mol0.addBond(0,1,IBond.Order.SINGLE);
44 Fragment frag0 = new Fragment(mol0, BBType.UNDEFINED);
45 frag0.addAP(0, APClass.make("A:0"), new Point3d(-2,0,0));
46 ClusterableFragment cf0 = new ClusterableFragment(frag0);
47 cf0.setNaturalNodeOrder();
48 sample.add(cf0);
49
50 IAtomContainer mol1 = builder.newAtomContainer();
51 mol1.addAtom(new Atom("C", new Point3d(0,0,0)));
52 mol1.addAtom(new Atom("H", new Point3d(1,0,0)));
53 mol1.addBond(0,1,IBond.Order.SINGLE);
54 Fragment frag1 = new Fragment(mol1, BBType.UNDEFINED);
55 frag1.addAP(0, APClass.make("A:0"), new Point3d(-1,0,0));
56 ClusterableFragment cf1 = new ClusterableFragment(frag1);
57 cf1.setNaturalNodeOrder();
58 sample.add(cf1);
59
60 IAtomContainer mol2 = builder.newAtomContainer();
61 mol2.addAtom(new Atom("C", new Point3d(0,0,0)));
62 mol2.addAtom(new Atom("H", new Point3d(1.5,0,0)));
63 mol2.addBond(0,1,IBond.Order.SINGLE);
64 Fragment frag2 = new Fragment(mol2, BBType.UNDEFINED);
65 frag2.addAP(0, APClass.make("A:0"), new Point3d(-1.5,0,0));
66 ClusterableFragment cf2 = new ClusterableFragment(frag2);
67 cf2.setNaturalNodeOrder();
68 sample.add(cf2);
69
70 DynamicCentroidCluster cluster = new DynamicCentroidCluster();
71 cluster.addPoint(cf0);
72 cluster.addPoint(cf1);
73 cluster.addPoint(cf2);
74
75 ClusterableFragment centroid = cluster.getCentroid();
76
77 DistanceAsRMSD measure = new DistanceAsRMSD();
78 assertTrue(measure.compute(centroid.getPoint(), cf2.getPoint())<0.0001);
79 assertTrue(centroid != cf2);
80 }
81
82//------------------------------------------------------------------------------
83
84 @Test
85 public void testGetNearestToCentroid() throws Exception
86 {
87 List<ClusterableFragment> sample = new ArrayList<ClusterableFragment>();
88
89 IAtomContainer mol0 = builder.newAtomContainer();
90 mol0.addAtom(new Atom("C", new Point3d(0,0,0)));
91 mol0.addAtom(new Atom("H", new Point3d(2,0,0)));
92 mol0.addBond(0,1,IBond.Order.SINGLE);
93 Fragment frag0 = new Fragment(mol0, BBType.UNDEFINED);
94 frag0.addAP(0, APClass.make("A:0"), new Point3d(-2,0,0));
95 ClusterableFragment cf0 = new ClusterableFragment(frag0);
96 cf0.setNaturalNodeOrder();
97 sample.add(cf0);
98
99 IAtomContainer mol1 = builder.newAtomContainer();
100 mol1.addAtom(new Atom("C", new Point3d(0,0,0)));
101 mol1.addAtom(new Atom("H", new Point3d(1,0,0)));
102 mol1.addBond(0,1,IBond.Order.SINGLE);
103 Fragment frag1 = new Fragment(mol1, BBType.UNDEFINED);
104 frag1.addAP(0, APClass.make("A:0"), new Point3d(-1,0,0));
105 ClusterableFragment cf1 = new ClusterableFragment(frag1);
106 cf1.setNaturalNodeOrder();
107 sample.add(cf1);
108
109 IAtomContainer mol2 = builder.newAtomContainer();
110 mol2.addAtom(new Atom("C", new Point3d(0,0,0)));
111 mol2.addAtom(new Atom("H", new Point3d(1.5,0,0)));
112 mol2.addBond(0,1,IBond.Order.SINGLE);
113 Fragment frag2 = new Fragment(mol2, BBType.UNDEFINED);
114 frag2.addAP(0, APClass.make("A:0"), new Point3d(-1.5,0,0));
115 ClusterableFragment cf2 = new ClusterableFragment(frag2);
116 cf2.setNaturalNodeOrder();
117 sample.add(cf2);
118
119 DynamicCentroidCluster cluster = new DynamicCentroidCluster();
120 cluster.addPoint(cf0);
121 cluster.addPoint(cf1);
122 cluster.addPoint(cf2);
123
124
125 DistanceAsRMSD measure = new DistanceAsRMSD();
126 ClusterableFragment nearest = cluster.getNearestToCentroid(measure);
127 assertTrue(measure.compute(nearest.getPoint(), cf2.getPoint())<0.0001);
128 assertTrue(nearest == cf2);
129 }
130
131//------------------------------------------------------------------------------
132
133}
denoptim.fragmenter.ClusterableFragment
Represents a fragment that can be clustered based on the 3*N coordinate of atoms and attachment point...
Definition: ClusterableFragment.java:29
denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder
void setNaturalNodeOrder()
Define the node order from the list of atoms and attachment points.
Definition: ClusterableFragment.java:91
denoptim.fragmenter.DynamicCentroidCluster
A cluster with a centroid that can be updated after definition of the cluster.
Definition: DynamicCentroidCluster.java:20
denoptim.fragmenter.DynamicCentroidCluster.getCentroid
ClusterableFragment getCentroid()
Get the point chosen to be the centroid of this cluster.
Definition: DynamicCentroidCluster.java:69
denoptim.fragmenter.DynamicCentroidCluster.getNearestToCentroid
ClusterableFragment getNearestToCentroid(DistanceMeasure measure)
Gets the original data that upon clustering is closest to the cluster centroid according to the given...
Definition: DynamicCentroidCluster.java:96
denoptim.fragmenter.DynamicCentroidCluster.addPoint
void addPoint(ClusterableFragment point)
Add a new member of this cluster.
Definition: DynamicCentroidCluster.java:123
denoptim.fragmenter.DynamicCentroidClusterTest.builder
IChemObjectBuilder builder
Private builder of atom containers.
Definition: DynamicCentroidClusterTest.java:31
denoptim.fragmenter.FragmentClusterer.DistanceAsRMSD
Distance in terms of RMSD between sets of 3D points expressed as a single vector of coordinates [x1,...
Definition: FragmentClusterer.java:384
denoptim.fragmenter.FragmentClusterer.DistanceAsRMSD.compute
double compute(double[] coordsA, double[] coordsB)
Definition: FragmentClusterer.java:386
denoptim.graph.APClass.make
static APClass make(String ruleAndSubclass)
Creates an APClass if it does not exist already, or returns the reference to the existing instance.
Definition: APClass.java:136
denoptim.graph.Fragment
Class representing a continuously connected portion of chemical object holding attachment points.
Definition: Fragment.java:61
denoptim.graph.Fragment.addAP
void addAP(int atomPositionNumber)
Adds an attachment point with a dummy APClass.
Definition: Fragment.java:343
denoptim.graph.Vertex.BBType
The type of building block.
Definition: Vertex.java:86