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DENOPTIM
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denoptim.fragspace.FragmentSpaceTest Class Reference

Unit test for fragment space. More...

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Classes

class  TestCase
 

Public Member Functions

void testSymmetry () throws Exception
 
void testGetFragsWithAPClass () throws Exception
 
void testGetVerticesWithAPClass () throws Exception
 
void testGetVerticesWithAPClasses () throws Exception
 
void testGetVerticesWithAPFingerprint () throws Exception
 
void testGetFragsWithAPClassStartingWith () throws Exception
 
void testGetFragAPsCompatibleWithClass () throws Exception
 
void testGetFragAPsCompatibleWithTheseAPs () throws Exception
 
void testGetFragmentsCompatibleWithTheseAPs () throws Exception
 
void testGetRCVsForAPClass () throws Exception
 
void testGetRCVsWithAPClass () throws Exception
 
void testFusedRingAddedToFragmentLibrary () throws Exception
 Check that the following graph's fused ring gets added to the fragment library. More...
 
void testFusedRingAddedToScaffoldLibrary () throws Exception
 Checks that a graph with a fused ring containing a scaffold vertex is added to the scaffold library. More...
 
void testFusedRingOnlyAddedOnce () throws DENOPTIMException
 
void testUseWholeMolGeometryForExtractedTemplates () throws Exception
 Works with this graph: More...
 

Static Package Attributes

static File tempDir
 

Private Member Functions

FragmentSpaceParameters buildFragmentSpace () throws DENOPTIMException
 
TestCase getTestCase () throws DENOPTIMException
 
Template getExpectedTemplate (DGraph g, Vertex c3) throws DENOPTIMException
 
Fragment getCarbonVertex () throws DENOPTIMException
 
Vertex getRCV () throws DENOPTIMException
 
Point3d getRandomVector ()
 

Private Attributes

final Random rng = new Random()
 

Static Private Attributes

static final String SEP = System.getProperty("file.separator")
 
static final int APSUBRULE = 0
 
static final String RULAPCS = "apc-S"
 
static final String RULAPC1 = "apc-1"
 
static final String RULAPC2 = "apc-2"
 
static final String RULAPC3 = "apc-3"
 
static final String RULAPC4 = "apc-4"
 
static final String RULAPC5 = "a_p_c-5"
 
static final String RULAPC6 = "a_p_c-6"
 
static final String RULAPCC1 = "cap-1"
 
static final String RULAPCC2 = "cap-2"
 
static final BBType BBTFRAG = BBType.FRAGMENT
 
static APClass APCS
 
static APClass APC1
 
static APClass APC2
 
static APClass APC3
 
static APClass APC4
 
static APClass APC5
 
static APClass APC6
 
static APClass APCC1
 
static APClass APCC2
 

Detailed Description

Unit test for fragment space.

Author
Marco Foscato

Definition at line 74 of file FragmentSpaceTest.java.

Member Function Documentation

◆ buildFragmentSpace()

FragmentSpaceParameters denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace ( ) throws DENOPTIMException
private

Definition at line 109 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.fragspace.FragmentSpaceTest.APC1, denoptim.fragspace.FragmentSpaceTest.APC2, denoptim.fragspace.FragmentSpaceTest.APC3, denoptim.fragspace.FragmentSpaceTest.APC4, denoptim.fragspace.FragmentSpaceTest.APC5, denoptim.fragspace.FragmentSpaceTest.APC6, denoptim.fragspace.FragmentSpaceTest.APCC1, denoptim.fragspace.FragmentSpaceTest.APCC2, denoptim.fragspace.FragmentSpaceTest.APCS, denoptim.fragspace.FragmentSpaceTest.APSUBRULE, denoptim.graph.Edge.BondType.DOUBLE, denoptim.graph.APClass.make(), denoptim.graph.Fragment.projectAPsToProperties(), denoptim.fragspace.FragmentSpaceTest.RULAPC1, denoptim.fragspace.FragmentSpaceTest.RULAPC2, denoptim.fragspace.FragmentSpaceTest.RULAPC3, denoptim.fragspace.FragmentSpaceTest.RULAPC4, denoptim.fragspace.FragmentSpaceTest.RULAPC5, denoptim.fragspace.FragmentSpaceTest.RULAPC6, denoptim.fragspace.FragmentSpaceTest.RULAPCC1, denoptim.fragspace.FragmentSpaceTest.RULAPCC2, denoptim.fragspace.FragmentSpaceTest.RULAPCS, denoptim.fragspace.FragmentSpaceTest.SEP, denoptim.graph.Edge.BondType.SINGLE, denoptim.fragspace.FragmentSpaceTest.tempDir, denoptim.io.DenoptimIO.writeCompatibilityMatrix(), and denoptim.io.DenoptimIO.writeVertexesToSDF().

Referenced by denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce(), denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithClass(), denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceTest.testGetFragmentsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClassStartingWith(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClasses(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPFingerprint(), denoptim.fragspace.FragmentSpaceTest.testSymmetry(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ getCarbonVertex()

Fragment denoptim.fragspace.FragmentSpaceTest.getCarbonVertex ( ) throws DENOPTIMException
private

Definition at line 892 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.fragspace.FragmentSpaceTest.APC1, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.fragspace.FragmentSpaceTest.getRandomVector(), and denoptim.utils.GraphUtils.getUniqueVertexIndex().

Referenced by denoptim.fragspace.FragmentSpaceTest.getTestCase().

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◆ getExpectedTemplate()

Template denoptim.fragspace.FragmentSpaceTest.getExpectedTemplate ( DGraph  g,
Vertex  c3 
) throws DENOPTIMException
private

Definition at line 876 of file FragmentSpaceTest.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.removeVertex(), denoptim.graph.DGraph.renumberGraphVertices(), denoptim.graph.Vertex.setBuildingBlockId(), and denoptim.graph.Template.setInnerGraph().

Referenced by denoptim.fragspace.FragmentSpaceTest.getTestCase().

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◆ getRandomVector()

Point3d denoptim.fragspace.FragmentSpaceTest.getRandomVector ( )
private

Definition at line 929 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.rng.

Referenced by denoptim.fragspace.FragmentSpaceTest.getCarbonVertex(), and denoptim.fragspace.FragmentSpaceTest.getRCV().

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◆ getRCV()

Vertex denoptim.fragspace.FragmentSpaceTest.getRCV ( ) throws DENOPTIMException
private

Definition at line 911 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.fragspace.FragmentSpaceTest.APC1, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.fragspace.FragmentSpaceTest.getRandomVector(), and denoptim.utils.GraphUtils.getUniqueVertexIndex().

Referenced by denoptim.fragspace.FragmentSpaceTest.getTestCase().

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◆ getTestCase()

TestCase denoptim.fragspace.FragmentSpaceTest.getTestCase ( ) throws DENOPTIMException
private 
  ↑         ↑
← C1 - C2 - C3 →
  .  / |    ↓
  C4 . C5 →
  ↓    ↓

Definition at line 840 of file FragmentSpaceTest.java.

References denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.getAP(), denoptim.fragspace.FragmentSpaceTest.getCarbonVertex(), denoptim.fragspace.FragmentSpaceTest.getExpectedTemplate(), denoptim.fragspace.FragmentSpaceTest.getRCV(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), and denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce().

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◆ testFusedRingAddedToFragmentLibrary()

void denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary ( ) throws Exception

Check that the following graph's fused ring gets added to the fragment library.

Dots are chords ↑ ↑ ← C1 - C2 - C3 → . / | ↓ C4 . C5 → ↓ ↓

Exceptions
Exception

Definition at line 738 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.files.FileUtils.deleteFile(), denoptim.fragspace.FragmentSpaceTest.TestCase.expected, denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedFragments(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedScaffolds(), denoptim.fragspace.FragmentSpaceTest.getTestCase(), denoptim.fragspace.FragmentSpaceTest.TestCase.graph, and denoptim.graph.Template.sameAs().

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◆ testFusedRingAddedToScaffoldLibrary()

void denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary ( ) throws Exception

Checks that a graph with a fused ring containing a scaffold vertex is added to the scaffold library.

Exceptions
Exception

Definition at line 771 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.files.FileUtils.deleteFile(), denoptim.fragspace.FragmentSpaceTest.TestCase.expected, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.Template.getInnerGraph(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedFragments(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedScaffolds(), denoptim.fragspace.FragmentSpace.getScaffoldLibrary(), denoptim.fragspace.FragmentSpaceTest.getTestCase(), denoptim.graph.DGraph.getVertexList(), denoptim.fragspace.FragmentSpaceTest.TestCase.graph, denoptim.graph.Template.sameAs(), denoptim.graph.Vertex.BBType.SCAFFOLD, and denoptim.graph.Vertex.setBuildingBlockType().

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◆ testFusedRingOnlyAddedOnce()

void denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce ( ) throws DENOPTIMException

Definition at line 801 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.DGraph.clone(), denoptim.files.FileUtils.deleteFile(), denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedFragments(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedScaffolds(), denoptim.fragspace.FragmentSpaceTest.getTestCase(), and denoptim.fragspace.FragmentSpaceTest.TestCase.graph.

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◆ testGetFragAPsCompatibleWithClass()

void denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithClass ( ) throws Exception

Definition at line 464 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.APC1, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithClass(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.APClass.isCPMapCompatibleWith(), denoptim.fragspace.FragmentSpace.isDefined(), and denoptim.graph.Vertex.newVertexFromLibrary().

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◆ testGetFragAPsCompatibleWithTheseAPs()

void denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithTheseAPs ( ) throws Exception

Definition at line 489 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.BBTFRAG, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.fragspace.IdFragmentAndAP.getApId(), denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.IdFragmentAndAP.getVertexMolId(), denoptim.fragspace.IdFragmentAndAP.getVertexMolType(), denoptim.graph.APClass.isCPMapCompatibleWith(), denoptim.fragspace.FragmentSpace.isDefined(), and denoptim.graph.Vertex.newVertexFromLibrary().

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◆ testGetFragmentsCompatibleWithTheseAPs()

void denoptim.fragspace.FragmentSpaceTest.testGetFragmentsCompatibleWithTheseAPs ( ) throws Exception

Definition at line 539 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.BBTFRAG, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpace.getFragmentsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), and denoptim.fragspace.FragmentSpace.isDefined().

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◆ testGetFragsWithAPClass()

void denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClass ( ) throws Exception

Definition at line 302 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.APC2, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpace.getFragsWithAPClass(), denoptim.fragspace.FragmentSpace.isDefined(), and denoptim.graph.Vertex.newVertexFromLibrary().

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◆ testGetFragsWithAPClassStartingWith()

void denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClassStartingWith ( ) throws Exception

Definition at line 440 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClassStartingWith(), denoptim.fragspace.FragmentSpace.isDefined(), and denoptim.fragspace.FragmentSpaceTest.RULAPC5.

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◆ testGetRCVsForAPClass()

void denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass ( ) throws Exception

Definition at line 559 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.fragspace.FragmentSpace.getRCVsForAPClass(), denoptim.graph.APClass.make(), denoptim.graph.APClass.RCACLASSMINUS, denoptim.graph.APClass.RCACLASSPLUS, denoptim.graph.rings.RingClosingAttractor.RCALABELPERAPCLASS, denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), and denoptim.graph.Vertex.setAsRCV().

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◆ testGetRCVsWithAPClass()

void denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass ( ) throws Exception

Definition at line 653 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.fragspace.FragmentSpace.getRCVsWithAPClass(), denoptim.graph.APClass.make(), denoptim.graph.APClass.RCACLASSMINUS, denoptim.graph.APClass.RCACLASSPLUS, denoptim.graph.rings.RingClosingAttractor.RCALABELPERAPCLASS, denoptim.graph.Fragment.sameAs(), denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), and denoptim.graph.Vertex.setAsRCV().

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◆ testGetVerticesWithAPClass()

void denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClass ( ) throws Exception

Definition at line 324 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.APC2, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClass(), and denoptim.fragspace.FragmentSpace.isDefined().

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◆ testGetVerticesWithAPClasses()

void denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClasses ( ) throws Exception

Definition at line 341 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.APC1, denoptim.fragspace.FragmentSpaceTest.APC2, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClasses(), and denoptim.fragspace.FragmentSpace.isDefined().

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◆ testGetVerticesWithAPFingerprint()

void denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPFingerprint ( ) throws Exception

Definition at line 364 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.fragspace.FragmentSpaceTest.APC1, denoptim.fragspace.FragmentSpaceTest.APC2, denoptim.fragspace.FragmentSpaceTest.APCS, denoptim.fragspace.FragmentSpace.appendVertexToLibrary(), denoptim.fragspace.FragmentSpaceTest.BBTFRAG, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpace.getVerticesWithAPFingerprint(), denoptim.fragspace.FragmentSpace.isDefined(), and denoptim.graph.Fragment.projectAPsToProperties().

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◆ testSymmetry()

void denoptim.fragspace.FragmentSpaceTest.testSymmetry ( ) throws Exception

Definition at line 277 of file FragmentSpaceTest.java.

References denoptim.fragspace.FragmentSpaceTest.APC4, denoptim.fragspace.FragmentSpaceTest.APC5, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.Vertex.getSymmetricAPSets(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.fragspace.FragmentSpace.isDefined(), and denoptim.graph.Vertex.newVertexFromLibrary().

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◆ testUseWholeMolGeometryForExtractedTemplates()

void denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates ( ) throws Exception

Works with this graph: 

           c1 
           | 
  v1--v2--v3
       |   |
       |   v11
       |   (chord)
       |   v10          c3
       |   |            |
      v4--v6--v9--v5---v7
       |           \    |  
      c2            \   v12
                     |  (chord)
                     \  v13
                      \ |
                       v8-v13
                       |
                       c4

Definition at line 977 of file FragmentSpaceTest.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.graph.Fragment.addAtom(), denoptim.graph.Fragment.addBond(), denoptim.graph.DGraph.addEdge(), denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.fragspace.FragmentSpaceTest.APC2, denoptim.fragspace.FragmentSpaceTest.APC3, denoptim.fragspace.FragmentSpaceTest.APC4, denoptim.fragspace.FragmentSpace.appendVertexToLibrary(), denoptim.fragspace.FragmentSpaceTest.BBTFRAG, denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraph.clone(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.files.FileUtils.deleteFile(), denoptim.graph.Edge.BondType.DOUBLE, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.Vertex.getIAtomContainer(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedFragments(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedScaffolds(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.fragspace.FragmentSpace.getScaffoldLibrary(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), denoptim.graph.APClass.make(), denoptim.graph.Fragment.projectAPsToProperties(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.fragspace.FragmentSpaceTest.SEP, denoptim.graph.Vertex.setAsRCV(), denoptim.graph.Edge.BondType.SINGLE, and denoptim.fragspace.FragmentSpaceTest.tempDir.

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Member Data Documentation

◆ APC1

APClass denoptim.fragspace.FragmentSpaceTest.APC1
staticprivate

Definition at line 98 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpaceTest.getCarbonVertex(), denoptim.fragspace.FragmentSpaceTest.getRCV(), denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithClass(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClasses(), and denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPFingerprint().

◆ APC2

APClass denoptim.fragspace.FragmentSpaceTest.APC2
staticprivate

Definition at line 99 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPClasses(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPFingerprint(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

◆ APC3

APClass denoptim.fragspace.FragmentSpaceTest.APC3
staticprivate

Definition at line 100 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

◆ APC4

APClass denoptim.fragspace.FragmentSpaceTest.APC4
staticprivate

Definition at line 101 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpaceTest.testSymmetry(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

◆ APC5

APClass denoptim.fragspace.FragmentSpaceTest.APC5
staticprivate

Definition at line 102 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.fragspace.FragmentSpaceTest.testSymmetry().

◆ APC6

APClass denoptim.fragspace.FragmentSpaceTest.APC6
staticprivate

Definition at line 103 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ APCC1

APClass denoptim.fragspace.FragmentSpaceTest.APCC1
staticprivate

Definition at line 104 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ APCC2

APClass denoptim.fragspace.FragmentSpaceTest.APCC2
staticprivate

Definition at line 105 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ APCS

APClass denoptim.fragspace.FragmentSpaceTest.APCS
staticprivate

Definition at line 97 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPFingerprint().

◆ APSUBRULE

final int denoptim.fragspace.FragmentSpaceTest.APSUBRULE = 0
staticprivate

Definition at line 83 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ BBTFRAG

final BBType denoptim.fragspace.FragmentSpaceTest.BBTFRAG = BBType.FRAGMENT
staticprivate

Definition at line 95 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceTest.testGetFragmentsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceTest.testGetVerticesWithAPFingerprint(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

◆ rng

final Random denoptim.fragspace.FragmentSpaceTest.rng = new Random()
private

Definition at line 81 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.getRandomVector().

◆ RULAPC1

final String denoptim.fragspace.FragmentSpaceTest.RULAPC1 = "apc-1"
staticprivate

Definition at line 86 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPC2

final String denoptim.fragspace.FragmentSpaceTest.RULAPC2 = "apc-2"
staticprivate

Definition at line 87 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPC3

final String denoptim.fragspace.FragmentSpaceTest.RULAPC3 = "apc-3"
staticprivate

Definition at line 88 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPC4

final String denoptim.fragspace.FragmentSpaceTest.RULAPC4 = "apc-4"
staticprivate

Definition at line 89 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPC5

final String denoptim.fragspace.FragmentSpaceTest.RULAPC5 = "a_p_c-5"
staticprivate

Definition at line 90 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClassStartingWith().

◆ RULAPC6

final String denoptim.fragspace.FragmentSpaceTest.RULAPC6 = "a_p_c-6"
staticprivate

Definition at line 91 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPCC1

final String denoptim.fragspace.FragmentSpaceTest.RULAPCC1 = "cap-1"
staticprivate

Definition at line 92 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPCC2

final String denoptim.fragspace.FragmentSpaceTest.RULAPCC2 = "cap-2"
staticprivate

Definition at line 93 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ RULAPCS

final String denoptim.fragspace.FragmentSpaceTest.RULAPCS = "apc-S"
staticprivate

Definition at line 85 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace().

◆ SEP

final String denoptim.fragspace.FragmentSpaceTest.SEP = System.getProperty("file.separator")
staticprivate

Definition at line 76 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

◆ tempDir

File denoptim.fragspace.FragmentSpaceTest.tempDir
staticpackage

Definition at line 79 of file FragmentSpaceTest.java.

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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