Unit test for DENOPTIMTemplate. More...

Collaboration diagram for denoptim.graph.TemplateTest:

Public Member Functions
void	testClone () throws Exception

void	testNestedTemplateCloning ()

void	testGetAttachmentPoints_returnsAPsWithTemplateAsOwner () throws DENOPTIMException

void	testGetAttachmentPoints_returnsCorrectNumberOfAPs () throws DENOPTIMException

void	testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs () throws DENOPTIMException

void	testAddAP_after_setInnerGraph_throwsException ()

void	testGetIAtomContainer () throws Exception

void	testGetIAtomContainer_DeepVertex () throws Exception

Static Public Member Functions
static Template	getTestAmideTemplate () throws DENOPTIMException
	Builds a template object meant for tests. More...

Package Attributes
final long	SEED = 13

Random	rng = new Random(SEED)

File	tempDir

Static Package Attributes
static IChemObjectBuilder	chemBuilder = DefaultChemObjectBuilder.getInstance()

Private Member Functions
Template	getNestedTemplate () throws DENOPTIMException
	Creating a template that contains another template with the following structure: \|--------------------—\| \| \|-----—\| \| \| * - CH_2 - \| * - OH \| \| \| \|-----—\| \| \|--------------------—\| The box containing the 'OH' represents the nested template and the outermost box represents the outermost template. More...

Vertex	getOHFragment () throws DENOPTIMException

void	testSameAPClass (Template t, DGraph innerGraph)

void	testAtLeastSameNumberOfAPs (Template t, int expNumberOfAPs) throws DENOPTIMException

Template	getTemplateDeepTest () throws DENOPTIMException

Static Private Member Functions
static Vertex	getCH2Fragment () throws DENOPTIMException
	The coordinates hard coded in this method must not be changed because they are needed to reproduce results in `testGetIAtomContainer()`. More...

static Vertex	getAmideFragment () throws DENOPTIMException
	The coordinates hard coded in this method must not be changed because they are needed to reproduce results in `testGetIAtomContainer()`. More...

Private Attributes
final String	NL = System.getProperty("line.separator")

final String	SEP = System.getProperty("file.separator")

Detailed Description

Unit test for DENOPTIMTemplate.

Definition at line 55 of file TemplateTest.java.

Member Function Documentation

◆ getAmideFragment()

static Vertex denoptim.graph.TemplateTest.getAmideFragment ( ) throws DENOPTIMException

staticprivate

The coordinates hard coded in this method must not be changed because they are needed to reproduce results in testGetIAtomContainer().

Returns: 3D building block C(=O)N with three APs: one on C and two on N.

Exceptions

DENOPTIMException

Definition at line 238 of file TemplateTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.TemplateTest.chemBuilder, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.utils.GraphUtils.getUniqueVertexIndex(), and denoptim.graph.APClass.make().

Referenced by denoptim.graph.TemplateTest.getTestAmideTemplate().

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◆ getCH2Fragment()

static Vertex denoptim.graph.TemplateTest.getCH2Fragment ( ) throws DENOPTIMException

staticprivate

The coordinates hard coded in this method must not be changed because they are needed to reproduce results in testGetIAtomContainer().

Returns: 3D building block CH2 with two APs both on C.

Exceptions

DENOPTIMException

Definition at line 196 of file TemplateTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.TemplateTest.chemBuilder, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.utils.GraphUtils.getUniqueVertexIndex(), and denoptim.graph.APClass.make().

Referenced by denoptim.graph.TemplateTest.getNestedTemplate(), denoptim.graph.TemplateTest.getTemplateDeepTest(), and denoptim.graph.TemplateTest.getTestAmideTemplate().

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◆ getNestedTemplate()

Template denoptim.graph.TemplateTest.getNestedTemplate ( ) throws DENOPTIMException

private

Creating a template that contains another template with the following structure: |--------------------—| | |-----—| | | * - CH_2 - | * - OH | | | |-----—| | |--------------------—| The box containing the 'OH' represents the nested template and the outermost box represents the outermost template.

Definition at line 168 of file TemplateTest.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.TemplateTest.getCH2Fragment(), denoptim.graph.TemplateTest.getOHFragment(), and denoptim.graph.Template.setInnerGraph().

Referenced by denoptim.graph.TemplateTest.testNestedTemplateCloning().

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◆ getOHFragment()

Vertex denoptim.graph.TemplateTest.getOHFragment ( ) throws DENOPTIMException

private

Returns: 0D (no 3D coords!) for OH

Exceptions

DENOPTIMException

Definition at line 283 of file TemplateTest.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.TemplateTest.chemBuilder, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.APClass.make(), and denoptim.graph.TemplateTest.rng.

Referenced by denoptim.graph.TemplateTest.getNestedTemplate().

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◆ getTemplateDeepTest()

Template denoptim.graph.TemplateTest.getTemplateDeepTest ( ) throws DENOPTIMException

private

Definition at line 576 of file TemplateTest.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.getAP(), denoptim.graph.TemplateTest.getCH2Fragment(), denoptim.graph.TemplateTest.getTestAmideTemplate(), denoptim.graph.Template.setInnerGraph(), denoptim.graph.Vertex.setVertexId(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex().

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◆ getTestAmideTemplate()

static Template denoptim.graph.TemplateTest.getTestAmideTemplate ( ) throws DENOPTIMException

static

Builds a template object meant for tests.

The inner graph has the following structure;

                            -->AP
                           /
AP<--v7<--v5<--v3<--v1-->v9-->AP

Before calling this method from outside its class, you should call TemplateTest#setUp() to prepare the fragment space.

Returns

Exceptions

DENOPTIMException

Definition at line 456 of file TemplateTest.java.

References denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.TemplateTest.getAmideFragment(), denoptim.graph.Vertex.getAP(), denoptim.graph.TemplateTest.getCH2Fragment(), denoptim.graph.Template.setInnerGraph(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.graph.TemplateTest.getTemplateDeepTest(), denoptim.graph.TemplateTest.testGetIAtomContainer(), denoptim.io.DenoptimIOTest.testIOTemplate(), and denoptim.json.DENOPTIMgsonTest.testTemplateSerialization().

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◆ testAddAP_after_setInnerGraph_throwsException()

void denoptim.graph.TemplateTest.testAddAP_after_setInnerGraph_throwsException ( )

Definition at line 431 of file TemplateTest.java.

References denoptim.graph.Template.addRequiredAP(), denoptim.graph.APClass.make(), denoptim.graph.Vertex.BBType.NONE, and denoptim.graph.Template.setInnerGraph().

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◆ testAtLeastSameNumberOfAPs()

void denoptim.graph.TemplateTest.testAtLeastSameNumberOfAPs	(	Template	t,
		int	expNumberOfAPs
	)		throws DENOPTIMException

private

Definition at line 415 of file TemplateTest.java.

References denoptim.graph.EmptyVertex.addAP(), and denoptim.graph.DGraph.addVertex().

Referenced by denoptim.graph.TemplateTest.testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs().

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◆ testClone()

void denoptim.graph.TemplateTest.testClone ( ) throws Exception

Definition at line 70 of file TemplateTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Template.clone(), denoptim.graph.Template.freezeTemplate(), denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Vertex.getFreeAPCount(), denoptim.graph.Template.getInnerGraph(), denoptim.graph.Vertex.getProperty(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getRings(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.Vertex.BBType.NONE, denoptim.graph.Vertex.setAsRCV(), denoptim.graph.Template.setInnerGraph(), and denoptim.graph.Vertex.setProperty().

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◆ testGetAttachmentPoints_returnsAPsWithTemplateAsOwner()

void denoptim.graph.TemplateTest.testGetAttachmentPoints_returnsAPsWithTemplateAsOwner ( ) throws DENOPTIMException

Definition at line 314 of file TemplateTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Vertex.getAttachmentPoints(), and denoptim.graph.Vertex.BBType.NONE.

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◆ testGetAttachmentPoints_returnsCorrectNumberOfAPs()

void denoptim.graph.TemplateTest.testGetAttachmentPoints_returnsCorrectNumberOfAPs ( ) throws DENOPTIMException

Definition at line 335 of file TemplateTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.getAP(), and denoptim.graph.Vertex.BBType.NONE.

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◆ testGetIAtomContainer()

void denoptim.graph.TemplateTest.testGetIAtomContainer ( ) throws Exception

Definition at line 480 of file TemplateTest.java.

References denoptim.utils.MoleculeUtils.countAtomsOfElement(), denoptim.graph.Template.getAttachmentPoints(), denoptim.graph.Template.getIAtomContainer(), denoptim.graph.TemplateTest.getTestAmideTemplate(), denoptim.graph.TemplateTest.NL, denoptim.io.DenoptimIO.readSDFFile(), denoptim.graph.TemplateTest.SEP, denoptim.graph.TemplateTest.tempDir, and denoptim.io.DenoptimIO.writeData().

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◆ testGetIAtomContainer_DeepVertex()

void denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex ( ) throws Exception

Definition at line 600 of file TemplateTest.java.

References denoptim.utils.MoleculeUtils.countAtomsOfElement(), denoptim.graph.Template.getAttachmentPoints(), denoptim.graph.Template.getIAtomContainer(), denoptim.graph.TemplateTest.getTemplateDeepTest(), denoptim.graph.TemplateTest.NL, denoptim.io.DenoptimIO.readSDFFile(), denoptim.graph.TemplateTest.SEP, denoptim.graph.TemplateTest.tempDir, and denoptim.io.DenoptimIO.writeData().

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◆ testNestedTemplateCloning()

void denoptim.graph.TemplateTest.testNestedTemplateCloning ( )

Definition at line 144 of file TemplateTest.java.

References denoptim.graph.Template.clone(), denoptim.graph.TemplateTest.getNestedTemplate(), and denoptim.graph.Template.sameAs().

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◆ testSameAPClass()

void denoptim.graph.TemplateTest.testSameAPClass	(	Template	t,
		DGraph	innerGraph
	)

private

Definition at line 399 of file TemplateTest.java.

References denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.AttachmentPoint.setAPClass(), and denoptim.graph.Template.setInnerGraph().

Referenced by denoptim.graph.TemplateTest.testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs().

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◆ testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs()

void denoptim.graph.TemplateTest.testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs ( ) throws DENOPTIMException

Definition at line 370 of file TemplateTest.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addVertex(), denoptim.graph.APClass.make(), denoptim.graph.Vertex.BBType.NONE, denoptim.graph.TemplateTest.testAtLeastSameNumberOfAPs(), and denoptim.graph.TemplateTest.testSameAPClass().

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Member Data Documentation

◆ chemBuilder

IChemObjectBuilder denoptim.graph.TemplateTest.chemBuilder = DefaultChemObjectBuilder.getInstance()

staticpackage

Definition at line 59 of file TemplateTest.java.

Referenced by denoptim.graph.TemplateTest.getAmideFragment(), denoptim.graph.TemplateTest.getCH2Fragment(), and denoptim.graph.TemplateTest.getOHFragment().

◆ NL

final String denoptim.graph.TemplateTest.NL = System.getProperty("line.separator")

private

Definition at line 64 of file TemplateTest.java.

Referenced by denoptim.graph.TemplateTest.testGetIAtomContainer(), and denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex().

◆ rng

Random denoptim.graph.TemplateTest.rng = new Random(SEED)

package

Definition at line 58 of file TemplateTest.java.

Referenced by denoptim.graph.TemplateTest.getOHFragment().

◆ SEED

final long denoptim.graph.TemplateTest.SEED = 13

package

Definition at line 57 of file TemplateTest.java.

◆ SEP

final String denoptim.graph.TemplateTest.SEP = System.getProperty("file.separator")

private

Definition at line 65 of file TemplateTest.java.

Referenced by denoptim.graph.TemplateTest.testGetIAtomContainer(), and denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex().

◆ tempDir

File denoptim.graph.TemplateTest.tempDir

package

Definition at line 62 of file TemplateTest.java.

Referenced by denoptim.graph.TemplateTest.testGetIAtomContainer(), and denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex().

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

/github/workspace/src/test/java/denoptim/graph/TemplateTest.java

Public Member Functions

Static Public Member Functions

Package Attributes

Static Package Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Member Function Documentation

◆ getAmideFragment()

◆ getCH2Fragment()

◆ getNestedTemplate()

◆ getOHFragment()

◆ getTemplateDeepTest()

◆ getTestAmideTemplate()

◆ testAddAP_after_setInnerGraph_throwsException()

◆ testAtLeastSameNumberOfAPs()

◆ testClone()

◆ testGetAttachmentPoints_returnsAPsWithTemplateAsOwner()

◆ testGetAttachmentPoints_returnsCorrectNumberOfAPs()

◆ testGetIAtomContainer()

◆ testGetIAtomContainer_DeepVertex()

◆ testNestedTemplateCloning()

◆ testSameAPClass()

◆ testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs()

Member Data Documentation

◆ chemBuilder

◆ NL

◆ rng

◆ SEED

◆ SEP

◆ tempDir