Testsuite: org.openscience.cdk.modulesuites.Mbuilder3dTests
 Tests run: 39, Failures: 2, Errors: 2, Time elapsed: 138.944 sec
 
 ------------- Standard Output ---------------
 PartialTChargeMMFF94Descriptor: missing the expected test method: testCalculate_IAtom_IAtomContainer
 PartialTChargeMMFF94Descriptor: missing the expected test method: testPartialTChargeMMFF94Descriptor
 AtomPlacer3D: missing the expected test method: testInitilize_Map
 AtomPlacer3D: missing the expected test method: testMarkPlaced_IAtomContainer
 AtomPlacer3D: missing the expected test method: testPlaceAliphaticHeavyChain_IAtomContainer_IAtomContainer
 AtomPlacer3D: missing the expected test method: testZmatrixChainToCartesian_IAtomContainer_boolean
 AtomPlacer3D: missing the expected test method: testGetBondLengthValue_String_String
 AtomPlacer3D: missing the expected test method: testGetAngleValue_String_String_String
 AtomPlacer3D: missing the expected test method: testGetNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour_IAtomContainer
 AtomPlacer3D: missing the expected test method: testGetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour_IAtomContainer
 AtomPlacer3D: missing the expected test method: testGetNextPlacedHeavyAtomWithUnplacedRingNeighbour_IAtomContainer
 AtomPlacer3D: missing the expected test method: testGetFarthestAtom_Point3d_IAtomContainer
 AtomPlacer3D: missing the expected test method: testGetUnplacedRingHeavyAtom_IAtomContainer_IAtom
 AtomPlacer3D: missing the expected test method: testAtomPlacer3D
 ModelBuilder3D: missing the expected test method: testGenerate3DCoordinates_IMolecule_boolean
 ModelBuilder3D: missing the expected test method: testGetTemplateCount
 ModelBuilder3D: missing the expected test method: testGetFfTypes
 ModelBuilder3D: missing the expected test method: testGetInstance_TemplateHandler3D_String
 ModelBuilder3D: missing the expected test method: testGetInstance
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGetAngleValue_String_String_String
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testSetParameterSet_Map
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testMakeStereocenter_Point3d_IBond_Point3d_Point3d_arrayPoint3d
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testRescaleBondLength_IAtom_IAtom_Point3d
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGet3DCoordinatesForSPLigands_IAtom_IAtomContainer_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGet3DCoordinatesForSP2Ligands_IAtom_IAtomContainer_IAtomContainer_IAtom_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGet3DCoordinatesForSP3Ligands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testCalculate3DCoordinates0_Point3d_int_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testCalculate3DCoordinates1_Point3d_Point3d_Point3d_int_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testCalculate3DCoordinates2_Point3d_Point3d_Point3d_int_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testCalculate3DCoordinates3_Point3d_Point3d_Point3d_Point3d_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testCalculate3DCoordinatesSP2_1_Point3d_Point3d_Point3d_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testCalculate3DCoordinatesSP2_2_Point3d_Point3d_Point3d_double_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGetSpatproduct_Vector3d_Vector3d_Vector3d
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGetTorsionAngle_Point3d_Point3d_Point3d_Point3d
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGetPlacedAtomsInAtomContainer_IAtom_IAtomContainer
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGetUnsetAtomsInAtomContainer_IAtom_IAtomContainer
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testHasUnsetNeighbour_IAtom_IAtomContainer
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testGetPlacedHeavyAtomInAtomContainer_IAtom_IAtom_IAtomContainer
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testRotate_Vector3d_Vector3d_double
 AtomTetrahedralLigandPlacer3D: missing the expected test method: testAtomTetrahedralLigandPlacer3D
 TemplateHandler3D: missing the expected test method: testGetTemplateCount
 TemplateHandler3D: missing the expected test method: testGetBitSetFromFile_StringTokenizer
 TemplateHandler3D: missing the expected test method: testGetLargestRingSet_List
 TemplateHandler3D: missing the expected test method: testGetTemplateAt_int
 WARNING: Maybe RingTemplateError!
 KEYError:Unknown distance key in pSet: O= ;Csp2 take default bon length:1.5
 10
 Calculation done
 Calculation done
 Calculation done
 Calculation done
 Calculation done
 WARNING: Maybe RingTemplateError!
 KEYError:Unknown distance key in pSet: O= ;Csp2 take default bon length:1.5
 WARNING: Maybe RingTemplateError!
 WARNING: Maybe RingTemplateError!
 Read data file in ...ready
 Generated Fingerprints: 0    \/\/\/\/\/...ready with:10 molecules
 Write data...of data vector:10 fingerprintCounter:10------------- ---------------- ---------------
 Testcase: testCoverage(org.openscience.cdk.coverage.Builder3dCoverageTest):	FAILED
 The builder3d module is not fully tested! Missing number of method tests: 44 in number of classes: 5; Missing test classes: 0
 junit.framework.AssertionFailedError: The builder3d module is not fully tested! Missing number of method tests: 44 in number of classes: 5; Missing test classes: 0
 	at org.openscience.cdk.coverage.CoverageTest.runCoverageTest(CoverageTest.java:87)
 	at org.openscience.cdk.coverage.Builder3dCoverageTest.testCoverage(Builder3dCoverageTest.java:43)
 
 
 Testcase: testModelBuilder3D_c1ccccc1C0(org.openscience.cdk.modeling.builder3d.ModelBuilder3DTest):	Caused an ERROR
 Rings weren't properly closed. Check ring numbers
 org.openscience.cdk.exception.InvalidSmilesException: Rings weren't properly closed. Check ring numbers
 	at org.openscience.cdk.smiles.SmilesParser.parseString(SmilesParser.java:443)
 	at org.openscience.cdk.smiles.SmilesParser.parseSmiles(SmilesParser.java:188)
 	at org.openscience.cdk.modeling.builder3d.ModelBuilder3DTest.testModelBuilder3D_c1ccccc1C0(ModelBuilder3DTest.java:122)
 
 
 Testcase: testModel3D_bug_1610997(org.openscience.cdk.modeling.builder3d.ModelBuilder3DTest):	Caused an ERROR
 null
 java.lang.NullPointerException
 	at org.openscience.cdk.modeling.builder3d.AtomPlacer3D.getDoubleBondConfiguration2D(AtomPlacer3D.java:296)
 	at org.openscience.cdk.modeling.builder3d.AtomPlacer3D.placeAliphaticHeavyChain(AtomPlacer3D.java:169)
 	at org.openscience.cdk.modeling.builder3d.ModelBuilder3D.placeLinearChains3D(ModelBuilder3D.java:530)
 	at org.openscience.cdk.modeling.builder3d.ModelBuilder3D.searchAndPlaceBranches(ModelBuilder3D.java:494)
 	at org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordinates(ModelBuilder3D.java:217)
 	at org.openscience.cdk.modeling.builder3d.ModelBuilder3DTest.testModel3D_bug_1610997(ModelBuilder3DTest.java:344)
 
 
 Testcase: testFingerprints(org.openscience.cdk.modeling.builder3d.TemplateHandler3DTest):	FAILED
 expected:<{12, 19, 21, 35, 91, 95, 96, 103, 152, 203, 230, 259, 324, 327, 373, 389, 390, 393, 409, 433, 435, 475, 521, 542, 556, 581, 613, 645, 737, 754, 757, 766, 768, 796, 804, 842, 869, 894, 896, 914, 945, 959, 969, 986, 1002}> but was:<{29, 142, 144, 184, 188, 204, 400, 478, 524, 534, 553, 562, 567, 597, 626, 644, 686, 696, 710, 741, 767, 775, 786, 823, 898, 925, 965, 987, 1000}>
 junit.framework.AssertionFailedError: expected:<{12, 19, 21, 35, 91, 95, 96, 103, 152, 203, 230, 259, 324, 327, 373, 389, 390, 393, 409, 433, 435, 475, 521, 542, 556, 581, 613, 645, 737, 754, 757, 766, 768, 796, 804, 842, 869, 894, 896, 914, 945, 959, 969, 986, 1002}> but was:<{29, 142, 144, 184, 188, 204, 400, 478, 524, 534, 553, 562, 567, 597, 626, 644, 686, 696, 710, 741, 767, 775, 786, 823, 898, 925, 965, 987, 1000}>
 	at org.openscience.cdk.modeling.builder3d.TemplateHandler3DTest.testFingerprints(TemplateHandler3DTest.java:78)