Avoid another external dependency in test

josemduarte · josemduarte · commit 2d7dbf72b336 · 2020-07-22T14:06:13.000-07:00
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java
@@ -134,7 +134,9 @@ public void testBug1() throws IOException, StructureException, CompoundNotFoundE
 		String b = "----------------------------------------------------------------------lsYFSKqtqtynigkLFTIIELQSVLVTTYTDILGV----LTINVtsmeELARDMLNSMN----VAVVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPtfqLLNMIKMFSQ---IDRLEDLS----KDPEKFNARMATMLEYvrythgIVFDG--KRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKV---HEISARGLCAHILlyqmltsGEYkqCLSDLLNSMMN--RDKIPIYS--HTERDKKPGRHGFINIEKDIIVFnitlkiietylgrvpsvneyhmlksqarniqkitvfnkdifvslvkknkkrffsdvntsaseikdri";
 //		            ========================================================================KQTQ=========NIGKLFTIIELQSVLVTTYTD====LTINV====TSMEELARDML====VAVVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDP===TFQLLNMIKM===IDRLEDLS====KFNARMATMLEYVRYT======HGIVF==KRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKV===SARGLCAHILLYQ=======TSG==EYKQCLSDLLN==MNRDKIPI==HTERDKKPGRHGFINIEKDIIVF===================================================================
 //		            ========================================================================YFSK=========LFTIIELQSVLVTTYTDILGV====LTINV====ELARDMLNSMN====VAVVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDP===LLNMIKMFSQ===IDRLEDLS====KDPEKFNARMATMLEY======IVFDG==KRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKV===HEISARGLCAHIL=======GEY==CLSDLLNSMMN==RDKIPIYS==HTERDKKPGRHGFINIEKDIIVF===================================================================
-		Structure structure = StructureTools.getStructure("d3er9b_");
+		// Note: before BioJava 6.0.0, this used to get scop id d3er9b. The domain happens to be the whole of chain B. To avoid dependence on Berkeley Scop provider in tests we use directly the chain
+		//Structure structure = StructureTools.getStructure("d3er9b_");
+		Structure structure = StructureTools.getStructure("3er9.B");
 		AFPChain afpChain = FastaAFPChainConverter.cpFastaToAfpChain(a, b, structure, 67);
 		assertEquals("Wrong RMSD", 2.681, afpChain.getTotalRmsdOpt(), 0.001);
 		assertEquals("Wrong TM-score", 0.69848, afpChain.getTMScore(), 0.001);
