Fixing #671

josemduarte · josemduarte · commit 93832066d86b · 2019-09-02T16:30:01.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -50,6 +50,7 @@
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
+import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
 import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
@@ -513,7 +514,7 @@ public static void addSeqRes(Chain modelChain, String sequence) {
 				continue;
 			}
 			
-			group = getSeqResGroup(modelChain, singleLetterCode, chainType);
+			group = getSeqResGroup(singleLetterCode, chainType);
 			addGroupAtId(seqResGroups, group, i);
 			seqResGroups.set(i, group);
 		}
@@ -537,21 +538,28 @@ private static <T> void addGroupAtId(List<T> seqResGroups, T group, int sequence
 		}
 	}
 
-	private static Group getSeqResGroup(Chain modelChain, char singleLetterCode, GroupType type) {
+	private static Group getSeqResGroup(char singleLetterCode, GroupType type) {
 		if(type==GroupType.AMINOACID){
 			AminoAcidImpl a = new AminoAcidImpl();
 			a.setRecordType(AminoAcid.SEQRESRECORD);
 			a.setAminoType(singleLetterCode);
 			ChemComp chemComp = new ChemComp();
 			chemComp.setOne_letter_code(""+singleLetterCode);
 			a.setChemComp(chemComp);
+			chemComp.setPolymerType(PolymerType.peptide);
 			return a;
 
 		} else if (type==GroupType.NUCLEOTIDE) {
 			NucleotideImpl n = new NucleotideImpl();
 			ChemComp chemComp = new ChemComp();
 			chemComp.setOne_letter_code(""+singleLetterCode);
 			n.setChemComp(chemComp);
+			// TODO this could be either dna or rna, how to distinguish properly?
+			if (singleLetterCode == 'U') {
+				chemComp.setPolymerType(PolymerType.rna);
+			} else {
+				chemComp.setPolymerType(PolymerType.dna);
+			}
 			return n;
 		}
 		else{
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
@@ -94,7 +94,6 @@ public void testRoundTrip() throws IOException, StructureException {
 	 * Broad test of atom similarity
 	 * @param structOne the first input structure
 	 * @param structTwo the second input structure
-	 * @param mmtfParams
 	 * @return
 	 */
 	private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
@@ -44,7 +44,7 @@ public void testRead() throws IOException {
 	/**
 	 * Compare structures loaded from MMCIF and MMTF files.
 	 */
-	@Test @Ignore
+	@Test
 	public void compareMmcif() throws IOException, StructureException {
 		
 		// Get the MMTF and MMCIF files from the resources folder
