Fixed the logic of working out which type of group a group is.

abradle · abradle · commit 566d41c99801 · 2016-08-16T08:37:48.000-07:00
Fixed a typo
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -29,6 +29,7 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureImpl;
 import org.biojava.nbio.structure.StructureTools;
+import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
@@ -185,7 +186,8 @@ public void setGroupInfo(String groupName, int groupNumber,
 			char insertionCode, String chemCompType, int atomCount, int bondCount,
 			char singleLetterCode, int sequenceIndexId, int secStructType) {
 		// Get the polymer type
-		int polymerType = getGroupTypIndicator(chemCompType);
+		ResidueType residueType = ResidueType.getResidueTypeFromString(chemCompType);
+		int polymerType = getGroupTypIndicator(residueType.polymerType);
 		switch (polymerType) {
 		case 1:
 			AminoAcid aa = new AminoAcidImpl();
@@ -204,7 +206,6 @@ public void setGroupInfo(String groupName, int groupNumber,
 		ChemComp chemComp = new ChemComp();
 		chemComp.setOne_letter_code(String.valueOf(singleLetterCode));
 		chemComp.setType(chemCompType.toUpperCase());
-		ResidueType residueType = ResidueType.getResidueTypeFromString(chemCompType);
 		chemComp.setResidueType(residueType);
 		chemComp.setPolymerType(residueType.polymerType);
 		group.setChemComp(chemComp);
@@ -400,33 +401,14 @@ public void setXtalInfo(String spaceGroupString, float[] unitCell, double[][] nc
 	 * @param currentGroup
 	 * @return The type of group. (0,1 or 2) depending on whether it is an amino aicd (1), nucleic acid (2) or ligand (0)
 	 */
-	private int getGroupTypIndicator(String currentGroupType) {
-		// At the moment - peptide like is a HETATM group (consistent with biojava)
-		if("PEPTIDE-LIKE".equalsIgnoreCase(currentGroupType)){
-			return 0;
-		}
-		// Again to correspond with Biojava - but I suspect we really want this to be 1
-		if("D-PEPTIDE LINKING".equalsIgnoreCase(currentGroupType)){
-			return 0;
-		}
-		if(currentGroupType.toUpperCase().contains("D-GAMMA-PEPTIDE")){
-			return 0;
-		}
-		if(currentGroupType.toUpperCase().contains("D-BETA-PEPTIDE")){
-			return 0;
-		}	
-                if(currentGroupType.toUpperCase().contains("D-PEPTIDE")){
-                        return 0;
-                }
-		if(currentGroupType.toUpperCase().contains("PEPTIDE")){
+	private int getGroupTypIndicator(PolymerType polymerType) {
+		if(PolymerType.PROTEIN_ONLY.contains(polymerType)){
 			return 1;
 		}
-		if(currentGroupType.toUpperCase().contains("DNA") || currentGroupType.toUpperCase().contains("RNA")){
+		if(PolymerType.POLYNUCLEOTIDE_ONLY.contains(polymerType)){
 			return 2;
 		}
-		else{
-			return 0;
-		}
+		return 0;
 	}
 
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java
@@ -318,7 +318,7 @@ public void testWeirdCase() throws IOException, StructureException {
 
 
 	/**
-	 * Test that Sulphur atoms are not found to be bonded to them selves
+	 * Test that Sulphur atoms are not found to be bonded to themselves
 	 * @throws IOException an error getting the required file
 	 * @throws StructureException an error parsing the required file
 	 */
