Merge pull request #878 from valasatava/master

josemduarte · web-flow · commit d20fcd94fee3 · 2020-06-28T22:09:44.000-07:00
Case insensitive chem.comp type lookup
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.java
@@ -140,9 +140,9 @@ public static ResidueType getResidueTypeFromString(String chem_comp_type)
 			{
 				return rt;
 			}
-			if ( rt.chem_comp_type.startsWith(chem_comp_type))
+			if ( rt.chem_comp_type.toLowerCase().startsWith(chem_comp_type.toLowerCase()))
 				return rt;
-			if ( chem_comp_type.startsWith(rt.chem_comp_type))
+			if ( chem_comp_type.toLowerCase().startsWith(rt.chem_comp_type.toLowerCase()))
 				return rt;
 		}
 		return null;
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
@@ -214,6 +214,9 @@ public void setGroupInfo(String groupName, int groupNumber,
 			char singleLetterCode, int sequenceIndexId, int secStructType) {
 		// Get the polymer type
 		ResidueType residueType = ResidueType.getResidueTypeFromString(chemCompType);
+		if (residueType == null)
+			throw new IllegalStateException("Couldn't resolve residue type for "+ chemCompType);
+
 		int polymerType = getGroupTypIndicator(residueType.polymerType);
 		switch (polymerType) {
 		case 1:

Original file line number	Diff line number	Diff line change
`@@ -140,9 +140,9 @@ public static ResidueType getResidueTypeFromString(String chem_comp_type)`
`140`	`140`	`{`
`141`	`141`	`return rt;`
`142`	`142`	`}`
`143`		`- if ( rt.chem_comp_type.startsWith(chem_comp_type))`
	`143`	`+ if ( rt.chem_comp_type.toLowerCase().startsWith(chem_comp_type.toLowerCase()))`
`144`	`144`	`return rt;`
`145`		`- if ( chem_comp_type.startsWith(rt.chem_comp_type))`
	`145`	`+ if ( chem_comp_type.toLowerCase().startsWith(rt.chem_comp_type.toLowerCase()))`
`146`	`146`	`return rt;`
`147`	`147`	`}`
`148`	`148`	`return null;`