Merge branch 'pointgroups2' of https://github.com/sbliven/biojava-sbliven.git into pointgroups2

lafita · lafita · commit 881bda56c83a · 2016-06-14T11:32:33.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -72,8 +72,7 @@ public Structure loadStructure(AtomCache cache) throws StructureException,
 
 	@Override
 	public SubstructureIdentifier toCanonical() throws StructureException {
-		// null pdbCode indicates that the structure can't be loaded by AtomCache
-		return new SubstructureIdentifier(null, new ArrayList<ResidueRange>());
+		return new SubstructureIdentifier(pdbCode, new ArrayList<ResidueRange>());
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
@@ -525,15 +525,15 @@ private void getSymmetryAxes(List<Axis> symmAxes, Matrix4d prior, int level, int
 		symmAxes.add(currAxis);
 		
 		//Remember that all degrees are at least 2
-		getSymmetryAxes(symmAxes,prior,level+1,0);
+		getSymmetryAxes(symmAxes,prior,level+1,firstRepeat);
 		//New prior is elementary^d*prior
 		Matrix4d newPrior = new Matrix4d(elemOp);
 		newPrior.mul(prior);
 		int childSize = getNumRepeats(level+1);
-		getSymmetryAxes(symmAxes,newPrior,level+1,childSize);
+		getSymmetryAxes(symmAxes,newPrior,level+1,firstRepeat+childSize);
 		for(int d=2;d<elem.getOrder();d++) {
 			newPrior.mul(elemOp,newPrior);
-			getSymmetryAxes(symmAxes,newPrior,level+1,childSize*d);
+			getSymmetryAxes(symmAxes,newPrior,level+1,firstRepeat+childSize*d);
 		}
 	}
 	

Original file line number	Diff line number	Diff line change
`@@ -72,8 +72,7 @@ public Structure loadStructure(AtomCache cache) throws StructureException,`
`72`	`72`
`73`	`73`	`@Override`
`74`	`74`	`public SubstructureIdentifier toCanonical() throws StructureException {`
`75`		`- // null pdbCode indicates that the structure can't be loaded by AtomCache`
`76`		`- return new SubstructureIdentifier(null, new ArrayList<ResidueRange>());`
	`75`	`+ return new SubstructureIdentifier(pdbCode, new ArrayList<ResidueRange>());`
`77`	`76`	`}`
`78`	`77`
`79`	`78`	`@Override`