Merge pull request #711 from valasatava/master

josemduarte · web-flow · commit 482df9e2dfff · 2017-10-18T09:10:04.000-07:00
ignore chains that do not have representative atoms
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
@@ -72,8 +72,9 @@ public static List<Subunit> extractSubunits(Structure structure,
 			// Only take protein chains
 			if (c.isProtein()) {
 				Atom[] ca = StructureTools.getRepresentativeAtomArray(c);
-				logger.debug("Chain " + c.getId() + "; CA Atoms: "
-						+ ca.length + "; SEQRES: " + c.getSeqResSequence());
+				logger.debug("Chain " + c.getId() + "; CA Atoms: " + ca.length + "; SEQRES: " + c.getSeqResSequence());
+				if (ca.length==0)
+					continue;
 				subunits.add(new Subunit(ca, c.getName(), null, structure));
 			}
 		}

Original file line number	Diff line number	Diff line change
`@@ -72,8 +72,9 @@ public static List<Subunit> extractSubunits(Structure structure,`
`72`	`72`	`// Only take protein chains`
`73`	`73`	`if (c.isProtein()) {`
`74`	`74`	`Atom[] ca = StructureTools.getRepresentativeAtomArray(c);`
`75`		`- logger.debug("Chain " + c.getId() + "; CA Atoms: "`
`76`		`- + ca.length + "; SEQRES: " + c.getSeqResSequence());`
	`75`	`+ logger.debug("Chain " + c.getId() + "; CA Atoms: " + ca.length + "; SEQRES: " + c.getSeqResSequence());`
	`76`	`+ if (ca.length==0)`
	`77`	`+ continue;`
`77`	`78`	`subunits.add(new Subunit(ca, c.getName(), null, structure));`
`78`	`79`	`}`
`79`	`80`	`}`