Adding non-standard sg check to pdb parser

josemduarte · josemduarte · commit 617d6ec04036 · 2016-11-23T09:34:31.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1502,8 +1502,13 @@ private void pdb_CRYST1_Handler(String line) {
 		}
 
 		SpaceGroup sg = SymoplibParser.getSpaceGroup(spaceGroup);
-		if (sg==null) logger.warn("Space group '"+spaceGroup+"' not recognised as a standard space group");
-		crystallographicInfo.setSpaceGroup(sg);
+		if (sg==null) {
+			logger.warn("Space group '"+spaceGroup+"' not recognised as a standard space group");
+			crystallographicInfo.setNonStandardSg(true);
+		} else {
+			crystallographicInfo.setSpaceGroup(sg);
+			crystallographicInfo.setNonStandardSg(false);
+		}
 	}
 
 	/**

Original file line number	Diff line number	Diff line change
`@@ -1502,8 +1502,13 @@ private void pdb_CRYST1_Handler(String line) {`
`1502`	`1502`	`}`
`1503`	`1503`
`1504`	`1504`	`SpaceGroup sg = SymoplibParser.getSpaceGroup(spaceGroup);`
`1505`		`- if (sg==null) logger.warn("Space group '"+spaceGroup+"' not recognised as a standard space group");`
`1506`		`- crystallographicInfo.setSpaceGroup(sg);`
	`1505`	`+ if (sg==null) {`
	`1506`	`+ logger.warn("Space group '"+spaceGroup+"' not recognised as a standard space group");`
	`1507`	`+ crystallographicInfo.setNonStandardSg(true);`
	`1508`	`+ } else {`
	`1509`	`+ crystallographicInfo.setSpaceGroup(sg);`
	`1510`	`+ crystallographicInfo.setNonStandardSg(false);`
	`1511`	`+ }`
`1507`	`1512`	`}`
`1508`	`1513`
`1509`	`1514`	`/**`