Switching Jmol interchange format to MMCIF

sbliven · sbliven · commit 50595e08865e · 2016-08-29T15:06:10.000+02:00
Any bugs are probably due to the poor MMCIF writer. However,
at least we can use multi-letter chain Ids now.
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
@@ -117,8 +117,8 @@ public void executeCmd(String rasmolScript) {
 	public void setStructure(Structure s)
 	{
 		this.structure = s;
-		String pdb = s.toPDB();
-		viewer.openStringInline(pdb);
+		String serialized = s.toMMCIF();
+		viewer.openStringInline(serialized);
 		evalString("save STATE state_1");
 	}
 

Original file line number	Diff line number	Diff line change
`@@ -117,8 +117,8 @@ public void executeCmd(String rasmolScript) {`
`117`	`117`	`public void setStructure(Structure s)`
`118`	`118`	`{`
`119`	`119`	`this.structure = s;`
`120`		`- String pdb = s.toPDB();`
`121`		`- viewer.openStringInline(pdb);`
	`120`	`+ String serialized = s.toMMCIF();`
	`121`	`+ viewer.openStringInline(serialized);`
`122`	`122`	`evalString("save STATE state_1");`
`123`	`123`	`}`
`124`	`124`