Resolution defaults to 99 if no value is available.

aalhossary · aalhossary · commit 73343ef4c90d · 2021-12-07T08:02:15.000+08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -580,6 +580,16 @@ public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo
 		this.crystallographicInfo = crystallographicInfo;
 	}
 
+	/**
+	 * Returns the resolution (or effective resolution) of the experiment. This is
+	 * related to <code>_refine.ls_d_res_high</code> (DIFFRACTION) or
+	 * <code>_em_3d_reconstruction.resolution</code> (ELECTRON MICROSCOPY) for mmCif
+	 * format, or to <code>REMARK 2</code> or <code>REMARK 3</code> for PDB legacy
+	 * format. If more than one value is available (in rare cases), the last one is
+	 * reported. If no value is available, it defaults to 99.
+	 * 
+	 * @return The reported experiment resolution, 99 if no value is available.
+	 */
 	public float getResolution() {
 		return resolution;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -651,8 +651,10 @@ public void consumeDatabasePDBRevRecord(DatabasePDBRevRecord databasePDBrevRecor
     public void consumeEm3dReconstruction(Em3dReconstruction em3dReconstruction) {
     	this.em3dReconstruction = em3dReconstruction;
     	
-        for (int rowIndex = 0; rowIndex < em3dReconstruction.getRowCount(); rowIndex++) {
-        	pdbHeader.setResolution((float) em3dReconstruction.getResolution().get(rowIndex)); //can it have more than 1 value?
+        for (int rowIndex = 0; rowIndex < em3dReconstruction.getRowCount(); rowIndex++) { //can it have more than 1 value?
+        	final FloatColumn resolution = em3dReconstruction.getResolution();
+			if (ValueKind.PRESENT.equals(resolution.getValueKind(rowIndex)))
+        		pdbHeader.setResolution((float) resolution.get(rowIndex));
         }
         //TODO other fields (maybe RFree)?
     }

Original file line number	Diff line number	Diff line change
`@@ -651,8 +651,10 @@ public void consumeDatabasePDBRevRecord(DatabasePDBRevRecord databasePDBrevRecor`
`651`	`651`	`public void consumeEm3dReconstruction(Em3dReconstruction em3dReconstruction) {`
`652`	`652`	`this.em3dReconstruction = em3dReconstruction;`
`653`	`653`
`654`		`- for (int rowIndex = 0; rowIndex < em3dReconstruction.getRowCount(); rowIndex++) {`
`655`		`- pdbHeader.setResolution((float) em3dReconstruction.getResolution().get(rowIndex)); //can it have more than 1 value?`
	`654`	`+ for (int rowIndex = 0; rowIndex < em3dReconstruction.getRowCount(); rowIndex++) { //can it have more than 1 value?`
	`655`	`+ final FloatColumn resolution = em3dReconstruction.getResolution();`
	`656`	`+ if (ValueKind.PRESENT.equals(resolution.getValueKind(rowIndex)))`
	`657`	`+ pdbHeader.setResolution((float) resolution.get(rowIndex));`
`656`	`658`	`}`
`657`	`659`	`//TODO other fields (maybe RFree)?`
`658`	`660`	`}`