Parsing EM resolution in mmCif parser

aalhossary · aalhossary · commit c16c2a86a743 · 2021-12-03T05:28:39.000+08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumer.java
@@ -10,6 +10,7 @@
 import org.rcsb.cif.schema.mm.DatabasePDBRemark;
 import org.rcsb.cif.schema.mm.DatabasePDBRev;
 import org.rcsb.cif.schema.mm.DatabasePDBRevRecord;
+import org.rcsb.cif.schema.mm.Em3dReconstruction;
 import org.rcsb.cif.schema.mm.Entity;
 import org.rcsb.cif.schema.mm.EntityPoly;
 import org.rcsb.cif.schema.mm.EntityPolySeq;
@@ -107,7 +108,13 @@ public interface CifStructureConsumer extends CifFileConsumer<Structure> {
      */
     void consumeDatabasePDBRevRecord(DatabasePDBRevRecord databasePDBrevRecord);
 
-    /**
+	/**
+	 * Consume Electron Microscopy 3D reconstruction data
+	 * @param em3dReconstruction
+	 */
+	void consumeEm3dReconstruction(Em3dReconstruction em3dReconstruction);
+
+	/**
      * Consume a particular Cif category.
      * @param entity data
      */
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
@@ -69,6 +69,7 @@
 import org.rcsb.cif.schema.mm.DatabasePDBRemark;
 import org.rcsb.cif.schema.mm.DatabasePDBRev;
 import org.rcsb.cif.schema.mm.DatabasePDBRevRecord;
+import org.rcsb.cif.schema.mm.Em3dReconstruction;
 import org.rcsb.cif.schema.mm.Entity;
 import org.rcsb.cif.schema.mm.EntityPoly;
 import org.rcsb.cif.schema.mm.EntityPolySeq;
@@ -128,6 +129,7 @@ public class CifStructureConsumerImpl implements CifStructureConsumer {
     private List<Chain> currentModel;
     private PDBHeader pdbHeader;
     private String currentNmrModelNumber;
+	private Em3dReconstruction em3dReconstruction;
     private List<Chain> entityChains;
 
     private Entity entity;
@@ -644,6 +646,16 @@ public void consumeDatabasePDBRevRecord(DatabasePDBRevRecord databasePDBrevRecor
             revRecords.add(new org.biojava.nbio.structure.DatabasePDBRevRecord(databasePDBrevRecord, i));
         }
     }
+    
+    @Override
+    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?
+        }
+        //TODO other fields (maybe RFree)?
+    }
 
     @Override
     public void consumeEntity(Entity entity) {
@@ -831,6 +843,10 @@ public void consumePdbxStructOperList(PdbxStructOperList pdbxStructOperList) {
     public void consumeRefine(Refine refine) {
         for (int rowIndex = 0; rowIndex < refine.getRowCount(); rowIndex++) {
             // RESOLUTION
+        	ValueKind valueKind = refine.getLsDResHigh().getValueKind(rowIndex);
+        	if (ValueKind.NOT_PRESENT.equals(valueKind)) {
+        		continue;
+        	}
             // in very rare cases (for instance hybrid methods x-ray + neutron diffraction, e.g. 3ins, 4n9m)
             // there are 2 resolution values, one for each method
             // we take the last one found so that behaviour is like in PDB file parsing
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConverter.java
@@ -118,6 +118,7 @@ public static Structure fromCifFile(CifFile cifFile, FileParsingParameters param
         consumer.consumeDatabasePDBRemark(cifBlock.getDatabasePDBRemark());
         consumer.consumeDatabasePDBRev(cifBlock.getDatabasePDBRev());
         consumer.consumeDatabasePDBRevRecord(cifBlock.getDatabasePDBRevRecord());
+        consumer.consumeEm3dReconstruction(cifBlock.getEm3dReconstruction());
         consumer.consumeEntity(cifBlock.getEntity());
         consumer.consumeEntityPoly(cifBlock.getEntityPoly());
         consumer.consumeEntitySrcGen(cifBlock.getEntitySrcGen());
