biojava · lafita · Jul 6, 2017 · Jul 6, 2017 · Jul 6, 2017
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.java
@@ -310,6 +310,18 @@ public void newStructSite(StructSite site) {
 	public void newEntityPoly(EntityPoly entityPoly) {
 
 
+	}
+
+	@Override
+	public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history) {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void newPdbxDatabaseStatus(PdbxDatabaseStatus status) {
+		// TODO Auto-generated method stub
+
 	}
 }
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.java
@@ -68,6 +68,8 @@ public interface MMcifConsumer {
 	public void newStructRefSeqDif(StructRefSeqDif sref);
 	public void newStructSite(StructSite sref);
 	public void newStructSiteGen(StructSiteGen sref);
+	public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history);
+	public void newPdbxDatabaseStatus(PdbxDatabaseStatus status);
 	public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss);
 	public void newPdbxNonPolyScheme(PdbxNonPolyScheme ppss);
 	public void newPdbxEntityNonPoly(PdbxEntityNonPoly pen);

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
@@ -259,4 +259,16 @@ public FileParsingParameters getFileParsingParameters() {
     public Map<String,List<MetalBondDistance>> getDefinitions(){
         return definitions;
     }
+
+	@Override
+	public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history) {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void newPdbxDatabaseStatus(PdbxDatabaseStatus status) {
+		// TODO Auto-generated method stub
+
+	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -79,8 +79,10 @@
 import org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat;
 import org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn;
 import org.biojava.nbio.structure.io.mmcif.model.Exptl;
+import org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier;
+import org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme;
@@ -1413,6 +1415,68 @@ public void newDatabasePDBrev(DatabasePDBrev dbrev) {
 
 		structure.setPDBHeader(header);
 	}
+
+	@Override
+	public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history) {
+
+		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
+		PDBHeader header = structure.getPDBHeader();
+
+		if ( header == null) {
+			header = new PDBHeader();
+		}
+
+        // first entry in revision history is the release date
+		if (history.getOrdinal().equals("1")){
+			try {
+				Date releaseDate = dateFormat.parse(history.getRevision_date());
+// TODO uncomment when setRelDate method has been implemented
+				// header.setRelDate(releaseDate));
+			} catch (ParseException e){
+				logger.warn("Could not parse date string '{}', release date will be unavailable", history.getRevision_date());
+			}
+		} else {
+			// all other dates are revision dates;
+			// since this method may be called multiple times,
+			// the last revision date will "stick"
+			try {
+				Date revisionDate = dateFormat.parse(history.getRevision_date());
+				header.setModDate(revisionDate);
+			} catch (ParseException e){
+				logger.warn("Could not parse date string '{}', revision date will be unavailable", history.getRevision_date());
+			}
+		}
+
+		structure.setPDBHeader(header);
+	}
+
+	@Override
+	public void newPdbxDatabaseStatus(PdbxDatabaseStatus status) {
+
+		// the deposition date field is only available in mmCIF 5.0
+
+		if (status.getRecvd_initial_deposition_date() == null) {
+			// skip this method for older mmCIF versions
+			return;
+		}
+
+		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
+		PDBHeader header = structure.getPDBHeader();
+
+		if (header == null) {
+			header = new PDBHeader();
+		}
+
+		// first entry in revision history is the release date
+		try {
+			Date depositionDate = dateFormat.parse(status.getRecvd_initial_deposition_date());
+			header.setDepDate(depositionDate);
+		} catch (ParseException e){
+			logger.warn("Could not parse date string '{}', deposition date will be unavailable", status.getRecvd_initial_deposition_date());
+		}
+
+		structure.setPDBHeader(header);
+	}
 
 	@Override
 	public void newDatabasePDBremark(DatabasePDBremark remark) {

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -59,8 +59,10 @@
 import org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn;
 import org.biojava.nbio.structure.io.mmcif.model.Exptl;
 import org.biojava.nbio.structure.io.mmcif.model.IgnoreField;
+import org.biojava.nbio.structure.io.mmcif.model.PdbxAuditRevisionHistory;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier;
+import org.biojava.nbio.structure.io.mmcif.model.PdbxDatabaseStatus;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme;
 import org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme;
@@ -641,22 +643,30 @@ private void endLineChecks(String category,List<String> loopFields, List<String>
 
 			triggerNewDatabasePDBrev(dbrev);
 
-		} else if ( category.equals("_database_PDB_rev_record")){
+		} else if ( category.equals("_database_PDB_rev_record")) {
 			DatabasePdbrevRecord dbrev = (DatabasePdbrevRecord) buildObject(
 					DatabasePdbrevRecord.class.getName(),
 					loopFields, lineData, loopWarnings);
 
 			triggerNewDatabasePDBrevRecord(dbrev);
 
-		// MMCIF version 5 dates
-		} else if ( category.equals("_pdbx_database_status")){
-			// TODO
+    // MMCIF version 5 dates  
+		} else if ( category.equals("_pdbx_audit_revision_history")) {
+			PdbxAuditRevisionHistory history = (PdbxAuditRevisionHistory) buildObject(
+					PdbxAuditRevisionHistory.class.getName(),
+					loopFields, lineData, loopWarnings);
 
-		// MMCIF version 5 dates
-		} else if ( category.equals("_pdbx_audit_revision_history")){
-			// TODO
-
-		}else if (  category.equals("_database_PDB_remark")){
+			triggerNewPdbxAuditRevisionHistory(history);
+
+    // MMCIF version 5 dates
+		} else if ( category.equals("_pdbx_database_status")) {
+			PdbxDatabaseStatus status = (PdbxDatabaseStatus) buildObject(
+					PdbxDatabaseStatus.class.getName(),
+					loopFields, lineData, loopWarnings);
+
+			triggerNewPdbxDatabaseStatus(status);
+
+		}else if (  category.equals("_database_PDB_remark")) {
 			DatabasePDBremark remark = (DatabasePDBremark) buildObject(
 					DatabasePDBremark.class.getName(),
 					loopFields, lineData, loopWarnings);
@@ -1110,6 +1120,19 @@ private void triggerNewAuditAuthor(AuditAuthor aa){
 			c.newAuditAuthor(aa);
 		}
 	}
+
+	private void triggerNewPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history) {
+		for(MMcifConsumer c : consumers){
+			c.newPdbxAuditRevisionHistory(history);
+		}
+	}
+
+	private void triggerNewPdbxDatabaseStatus(PdbxDatabaseStatus status) {
+		for(MMcifConsumer c : consumers){
+			c.newPdbxDatabaseStatus(status);
+		}
+	}
+
 	private void triggerNewDatabasePDBrev(DatabasePDBrev dbrev){
 		for(MMcifConsumer c : consumers){
 			c.newDatabasePDBrev(dbrev);

diff --git a/...ure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxAuditRevisionHistory.java b/...ure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxAuditRevisionHistory.java
@@ -0,0 +1,46 @@
+package org.biojava.nbio.structure.io.mmcif.model;
+
+/**
+ * Bean to hold data for _pdbx_audit_revision_history mmCIF category.
+ * 
+ * @author Peter Rose
+ * @since 5.0
+ */
+public class PdbxAuditRevisionHistory extends AbstractBean {
+	private String ordinal;
+	private String data_content_type;
+	private String major_revision;
+	private String minor_revision;
+	private String revision_date;
+
+	public String getOrdinal() {
+		return ordinal;
+	}
+	public void setOrdinal(String ordinal) {
+		this.ordinal = ordinal;
+	}
+	public String getData_content_type() {
+		return data_content_type;
+	}
+	public void setData_content_type(String data_content_type) {
+		this.data_content_type = data_content_type;
+	}
+	public String getMajor_revision() {
+		return major_revision;
+	}
+	public void setMajor_revision(String major_revision) {
+		this.major_revision = major_revision;
+	}
+	public String getMinor_revision() {
+		return minor_revision;
+	}
+	public void setMinor_revision(String minor_revision) {
+		this.minor_revision = minor_revision;
+	}
+	public String getRevision_date() {
+		return revision_date;
+	}
+	public void setRevision_date(String revision_date) {
+		this.revision_date = revision_date;
+	}
+}
diff --git a/...structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxDatabaseStatus.java b/...structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/PdbxDatabaseStatus.java
@@ -0,0 +1,81 @@
+package org.biojava.nbio.structure.io.mmcif.model;
+
+/**
+ * Bean to hold data for _pdbx_database_status mmCIF category.
+ * 
+ * @author Peter Rose
+ * @since 5.0
+ */
+public class PdbxDatabaseStatus extends AbstractBean {
+	private String status_code;
+	private String entry_id;
+	private String recvd_initial_deposition_date;
+	private String deposit_site;
+	private String process_site;
+	private String SG_entry;
+	private String pdb_format_compatible;
+	private String status_code_mr;
+	private String status_code_sf;
+	private String status_code_cs;
+
+	public String getStatus_code() {
+		return status_code;
+	}
+	public void setStatus_code(String status_code) {
+		this.status_code = status_code;
+	}
+	public String getEntry_id() {
+		return entry_id;
+	}
+	public void setEntry_id(String entry_id) {
+		this.entry_id = entry_id;
+	}
+	public String getRecvd_initial_deposition_date() {
+		return recvd_initial_deposition_date;
+	}
+	public void setRecvd_initial_deposition_date(String recvd_initial_deposition_date) {
+		this.recvd_initial_deposition_date = recvd_initial_deposition_date;
+	}
+	public String getDeposit_site() {
+		return deposit_site;
+	}
+	public void setDeposit_site(String deposit_site) {
+		this.deposit_site = deposit_site;
+	}
+	public String getProcess_site() {
+		return process_site;
+	}
+	public void setProcess_site(String process_site) {
+		this.process_site = process_site;
+	}
+	public String getSG_entry() {
+		return SG_entry;
+	}
+	public void setSG_entry(String sG_entry) {
+		SG_entry = sG_entry;
+	}
+	public String getPdb_format_compatible() {
+		return pdb_format_compatible;
+	}
+	public void setPdb_format_compatible(String pdb_format_compatible) {
+		this.pdb_format_compatible = pdb_format_compatible;
+	}
+	public String getStatus_code_mr() {
+		return status_code_mr;
+	}
+	public void setStatus_code_mr(String status_code_mr) {
+		this.status_code_mr = status_code_mr;
+	}
+	public String getStatus_code_sf() {
+		return status_code_sf;
+	}
+	public void setStatus_code_sf(String status_code_sf) {
+		this.status_code_sf = status_code_sf;
+	}
+	public String getStatus_code_cs() {
+		return status_code_cs;
+	}
+	public void setStatus_code_cs(String status_code_cs) {
+		this.status_code_cs = status_code_cs;
+	}  
+}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestMmcifV5Changes.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestMmcifV5Changes.java
@@ -0,0 +1,60 @@
+package org.biojava.nbio.structure.io.mmcif;
+
+import static org.junit.Assert.*;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.Locale;
+
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.io.FileParsingParameters;
+import org.biojava.nbio.structure.io.MMCIFFileReader;
+import org.junit.Test;
+
+public class TestMmcifV5Changes {
+
+	/**
+	 * Test date related changes in mmCIF 5.0 format
+	 * @throws IOException
+	 * @throws ParseException 
+	 */
+
+    @Test
+	public void testReleaseDate() throws IOException, ParseException {
+		Structure s = getStructure("/1stp_v50.cif");
+	    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
+        Date releaseDate = dateFormat.parse("1992-10-15");
+        // TODO uncomment the following line once getRelDate has been implemented
+	    // assertEquals(releaseDate, s.getPDBHeader().getRelDate());    
+	}
+
+	@Test
+	public void testDepositionDate() throws IOException, ParseException {
+		Structure s = getStructure("/1stp_v50.cif");
+	    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
+        Date depositionDate = dateFormat.parse("1992-03-12");
+	    assertEquals(depositionDate, s.getPDBHeader().getDepDate());
+
+	}
+
+	@Test
+	public void testRevisionDate() throws IOException, ParseException {
+		Structure s = getStructure("/1stp_v50.cif");
+	    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
+        Date depositionDate = dateFormat.parse("2011-07-13");
+	    assertEquals(depositionDate, s.getPDBHeader().getModDate());
+
+	}
+
+	private Structure getStructure(String fileName) throws IOException{
+		InputStream inStream = this.getClass().getResourceAsStream(fileName);
+		assertNotNull(inStream);
+
+		MMCIFFileReader reader = new MMCIFFileReader();
+
+		return reader.getStructure(inStream) ;
+	}
+}