Updated to initialise all the arrays during the writing process

abradle · abradle · commit 62801b0c3cfe · 2016-04-08T19:07:26.000-07:00
diff --git a/biojava-structure/src/main/java/demo/DemoMmtfRoundTrip.java b/biojava-structure/src/main/java/demo/DemoMmtfRoundTrip.java
@@ -12,7 +12,7 @@ public class DemoMmtfRoundTrip {
 
 	public static void main(String[] args) throws IOException, StructureException {
 		MmtfUtils.setUpBioJava();
-		Structure structure = StructureIO.getStructure("4cup");
+		Structure structure = StructureIO.getStructure("/Users/abradley/Downloads/4cup.cif");
 		// We can do somme comparisons on the round tripped structure
 		MmtfActions.roundTrip(structure);
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
@@ -43,7 +43,6 @@ public MmtfStructureWriter(Structure data) {
 	public void write(MmtfDecoderInterface decoder) {
 		
 		this.mmtfDecoderInterface = decoder;
-		
 		// Reset structure to consider altloc groups with the same residue number but different group names as seperate groups
 		MmtfUtils.fixMicroheterogenity(structure);
 		// Generate the secondary structure
@@ -52,6 +51,8 @@ public void write(MmtfDecoderInterface decoder) {
 		Map<String, Integer> chainIdToIndexMap = MmtfUtils.getChainIdToIndexMap(structure);
 		List<Chain> allChains = MmtfUtils.getAllChains(structure);
 		List<Atom> allAtoms = MmtfUtils.getAllAtoms(structure);
+		
+		mmtfDecoderInterface.initStructure(allAtoms.size(), MmtfUtils.getNumGroups(structure), allChains.size(), structure.nrModels(), structure.getPDBCode());
 		// Get the header and the xtal info.
 		PDBHeader pdbHeader = structure.getPDBHeader();
 		PDBCrystallographicInfo xtalInfo = pdbHeader.getCrystallographicInfo();
@@ -89,6 +90,7 @@ public void write(MmtfDecoderInterface decoder) {
 				}
 			}
 		}
+		mmtfDecoderInterface.finalizeStructure();
 
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -325,5 +325,20 @@ public static List<Chain> getAllChains(Structure structure) {
 			chainList.addAll(structure.getChains(i));
 		}
 		return chainList;
+	}
+
+	/**
+	 * Count the total number of groups in the structure
+	 * @param structure the input structure
+	 * @return the total number of groups
+	 */
+	public static int getNumGroups(Structure structure) {
+		int count = 0;
+		for(int i=0; i<structure.nrModels(); i++) {
+			for(Chain chain : structure.getChains(i)){
+				count+= chain.getAtomGroups().size();
+			}
+		}
+		return count;
 	}	
 }

Original file line number	Diff line number	Diff line change
`@@ -12,7 +12,7 @@ public class DemoMmtfRoundTrip {`
`12`	`12`
`13`	`13`	`public static void main(String[] args) throws IOException, StructureException {`
`14`	`14`	`MmtfUtils.setUpBioJava();`
`15`		`- Structure structure = StructureIO.getStructure("4cup");`
	`15`	`+ Structure structure = StructureIO.getStructure("/Users/abradley/Downloads/4cup.cif");`
`16`	`16`	`// We can do somme comparisons on the round tripped structure`
`17`	`17`	`MmtfActions.roundTrip(structure);`
`18`	`18`	`}`
Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,6 @@ public MmtfStructureWriter(Structure data) {`
`43`	`43`	`public void write(MmtfDecoderInterface decoder) {`
`44`	`44`
`45`	`45`	`this.mmtfDecoderInterface = decoder;`
`46`		`-`
`47`	`46`	`// Reset structure to consider altloc groups with the same residue number but different group names as seperate groups`
`48`	`47`	`MmtfUtils.fixMicroheterogenity(structure);`
`49`	`48`	`// Generate the secondary structure`
`@@ -52,6 +51,8 @@ public void write(MmtfDecoderInterface decoder) {`
`52`	`51`	`Map<String, Integer> chainIdToIndexMap = MmtfUtils.getChainIdToIndexMap(structure);`
`53`	`52`	`List<Chain> allChains = MmtfUtils.getAllChains(structure);`
`54`	`53`	`List<Atom> allAtoms = MmtfUtils.getAllAtoms(structure);`
	`54`	`+`
	`55`	`+ mmtfDecoderInterface.initStructure(allAtoms.size(), MmtfUtils.getNumGroups(structure), allChains.size(), structure.nrModels(), structure.getPDBCode());`
`55`	`56`	`// Get the header and the xtal info.`
`56`	`57`	`PDBHeader pdbHeader = structure.getPDBHeader();`
`57`	`58`	`PDBCrystallographicInfo xtalInfo = pdbHeader.getCrystallographicInfo();`
`@@ -89,6 +90,7 @@ public void write(MmtfDecoderInterface decoder) {`
`89`	`90`	`}`
`90`	`91`	`}`
`91`	`92`	`}`
	`93`	`+ mmtfDecoderInterface.finalizeStructure();`
`92`	`94`
`93`	`95`	`}`
`94`	`96`