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Updates to the biojava structure decoder due to an API change in the interrface
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/BioJavaStructureDecoder.java‎

Lines changed: 48 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,11 @@
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import javax.vecmath.Matrix4d;
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@@ -31,6 +33,8 @@
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import org.biojava.nbio.structure.xtal.CrystalCell;
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import org.biojava.nbio.structure.xtal.SpaceGroup;
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import org.rcsb.mmtf.api.StructureDecoderInterface;
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import org.rcsb.mmtf.dataholders.BioAssemblyData;
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import org.rcsb.mmtf.dataholders.BioAssemblyTrans;
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/**
@@ -270,52 +274,6 @@ private Group getCorrectAltLocGroup(final Character altLoc) {
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}
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/* (non-Javadoc)
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* @see org.rcsb.mmtf.decoder.StructureDecoderInterface
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* #setBioAssembly(java.util.Map, java.util.Map,
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* java.util.Map, java.util.Map, java.util.Map)
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*/
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@Override
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public final void setBioAssembly(final Map<Integer,
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Integer> keyList, final Map<Integer, Integer> sizeList,
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final Map<Integer, List<String>> inputIds, final Map<Integer,
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List<String>> inputChainIds, final Map<Integer,
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List<double[]>> inputTransformations) {
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PDBHeader pdbHeader = structure.getPDBHeader();
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// Get the bioassebly data
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Map<Integer, BioAssemblyInfo> bioAssemblies = new HashMap<>();
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for (Entry<Integer, Integer> entry: keyList.entrySet()) {
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// Get the key and the value
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Integer key = entry.getKey();
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Integer value = entry.getValue();
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// Make a biojava bioassembly object
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BioAssemblyInfo bioAssInfo = new BioAssemblyInfo();
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bioAssInfo.setId(value);
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// Set size
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bioAssInfo.setMacromolecularSize(sizeList.get(key));
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// Now get the new sizes
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List<BiologicalAssemblyTransformation> newList = new ArrayList<>();
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for (int i = 0; i < inputIds.get(key).size(); i++) {
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BiologicalAssemblyTransformation bioAssTrans =
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new BiologicalAssemblyTransformation();
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bioAssTrans.setId(inputIds.get(key).get(i));
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bioAssTrans.setChainId(inputChainIds.get(key).get(i));
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// Now set matrix
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Matrix4d mat4d = new Matrix4d(inputTransformations.get(key).get(i));
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bioAssTrans.setTransformationMatrix(mat4d);
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// Now add this
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newList.add(bioAssTrans);
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}
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// Now set the transform list
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bioAssInfo.setTransforms(newList);
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// Now set this
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bioAssemblies.put(key, bioAssInfo);
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}
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// Now actually set them
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pdbHeader.setBioAssemblies(bioAssemblies);
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structure.setPDBHeader(pdbHeader);
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}
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/* (non-Javadoc)
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* @see org.rcsb.mmtf.decoder.StructureDecoderInterface#
@@ -378,5 +336,49 @@ private int getGroupTypIndicator(String currentGroupType) {
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}
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}
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@Override
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public void setBioAssembly(Map<Integer, BioAssemblyData> inputBioassemblies) {
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PDBHeader pdbHeader = structure.getPDBHeader();
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// Get the bioassebly data
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Map<Integer, BioAssemblyInfo> bioAssemblies = new HashMap<>();
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int bioassemlyCounter = 0;
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for (Entry<Integer, BioAssemblyData> entry: inputBioassemblies.entrySet()) {
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bioassemlyCounter++;
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// Get the key and the value
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Integer key = entry.getKey();
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BioAssemblyData value = entry.getValue();
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// Make a biojava bioassembly object
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BioAssemblyInfo bioAssInfo = new BioAssemblyInfo();
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bioAssInfo.setId(bioassemlyCounter);
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// Now get the new sizes
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List<BiologicalAssemblyTransformation> newList = new ArrayList<>();
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Integer transIdCounter =0;
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for (BioAssemblyTrans transform : value.getTransforms()) {
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transIdCounter++;
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// Now loop over the chains
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for(String currChainId : transform.getChainId()){
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BiologicalAssemblyTransformation bioAssTrans =
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new BiologicalAssemblyTransformation();
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bioAssTrans.setId(transIdCounter.toString());
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bioAssTrans.setChainId(currChainId);
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// Now set matrix
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Matrix4d mat4d = new Matrix4d(transform.getTransformation());
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bioAssTrans.setTransformationMatrix(mat4d);
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// Now add this
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newList.add(bioAssTrans);
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}
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}
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// Now set the transform list
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bioAssInfo.setTransforms(newList);
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bioAssInfo.setMacromolecularSize(value.getMacroMolecularSize());
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// Now set this
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bioAssemblies.put(key, bioAssInfo);
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}
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// Now actually set them
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pdbHeader.setBioAssemblies(bioAssemblies);
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structure.setPDBHeader(pdbHeader);
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}
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}

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