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Added three new demos (reader, writer and roundtrip) to Biojava.
Updated the Writer to use the writer interface. Updated the others to comply with upstrea formatting
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6 files changed

+131
-38
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6 files changed

+131
-38
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‎biojava-structure/src/main/java/demo/DemoMmtfReader.java‎

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package demo;
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import java.io.IOException;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.io.mmtf.MmtfStructureReader;
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import org.rcsb.mmtf.dataholders.MmtfBean;
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import org.rcsb.mmtf.decoder.BeanToGet;
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import org.rcsb.mmtf.decoder.GetToInflator;
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import org.rcsb.mmtf.deserializers.MessagePackDeserializer;
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public class DemoMmtfReader {
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/**
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* Utility function to get a Biojava structure from a byte array.
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* @param inputByteArray Must be uncompressed (i.e. with entropy compression methods like gzip)
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* @param parsingParams
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* @return
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* @throws IOException
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*/
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public static Structure getBiojavaStruct(byte[] inputByteArray) throws IOException {
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// Get the reader - this is the bit that people need to implement.
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MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
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// Set up the deserializer
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MessagePackDeserializer messagePackDeserializer = new MessagePackDeserializer();
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// Get the data
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MmtfBean mmtfBean = messagePackDeserializer.deserialize(inputByteArray);
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// Set up the data API
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BeanToGet beanToGet = new BeanToGet(mmtfBean);
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// Set up the inflator
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GetToInflator getToInflator = new GetToInflator();
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// Do the inflation
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getToInflator.read(beanToGet, mmtfStructureReader);
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// Get the structue
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return mmtfStructureReader.getStructure();
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}
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}

‎biojava-structure/src/main/java/demo/DemoMmtfRoundTrip.java‎

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package demo;
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import java.io.IOException;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.io.mmtf.MmtfStructureReader;
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import org.biojava.nbio.structure.io.mmtf.MmtfStructureWriter;
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import org.rcsb.mmtf.dataholders.MmtfBean;
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import org.rcsb.mmtf.decoder.BeanToGet;
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import org.rcsb.mmtf.decoder.GetToInflator;
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import org.rcsb.mmtf.deserializers.MessagePackDeserializer;
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import org.rcsb.mmtf.encoder.GetToBean;
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import org.rcsb.mmtf.encoder.InflatorToGet;
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import org.rcsb.mmtf.serializers.MessagePackSerializer;
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public class DemoMmtfRoundTrip {
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public static Structure roundTrip(Structure structure) throws IOException {
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// Set up the transform from the inflator to the get api
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InflatorToGet inflatorToGet = new InflatorToGet();
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// Get the writer - this is what people implement
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MmtfStructureWriter mmtfStructureWriter = new MmtfStructureWriter(structure);
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// Do thte inflation
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mmtfStructureWriter.write(inflatorToGet);
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// Get the bean
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GetToBean getToBean = new GetToBean(inflatorToGet);
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// Serialize
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MessagePackSerializer messagePackSerializer = new MessagePackSerializer();
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byte[] byteArr = messagePackSerializer.serialize(getToBean.getMmtfBean());
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// Get the reader - this is the bit that people need to implement.
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MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
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// Set up the deserializer
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MessagePackDeserializer messagePackDeserializer = new MessagePackDeserializer();
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// Get the data
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MmtfBean mmtfBean = messagePackDeserializer.deserialize(byteArr);
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// Set up the data API
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BeanToGet beanToGet = new BeanToGet(mmtfBean);
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// Set up the inflator
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GetToInflator getToInflator = new GetToInflator();
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// Do the inflation
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getToInflator.read(beanToGet, mmtfStructureReader);
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// Get the structue
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return mmtfStructureReader.getStructure();
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}
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}

‎biojava-structure/src/main/java/demo/DemoMmtfWriter.java‎

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package demo;
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import java.io.IOException;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.io.mmtf.MmtfStructureWriter;
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import org.rcsb.mmtf.encoder.GetToBean;
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import org.rcsb.mmtf.encoder.InflatorToGet;
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import org.rcsb.mmtf.serializers.MessagePackSerializer;
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public class DemoMmtfWriter {
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/**
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* Utility function to get a byte array from a Biojava structure
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* @param inputByteArray Must be uncompressed (i.e. with entropy compression methods like gzip)
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* @param parsingParams
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* @return
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* @throws IOException
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*/
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public static byte[] getByteArray(Structure structure) throws IOException {
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// Set up the transform from the inflator to the get api
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InflatorToGet inflatorToGet = new InflatorToGet();
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// Get the writer - this is what people implement
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MmtfStructureWriter mmtfStructureWriter = new MmtfStructureWriter(structure);
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// Now deflate
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mmtfStructureWriter.write(inflatorToGet);
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// Get to bean
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GetToBean getToBean = new GetToBean(inflatorToGet);
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MessagePackSerializer messagePackSerializer = new MessagePackSerializer();
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return messagePackSerializer.serialize(getToBean.getMmtfBean());
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java‎

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@@ -30,7 +30,6 @@
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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.MmtfDecoderInterface;
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import org.rcsb.mmtf.decoder.GetApiToInflatorInterface;
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/**
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}
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}
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/**
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* Utility function to get a Biojava structure from a byte array.
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* @param inputByteArray Must be uncompressed (i.e. with entropy compression methods like gzip)
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* @param parsingParams
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* @return
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*/
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public static Structure getBiojavaStruct(byte[] inputByteArray) {
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// Make the decoder
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MmtfStructureReader biojavaStructureDecoder = new MmtfStructureReader();
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GetApiToInflatorInterface ds = new GetApiToInflatorInterface(inputByteArray);
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ds.getStructFromByteArray(biojavaStructureDecoder);
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// Now return this structure
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return biojavaStructureDecoder.getStructure();
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java‎

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import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
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import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
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import org.rcsb.mmtf.api.MmtfDecoderInterface;
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import org.rcsb.mmtf.api.MmtfWriter;
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/**
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* Class to take Biojava structure data and covert to the DataApi for encoding.
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* Must implement all the functions in {@link MmtfDecoderInterface}.
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* @author Anthony Bradley
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*
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*/
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public class MmtfStructureWriter {
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public class MmtfStructureWriter implements MmtfWriter {
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private MmtfDecoderInterface mmtfDecoderInterface;
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private Structure structure;
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/**
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* The constructor requires a structre input.
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* @param structure ths structure to be encoded
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* @param mmtfDecoderInterface the interface to be used
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* @param structure the structure to be encoded
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*/
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public MmtfStructureWriter(MmtfDecoderInterface mmtfDecoderInterface) {
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this.mmtfDecoderInterface = mmtfDecoderInterface;
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public MmtfStructureWriter(Structure data) {
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this.structure = data;
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}
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public void encodeStructure(Structure structure) {
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public void write(MmtfDecoderInterface decoder) {
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this.mmtfDecoderInterface = decoder;
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// Reset structure to consider altloc groups with the same residue number but different group names as seperate groups
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MmtfUtils.fixMicroheterogenity(structure);
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// Generate the secondary structure
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Chain chain = modelChains.get(chainInModelIndex);
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List<Group> groups = chain.getAtomGroups();
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List<Group> sequenceGroups = chain.getSeqResGroups();
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// TODO we need to include the sequence to group mapping information....
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mmtfDecoderInterface.setChainInfo(chain.getChainID(), chain.getInternalChainID(), groups.size());
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for(int groupInChainIndex=0; groupInChainIndex<groups.size(); groupInChainIndex++){
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// Get the major compy of this group
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Group group = groups.get(groupInChainIndex);
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List<Atom> atomsInGroup = MmtfUtils.getAtomsForGroup(group);
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// Get the group type
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ChemComp chemComp = group.getChemComp();
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// TODO We need to specify what type of group is being added
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mmtfDecoderInterface.setGroupInfo(group.getPDBName(), group.getResidueNumber().getSeqNum(), group.getResidueNumber().getInsCode().charValue(),
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chemComp.getPdbx_type(), atomsInGroup.size(), chemComp.getOne_letter_code().charAt(0), sequenceGroups.indexOf(group));
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for (Atom atom : atomsInGroup){
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}
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}
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java‎

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import org.biojava.nbio.structure.secstruc.SecStrucCalc;
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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.utils.CodecUtils;
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/**
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* A utils class of functions needed for Biojava.
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* A utils class of functions needed for Biojava to read and write to mmtf.
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* @author Anthony Bradley
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*
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*/
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/**
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* Set up the configuration parameters for BioJava. - with an extra URL
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*/
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public AtomCache setUpBioJava(String extraUrl) {
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public static AtomCache setUpBioJava(String extraUrl) {
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// Set up the atom cache etc
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AtomCache cache = new AtomCache();
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cache.setUseMmCif(true);
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}
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Map<double[], int[]> outMap = new HashMap<>();
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for (Entry<Matrix4d, List<Integer>> entry : matMap.entrySet()) {
293-
outMap.put(convertToDoubleArray(entry.getKey()), convertToIntArray(entry.getValue()));
294+
outMap.put(convertToDoubleArray(entry.getKey()), CodecUtils.convertToIntArray(entry.getValue()));
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}
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return outMap;
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}
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/**
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* Convert a List<Integer> to an int[]
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* @param integerList the input list
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* @return the output array
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*/
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private static int[] convertToIntArray(List<Integer> integerList) {
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int[] integerArray = new int[integerList.size()];
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for(int i=0; i<integerList.size(); i++){
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integerArray[i] = integerList.get(i);
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}
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return integerArray;
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}
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/**
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* Convert a four-d matrix to a double array. Row-packed.
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* @param transformationMatrix the input matrix4d object

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