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abradleabradle
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Added a new implementation of an interface to allow data transfer from Biojava structures to the mmtf encoder
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2 files changed

Lines changed: 338 additions & 3 deletions

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‎biojava-structure/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>biojava</artifactId>
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<dependency>
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<groupId>org.rcsb</groupId>
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<artifactId>mmtf-api</artifactId>
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<version>0.0.1-alpha4-SNAPSHOT</version>
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<version>0.0.1-alpha4-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.rcsb</groupId>
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<artifactId>mmtf-common</artifactId>
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<version>0.0.1-alpha4-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.rcsb</groupId>
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<artifactId>mmtf-decoder</artifactId>
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<version>0.0.1-alpha4-SNAPSHOT</version>
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<version>0.0.1-alpha4-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.rcsb</groupId>
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<artifactId>mmtf-encoder</artifactId>
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<version>0.0.1-alpha4-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

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

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package org.biojava.nbio.structure.io.mmtf;
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import org.rcsb.mmtf.api.MmtfDecodedDataInterface;
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import org.rcsb.mmtf.api.MmtfInputDataInterface;
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import org.rcsb.mmtf.api.ObjectToByteArrayConverterInterface;
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import org.rcsb.mmtf.dataholders.MmtfBean;
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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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* @author Anthony Bradley
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*
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*/
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public class MmtfStructureEncoder implements MmtfInputDataInterface {
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@Override
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public void setxCoords(float[] xCoords) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setyCoords(float[] yCoords) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setzCoords(float[] zCoords) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setbFactors(float[] bFactors) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setOccupancies(float[] occupancies) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setAtomIds(int[] atomIds) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setAltLocIds(char[] altLocIds) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setInsCodes(char[] insCodes) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupIds(int[] groupIds) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupName(int groupInd, String groupName) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumAtomsInGroup(int groupInd, int numAtomsInGroup) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupAtomNames(int groupInd, String[] groupAtomNames) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupElementNames(int groupInd, String[] groupElements) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupBondOrders(int groupInd, int[] groupBondOrders) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupBondIndices(int groupInd, int[] groupBondIndices) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupAtomCharges(int groupInd, int[] groupAtomCharges) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupSingleLetterCode(int groupInd, char groupSingleLetterCode) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupChemCompType(int groupInd, String groupChemCompType) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupTypeIndices(int[] groupTypeIndices) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupSequenceIndices(int[] groupSequenceIndices) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setChainIds(String[] chainIds) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setChainNames(String[] chainNames) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setChainsPerModel(int[] chainsPerModel) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setGroupsPerChain(int[] groupsPerChain) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setSpaceGroup(String spaceGroup) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setUnitCell(float[] unitCell) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumBioassemblies(int numBioassemblies) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumTransInBioassembly(int bioassemblyIndex, int numTransInBioassembly) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setChainIndexListForTransform(int bioassemblyIndex, int transformationIndex,
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int[] transChainIndexList) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setMatrixForTransform(int bioassemblyIndex, int transformationIndex, double[] transformationMatrix) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setInterGroupBondIndices(int[] interGroupBondIndices) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setInterGroupBondOrders(int[] interGroupBondOrders) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setMmtfVersion(String mmtfVersion) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setMmtfProducer(String mmtfProducer) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumEntities(int numEntities) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setEntityDescription(int entityInd, String entityDescription) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setEntityType(int entityInd, String entityType) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setEntityChainIndexList(int entityInd, int[] chainIndexList) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setEntitySequence(int entityInd, String sequence) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setStructureId(String structureId) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumModels(int numModels) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumChains(int numChains) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumGroups(int numGroups) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setNumAtoms(int numAtoms) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setRfree(float rFree) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setRwork(float rWork) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setResolution(float resolution) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setTitle(String title) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setExperimentalMethods(String[] experimentalMethods) {
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// TODO Auto-generated method stub
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}
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@Override
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public void setDepositionDate(String depositionDate) {
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// TODO Auto-generated method stub
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}
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@Override
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public MmtfDecodedDataInterface getDataAsDecodedDataInterface() {
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// TODO Auto-generated method stub
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return null;
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}
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}

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