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josemduartejosemduarte
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Removing utility method that shouldn't be here
1 parent 4d1cf58 commit f1bcdb2

4 files changed

Lines changed: 26 additions & 52 deletions

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‎CHANGELOG.md‎

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@@ -17,6 +17,7 @@ BioJava 6.0.0 (future release)
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* `org.biojava.nbio.structure.PDBStatus`: removed `getReplacement` and `getReplaces`
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* Removed `org.biojava.nbio.structure.io.mmcif` package
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* Removed functionality to write isolated CIF headers from `FileConvert`
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* Removed `org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()`
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### Breaking API changes
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* Extracted `StructureIO.StructureFiletype` enum to `org.biojava.nbio.structure.io.StructureFiletype` (supports `PDB`, `MMTF`, `CIF`, and `BCIF`)

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

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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.io.mmtf.MmtfActions;
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import org.biojava.nbio.structure.io.mmtf.MmtfUtils;
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public class DemoMmtfWriter {
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public static void main(String[] args) throws IOException, StructureException {
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MmtfUtils.setUpBioJava();
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Structure structure = StructureIO.getStructure("4cup");
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MmtfActions.writeToFile(structure, Paths.get("/tmp/4cup.mmtf"));
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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.PDBCrystallographicInfo;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.io.StructureFiletype;
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import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.chem.ChemComp;
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import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
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import org.biojava.nbio.structure.chem.ChemCompTools;
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import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
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import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
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import org.biojava.nbio.structure.secstruc.SecStrucCalc;
@@ -74,49 +69,6 @@ public class MmtfUtils {
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private static final Logger LOGGER = LoggerFactory.getLogger(MmtfUtils.class);
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/**
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* Set up the configuration parameters for BioJava.
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*/
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public static AtomCache setUpBioJava() {
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// Set up the atom cache etc
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AtomCache cache = new AtomCache();
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cache.setFiletype(StructureFiletype.MMTF);
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FileParsingParameters params = cache.getFileParsingParams();
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params.setCreateAtomBonds(true);
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params.setAlignSeqRes(true);
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params.setParseBioAssembly(true);
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DownloadChemCompProvider cc = new DownloadChemCompProvider();
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ChemCompGroupFactory.setChemCompProvider(cc);
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cc.checkDoFirstInstall();
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cache.setFileParsingParams(params);
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StructureIO.setAtomCache(cache);
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return cache;
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}
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/**
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* Set up the configuration parameters for BioJava.
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* @param extraUrl the string describing the URL (or file path) from which
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* to get missing CCD entries.
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*/
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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.setFiletype(StructureFiletype.MMTF);
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FileParsingParameters params = cache.getFileParsingParams();
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params.setCreateAtomBonds(true);
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params.setAlignSeqRes(true);
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params.setParseBioAssembly(true);
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DownloadChemCompProvider.serverBaseUrl = extraUrl;
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DownloadChemCompProvider.useDefaultUrlLayout = false;
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DownloadChemCompProvider cc = new DownloadChemCompProvider();
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ChemCompGroupFactory.setChemCompProvider(cc);
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cc.checkDoFirstInstall();
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cache.setFileParsingParams(params);
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StructureIO.setAtomCache(cache);
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return cache;
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}
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/**
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* This sets all microheterogeneous groups
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* (previously alternate location groups) as separate groups.

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java‎

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*/
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package org.biojava.nbio.structure.io.mmtf;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
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import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.StructureFiletype;
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import org.junit.Test;
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import static org.junit.Assert.*;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.StructureImpl;
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import org.biojava.nbio.structure.io.mmtf.MmtfUtils;
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import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
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import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
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import org.biojava.nbio.structure.xtal.BravaisLattice;
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*/
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public class TestMmtfUtils {
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/**
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* Set up the configuration parameters for BioJava.
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*/
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public static AtomCache setUpBioJava() {
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// Set up the atom cache etc
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AtomCache cache = new AtomCache();
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cache.setFiletype(StructureFiletype.CIF);
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FileParsingParameters params = cache.getFileParsingParams();
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params.setCreateAtomBonds(true);
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params.setAlignSeqRes(true);
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params.setParseBioAssembly(true);
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DownloadChemCompProvider cc = new DownloadChemCompProvider();
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ChemCompGroupFactory.setChemCompProvider(cc);
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cc.checkDoFirstInstall();
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cache.setFileParsingParams(params);
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StructureIO.setAtomCache(cache);
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return cache;
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}
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/**
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* Integration test to see that the microheterogenity is being dealt with correctly.
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*
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*/
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@Test
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public void microHeterogenity() throws IOException, StructureException {
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MmtfUtils.setUpBioJava();
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setUpBioJava();
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Structure inputStructure = StructureIO.getStructure("4ck4");
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// Count the number of groups
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Group before = inputStructure.getChains().get(0).getAtomGroup(17);

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