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Test parsing the release date from MMCIF
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biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseHeader.java

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package org.biojava.nbio.structure.io.mmcif;
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import static org.junit.Assert.assertEquals;
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import java.io.IOException;
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import org.biojava.nbio.structure.PDBHeader;
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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.StructureIO;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.junit.Ignore;
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import org.junit.Test;
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/**
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* Test parsing header information from MmCif files.
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*
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* @author Anthony Bradley
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* @author Aleix Lafita
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*
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*/
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public class TestParseMmcifHeader {
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/**
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* Test we can parse R-work and R-free effectively.
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*/
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@Test
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public void testRfactors() throws IOException, StructureException {
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AtomCache atomCache = new AtomCache();
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atomCache.setUseMmCif(true);
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Structure structure = atomCache.getStructure("4cup");
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PDBHeader pdbHeader = structure.getPDBHeader();
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// Check they are the same
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assertEquals(pdbHeader.getRfree(), 0.2078f, 0.000001f);
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assertEquals(pdbHeader.getRwork(), 0.1763f, 0.000001f);
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}
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/**
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* Test parsing dates from MMCIF file version 4.
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*/
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@Test
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public void testDatesV4() throws IOException, StructureException {
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ClassLoader classLoader = this.getClass().getClassLoader();
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String file4 = classLoader.getResource("org/biojava/nbio/structure/io/mmcif/1stp_v4.cif").getPath();
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Structure s = StructureIO.getStructure(file4);
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// The latest modified year should be 2011
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assertEquals(s.getPDBHeader().getModDate().getYear() + 1900, 2011);
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// The release date should be october 1992
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assertEquals(s.getPDBHeader().getRelDate().getMonth() + 1, 10);
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assertEquals(s.getPDBHeader().getRelDate().getYear() + 1900, 1992);
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// The deposition date should be march 1992
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assertEquals(s.getPDBHeader().getDepDate().getMonth() + 1, 3);
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assertEquals(s.getPDBHeader().getDepDate().getYear() + 1900, 1992);
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}
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/**
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* Test parsing dates from MMCIF file version 5.
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*/
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@Test @Ignore
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public void testDatesV5() throws IOException, StructureException {
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ClassLoader classLoader = this.getClass().getClassLoader();
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String file4 = classLoader.getResource("org/biojava/nbio/structure/io/mmcif/1stp_v5.cif").getPath();
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Structure s = StructureIO.getStructure(file4);
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// The latest modified year should be 2011
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assertEquals(s.getPDBHeader().getModDate().getYear() + 1900, 2011);
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// The release date should be october 1992
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assertEquals(s.getPDBHeader().getRelDate().getMonth() + 1, 10);
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assertEquals(s.getPDBHeader().getRelDate().getYear() + 1900, 1992);
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// The deposition date should be march 1992
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assertEquals(s.getPDBHeader().getDepDate().getMonth() + 1, 3);
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assertEquals(s.getPDBHeader().getDepDate().getYear() + 1900, 1992);
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}
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}

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