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Sebastian Bittrich
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moves some tests to integration
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerImplTest.java‎

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package org.biojava.nbio.structure.test.io.cif;
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.io.*;
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import org.junit.Test;
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import org.rcsb.cif.CifReader;
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import org.rcsb.cif.model.CifFile;
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import org.rcsb.cif.model.Column;
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import org.rcsb.cif.model.ValueKind;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.List;
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import java.util.Locale;
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import java.util.Objects;
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import java.util.zip.GZIPInputStream;
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import static org.junit.Assert.*;
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public class CifFileConsumerImplTest {
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private static boolean headerOnly;
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private static boolean binary;
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@Test
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public void testLoad() throws IOException {
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headerOnly = false;
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doTestLoad();
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}
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@Test
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public void testLoadHeaderOnly() throws IOException {
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headerOnly = true;
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doTestLoad();
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}
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@Test
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public void testLoadBinary() throws IOException {
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headerOnly = false;
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binary = true;
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doTestLoad();
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}
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@Test
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public void testLoadHeaderOnlyBinary() throws IOException {
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headerOnly = true;
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binary = true;
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doTestLoad();
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}
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private void doTestLoad() throws IOException {
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// test a simple protein
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comparePDB2cif("5pti","A");
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// test a protein with modified residues
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comparePDB2cif("1a4w","L");
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comparePDB2cif("1a4w","H");
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comparePDB2cif("1a4w","I");
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//non-standard encoded amino acid
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comparePDB2cif("1fdo","A");
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// test a DNA binding protein
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comparePDB2cif("1j59","A");
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comparePDB2cif("1j59","E");
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// test a NMR protein
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comparePDB2cif("2kc9","A");
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}
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private void comparePDB2cif(String id, String chainId) throws IOException {
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String fileName = binary ? "/" + id + ".bcif" : "/" + id + ".cif";
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System.out.println(fileName);
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InputStream inStream = getClass().getResourceAsStream(fileName);
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assertNotNull("Could not find file " + fileName + ". Config problem?" , inStream);
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LocalPDBDirectory reader = binary ? new BcifFileReader() : new CifFileReader();
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FileParsingParameters params = new FileParsingParameters();
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params.setHeaderOnly(headerOnly);
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reader.setFileParsingParameters(params);
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Structure cifStructure = reader.getStructure(inStream);
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assertNotNull(cifStructure);
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// load the PDB file via the PDB parser
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Structure pdbStructure;
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InputStream pinStream = this.getClass().getResourceAsStream("/" + id + ".pdb");
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assertNotNull(inStream);
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PDBFileParser pdbParser = new PDBFileParser();
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pdbParser.setFileParsingParameters(params);
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pdbStructure = pdbParser.parsePDBFile(pinStream);
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assertNotNull(pdbStructure);
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// check NMR data
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assertEquals(id + ": the isNMR flag is not the same!",
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pdbStructure.isNmr(),
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cifStructure.isNmr());
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if ( pdbStructure.isNmr()){
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assertEquals(id + ": the nr of NMR models is not the same!",
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pdbStructure.nrModels(),
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pdbStructure.nrModels());
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checkNMR(pdbStructure);
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checkNMR(cifStructure);
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}
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Chain a_pdb = pdbStructure.getPolyChainByPDB(chainId);
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Chain a_cif = cifStructure.getPolyChainByPDB(chainId);
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String pdb_SEQseq = a_pdb.getSeqResSequence();
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String cif_SEQseq = a_cif.getSeqResSequence();
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assertEquals(id + ": the SEQRES sequences don't match!",
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pdb_SEQseq,
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cif_SEQseq);
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assertEquals(id + ": The nr of ATOM groups does not match!",
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a_pdb.getAtomGroups(GroupType.AMINOACID).size(),
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a_cif.getAtomGroups(GroupType.AMINOACID).size());
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// actually this check not necessarily works, since there can be waters in PDB that we don;t deal with yet in cif...
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for (int i = 0 ; i < a_pdb.getAtomGroups(GroupType.AMINOACID).size(); i++){
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Group gp = a_pdb.getAtomGroups(GroupType.AMINOACID).get(i);
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List<Group> cifGroups = a_cif.getAtomGroups(GroupType.AMINOACID);
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Group gc = cifGroups.get(i);
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checkGroups(gp, gc);
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}
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String pdb_seq = a_pdb.getAtomSequence();
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String cif_seq = a_cif.getAtomSequence();
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assertEquals("the sequences obtained from PDB and mmCif don't match!", pdb_seq, cif_seq);
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List<DBRef> pdb_dbrefs= pdbStructure.getDBRefs();
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List<DBRef> cif_dbrefs= cifStructure.getDBRefs();
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assertEquals("nr of DBrefs found does not match!", pdb_dbrefs.size(), cif_dbrefs.size());
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DBRef p = pdb_dbrefs.get(0);
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DBRef c = cif_dbrefs.get(0);
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String pdb_dbref = p.toPDB();
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String cif_dbref = c.toPDB();
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assertEquals("DBRef is not equal", pdb_dbref, cif_dbref);
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PDBHeader h1 = pdbStructure.getPDBHeader();
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PDBHeader h2 = cifStructure.getPDBHeader();
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if (!h1.toPDB().toUpperCase().equals(h2.toPDB().toUpperCase())) {
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System.err.println(h1.toPDB());
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System.err.println(h2.toPDB());
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assertEquals(h1.toPDB(), h2.toPDB());
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}
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assertEquals("the PDBHeader.toPDB representation is not equivalent",
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h1.toPDB().toUpperCase(),
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h2.toPDB().toUpperCase());
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}
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private void checkGroups(Group g1, Group g2){
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String pdbId1 = g1.getChain().getStructure().getPDBCode();
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String pdbId2 = g1.getChain().getStructure().getPDBCode();
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assertEquals(pdbId1, pdbId2);
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assertEquals(g1.getType(), g2.getType());
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assertEquals(g1.getResidueNumber().getSeqNum(), g2.getResidueNumber().getSeqNum());
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assertEquals(g1.getResidueNumber().getInsCode(), g2.getResidueNumber().getInsCode());
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assertEquals(g1.getPDBName(), g2.getPDBName());
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assertEquals(g1.has3D(), g2.has3D());
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assertEquals(g1.hasAltLoc(), g2.hasAltLoc());
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assertEquals(pdbId1 + ":" + g1 + " - " + pdbId2 + ":"+ g2, g1.getAltLocs().size(), g2.getAltLocs().size());
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assertEquals(pdbId1 + ":" + g1 + " - " + pdbId2 + ":"+ g2, g1.getAtoms().size(), g2.getAtoms().size());
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if (g1.has3D()){
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Atom a1 = g1.getAtom(0);
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Atom a2 = g2.getAtom(0);
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if ( a1 == null)
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fail("could not get atom for group " + g1);
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if (a2 == null)
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fail("could not get atom for group " + g2);
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assertEquals(a1.getX(),a2.getX(), 0.0001);
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assertEquals(a1.getOccupancy(), a2.getOccupancy(), 0.0001);
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assertEquals(a1.getTempFactor(), a2.getTempFactor(), 0.0001);
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assertEquals(a1.getName(), a2.getName());
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}
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}
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private void checkNMR(Structure s){
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assertTrue(s.isNmr());
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int models = s.nrModels();
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assertTrue(models > 0);
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List<Chain> model0 = s.getModel(0);
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// compare with all others
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for (int i = 1 ; i < models; i++){
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List<Chain> modelX = s.getModel(i);
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assertEquals(model0.size(),modelX.size());
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// compare lengths:
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for (int j=0 ; j< model0.size(); j++){
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Chain c1 = model0.get(j);
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Chain cx = modelX.get(j);
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assertEquals(c1.getAtomLength(), cx.getAtomLength());
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assertEquals(c1.getAtomSequence(), cx.getAtomSequence());
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assertEquals(c1.getAtomGroups(GroupType.AMINOACID).size(), cx.getAtomGroups(GroupType.AMINOACID).size());
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assertEquals(c1.getAtomGroups(GroupType.NUCLEOTIDE).size(), cx.getAtomGroups(GroupType.NUCLEOTIDE).size());
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assertEquals(c1.getAtomGroups(GroupType.HETATM).size(), cx.getAtomGroups(GroupType.HETATM).size());
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}
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}
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}
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}

biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java renamed to biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierImplTest.java

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package org.biojava.nbio.structure.io.cif;
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package org.biojava.nbio.structure.test.io.cif;
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.cif.CifFileConverter;
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import org.junit.Test;
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import org.rcsb.cif.CifReader;
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import org.rcsb.cif.CifWriter;

biojava-structure/src/test/resources/1a4w.bcif renamed to biojava-integrationtest/src/test/resources/1a4w.bcif

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biojava-structure/src/test/resources/1fdo.bcif renamed to biojava-integrationtest/src/test/resources/1fdo.bcif

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biojava-structure/src/test/resources/1j59.bcif renamed to biojava-integrationtest/src/test/resources/1j59.bcif

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biojava-structure/src/test/resources/2kc9.bcif renamed to biojava-integrationtest/src/test/resources/2kc9.bcif

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biojava-structure/src/test/resources/5pti.bcif renamed to biojava-integrationtest/src/test/resources/5pti.bcif

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