import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.util.Vector;
-
-import MCview.PDBfile;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
+import java.util.Vector;
+
+import org.jmol.c.STR;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
+
/**
* @author jimp
*
*/
public class PDBFileWithJmolTest
{
- String[] testFile = new String[]
- { "./examples/1GAQ.txt", "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+ /*
+ * 1GAQ has been reduced to alpha carbons only
+ * 1QCF is the full PDB file including headers, HETATM etc
+ */
+ String[] testFile = new String[] { "./examples/1GAQ.txt",
+ "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+
+ //@formatter:off
+ // a modified and very cut-down extract of 4UJ4
+ String pdbWithChainBreak =
+ "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
+ // chain B has missing residues; these should all go in the same sequence:
+ "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
+ "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
+ "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
+ "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
+ // switch to chain C; should be a separate sequence
+ "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
+ "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
+ //@formatter:on
- // "./examples/DNMT1_MOUSE.pdb"
- // };
+ //@formatter:off
+ // a very cut-down extract of 1ejg
+ String pdbWithAltLoc =
+ "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
+ "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
+ "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
+ // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
+ "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
+ // including the next altloc causes the unit test to fail but it works with the full file
+ // not sure why!
+ // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
+ "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
+ //@formatter:on
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
}
- @Test
+ @Test(groups = { "Functional" })
public void testAlignmentLoader() throws Exception
{
for (String f : testFile)
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testFileParser() throws Exception
{
for (String pdbStr : testFile)
+ " to the same sequence as MCView",
sq.getSequenceAsString(), mcseqs.remove(0)
.getSequenceAsString());
- AlignmentI al = new Alignment(new SequenceI[]
- { sq });
+ AlignmentI al = new Alignment(new SequenceI[] { sq });
validateSecStrRows(al);
}
}
}
-
private void validateSecStrRows(AlignmentI al)
{
if (!al.isNucleotide())
"Secondary structure not associated for sequence "
+ sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
}
+
+ /**
+ * Test parsing a chain with missing residues
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testParse_missingResidues() throws Exception
+ {
+ PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
+ AppletFormatAdapter.PASTE);
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithChainBreak,
+ jalview.io.AppletFormatAdapter.PASTE);
+ Vector<SequenceI> seqs = jtest.getSeqs();
+ Vector<SequenceI> mcseqs = mctest.getSeqs();
+
+ assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
+ assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
+ assertEquals("VGKA", seqs.get(0).getSequenceAsString());
+ assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
+ assertEquals("SA", seqs.get(1).getSequenceAsString());
+ assertEquals("SA", mcseqs.get(1).getSequenceAsString());
+ }
+
+ /**
+ * Test parsing a chain with 'altloc' residues
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testParse_alternativeResidues() throws Exception
+ {
+ PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
+ AppletFormatAdapter.PASTE);
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithAltLoc,
+ jalview.io.AppletFormatAdapter.PASTE);
+ Vector<SequenceI> seqs = jtest.getSeqs();
+ Vector<SequenceI> mcseqs = mctest.getSeqs();
+
+ assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
+ assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
+ assertEquals("ALC", seqs.get(0).getSequenceAsString());
+ assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
+ }
+
+ @Test(groups = "Functional")
+ public void testSetSecondaryStructure()
+ {
+ PDBFileWithJmol testee = new PDBFileWithJmol();
+ char[] struct = new char[10];
+ char[] structCode = new char[10];
+ struct[0] = '1';
+ structCode[0] = '1';
+
+ testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
+ testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
+ testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
+
+ assertEquals(0, struct[0]);
+ assertEquals('H', struct[1]);
+ assertEquals('3', struct[2]);
+ assertEquals('H', struct[3]);
+ assertEquals('P', struct[4]);
+ assertEquals('E', struct[5]);
+
+ assertEquals(0, structCode[0]);
+ assertEquals('H', structCode[1]);
+ assertEquals('H', structCode[2]);
+ assertEquals('H', structCode[3]);
+ assertEquals('H', structCode[4]);
+ assertEquals('E', structCode[5]);
+ }
}
git://source.jalview.org / jalview.git / blobdiff