*/
public class PDBFileWithJmolTest
{
+ /*
+ * 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" }; // ,
- // "./examples/DNMT1_MOUSE.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
+
+ //@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(alwaysRun = true)
public void setUp()
"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());
+ }
}