2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.jmol;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.bin.Cache;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.SequenceI;
31 import jalview.gui.AlignFrame;
32 import jalview.io.AppletFormatAdapter;
33 import jalview.io.FileLoader;
34 import jalview.structure.StructureImportSettings;
35 import jalview.structure.StructureImportSettings.StructureParser;
37 import java.io.IOException;
38 import java.util.Vector;
40 import org.jmol.c.STR;
41 import org.testng.annotations.BeforeMethod;
42 import org.testng.annotations.Test;
44 import MCview.PDBfile;
50 public class JmolParserTest
53 * 1GAQ has been reduced to alpha carbons only
54 * 1QCF is the full PDB file including headers, HETATM etc
56 String[] testFile = new String[] { "./examples/1GAQ.txt",
57 "./test/jalview/ext/jmol/1xyz.pdb",
58 "./test/jalview/ext/jmol/1qcf.pdb" };
61 // a modified and very cut-down extract of 4UJ4
62 String pastePDBDataWithChainBreak =
63 "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
64 // chain B has missing residues; these should all go in the same sequence:
65 "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
66 "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
67 "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
68 "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
69 // switch to chain C; should be a separate sequence
70 "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
71 "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
75 // a very cut-down extract of 1ejg
76 String pdbWithAltLoc =
77 "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
78 "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
79 "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
80 // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
81 "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
82 // including the next altloc causes the unit test to fail but it works with the full file
84 // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
85 "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
88 @BeforeMethod(alwaysRun = true)
91 Cache.loadProperties("test/jalview/io/testProps.jvprops");
92 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
93 Boolean.TRUE.toString());
94 Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
95 Boolean.FALSE.toString());
96 Cache.applicationProperties.setProperty("ADD_SS_ANN",
97 Boolean.TRUE.toString());
98 StructureImportSettings.setDefaultStructureFileFormat("PDB");
99 StructureImportSettings
100 .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
103 @Test(groups = { "Functional" })
104 public void testAlignmentLoader() throws Exception
106 for (String f : testFile)
108 FileLoader fl = new jalview.io.FileLoader(false);
110 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
111 validateSecStrRows(af.getViewport().getAlignment());
115 @Test(groups = { "Functional" })
116 public void testFileParser() throws Exception
118 for (String pdbStr : testFile)
120 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
121 AppletFormatAdapter.FILE);
122 JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
123 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
126 "No sequences extracted from testfile\n"
127 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
128 : "(No warnings raised)"), seqs != null
130 for (SequenceI sq : seqs)
132 assertEquals("JMol didn't process " + pdbStr
133 + " to the same sequence as MCView",
134 sq.getSequenceAsString(), mcseqs.remove(0)
135 .getSequenceAsString());
136 AlignmentI al = new Alignment(new SequenceI[] { sq });
137 validateSecStrRows(al);
143 private void validateSecStrRows(AlignmentI al)
145 if (!al.isNucleotide())
147 for (SequenceI asq : al.getSequences())
150 boolean hasDs = false;
151 while (sq.getDatasetSequence() != null
152 && sq.getAnnotation() == null)
154 sq = sq.getDatasetSequence();
157 checkFirstAAIsAssoc(sq);
160 // also verify if alignment sequence has annotation on it
161 // that is correctly mapped
162 checkFirstAAIsAssoc(asq);
168 private void checkFirstAAIsAssoc(SequenceI sq)
170 assertTrue("No secondary structure assigned for protein sequence for "
172 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
173 && sq.getAnnotation()[0].hasIcons);
175 "Secondary structure not associated for sequence "
176 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
180 * Test parsing a chain with missing residues
184 @Test(groups = { "Functional" })
185 public void testParse_missingResidues() throws Exception
187 PDBfile mctest = new PDBfile(false, false, false,
188 pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
189 JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
190 AppletFormatAdapter.PASTE);
191 Vector<SequenceI> seqs = jtest.getSeqs();
192 Vector<SequenceI> mcseqs = mctest.getSeqs();
194 assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
195 assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
196 assertEquals("VGKA", seqs.get(0).getSequenceAsString());
197 assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
198 assertEquals("SA", seqs.get(1).getSequenceAsString());
199 assertEquals("SA", mcseqs.get(1).getSequenceAsString());
203 * Test parsing a chain with 'altloc' residues
207 @Test(groups = { "Functional" })
208 public void testParse_alternativeResidues() throws Exception
210 PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
211 AppletFormatAdapter.PASTE);
212 JmolParser jtest = new JmolParser(pdbWithAltLoc,
213 AppletFormatAdapter.PASTE);
214 Vector<SequenceI> seqs = jtest.getSeqs();
215 Vector<SequenceI> mcseqs = mctest.getSeqs();
217 assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
218 assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
219 assertEquals("ALC", seqs.get(0).getSequenceAsString());
220 assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
223 @Test(groups = "Functional")
224 public void testSetSecondaryStructure()
226 JmolParser testee = new JmolParser();
227 char[] struct = new char[10];
228 char[] structCode = new char[10];
232 testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
233 testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
234 testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
235 testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
236 testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
237 testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
239 assertEquals(0, struct[0]);
240 assertEquals('H', struct[1]);
241 assertEquals('3', struct[2]);
242 assertEquals('H', struct[3]);
243 assertEquals('P', struct[4]);
244 assertEquals('E', struct[5]);
246 assertEquals(0, structCode[0]);
247 assertEquals('H', structCode[1]);
248 assertEquals('H', structCode[2]);
249 assertEquals('H', structCode[3]);
250 assertEquals('H', structCode[4]);
251 assertEquals('E', structCode[5]);
254 @Test(groups = "Functional")
255 public void testLocalPDBId()
257 JmolParser structureData;
260 structureData = new JmolParser("examples/DNMT1_MOUSE.pdb",
261 AppletFormatAdapter.FILE);
262 assertNotNull(structureData);
263 assertNotNull(structureData.getId());
264 assertEquals(structureData.getId(), "DNMT1_MOUSE.pdb");
265 assertNotNull(structureData.getSeqs());
266 assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
268 structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
270 } catch (IOException e)