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.assertTrue;
26 import jalview.bin.Cache;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.SequenceI;
30 import jalview.gui.AlignFrame;
31 import jalview.io.AppletFormatAdapter;
32 import jalview.io.FileLoader;
33 import jalview.structure.StructureImportSettings;
34 import jalview.structure.StructureImportSettings.StructureParser;
36 import java.util.Vector;
38 import org.jmol.c.STR;
39 import org.testng.annotations.BeforeMethod;
40 import org.testng.annotations.Test;
42 import MCview.PDBfile;
48 public class JmolParserTest
51 * 1GAQ has been reduced to alpha carbons only
52 * 1QCF is the full PDB file including headers, HETATM etc
54 String[] testFile = new String[] { "./examples/1GAQ.txt",
55 "./test/jalview/ext/jmol/1xyz.pdb",
56 "./test/jalview/ext/jmol/1qcf.pdb" };
59 // a modified and very cut-down extract of 4UJ4
60 String pastePDBDataWithChainBreak =
61 "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
62 // chain B has missing residues; these should all go in the same sequence:
63 "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
64 "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
65 "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
66 "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
67 // switch to chain C; should be a separate sequence
68 "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
69 "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
73 // a very cut-down extract of 1ejg
74 String pdbWithAltLoc =
75 "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
76 "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
77 "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
78 // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
79 "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
80 // including the next altloc causes the unit test to fail but it works with the full file
82 // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
83 "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
86 @BeforeMethod(alwaysRun = true)
89 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
90 Boolean.TRUE.toString());
91 Cache.applicationProperties.setProperty("ADD_SS_ANN",
92 Boolean.TRUE.toString());
93 StructureImportSettings.setDefaultStructureFileFormat("PDB");
94 StructureImportSettings
95 .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
98 @Test(groups = { "Functional" })
99 public void testAlignmentLoader() throws Exception
101 for (String f : testFile)
103 FileLoader fl = new jalview.io.FileLoader(false);
105 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
106 validateSecStrRows(af.getViewport().getAlignment());
110 @Test(groups = { "Functional" })
111 public void testFileParser() throws Exception
113 for (String pdbStr : testFile)
115 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
116 AppletFormatAdapter.FILE);
117 JmolParser jtest = new JmolParser(false, false, false, pdbStr,
118 jalview.io.AppletFormatAdapter.FILE);
119 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
122 "No sequences extracted from testfile\n"
123 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
124 : "(No warnings raised)"), seqs != null
126 for (SequenceI sq : seqs)
128 assertEquals("JMol didn't process " + pdbStr
129 + " to the same sequence as MCView",
130 sq.getSequenceAsString(), mcseqs.remove(0)
131 .getSequenceAsString());
132 AlignmentI al = new Alignment(new SequenceI[] { sq });
133 validateSecStrRows(al);
139 private void validateSecStrRows(AlignmentI al)
141 if (!al.isNucleotide())
143 for (SequenceI asq : al.getSequences())
146 boolean hasDs = false;
147 while (sq.getDatasetSequence() != null
148 && sq.getAnnotation() == null)
150 sq = sq.getDatasetSequence();
153 checkFirstAAIsAssoc(sq);
156 // also verify if alignment sequence has annotation on it
157 // that is correctly mapped
158 checkFirstAAIsAssoc(asq);
164 private void checkFirstAAIsAssoc(SequenceI sq)
166 assertTrue("No secondary structure assigned for protein sequence.",
167 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
168 && sq.getAnnotation()[0].hasIcons);
170 "Secondary structure not associated for sequence "
171 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
175 * Test parsing a chain with missing residues
179 @Test(groups = { "Functional" })
180 public void testParse_missingResidues() throws Exception
182 PDBfile mctest = new PDBfile(false, false, false,
183 pastePDBDataWithChainBreak,
184 AppletFormatAdapter.PASTE);
185 boolean annotFromStructure = false;
186 boolean localSecondaryStruct = false;
187 boolean serviceSecondaryStruct = false;
188 JmolParser jtest = new JmolParser(annotFromStructure,
189 localSecondaryStruct, serviceSecondaryStruct,
190 pastePDBDataWithChainBreak,
191 jalview.io.AppletFormatAdapter.PASTE);
192 Vector<SequenceI> seqs = jtest.getSeqs();
193 Vector<SequenceI> mcseqs = mctest.getSeqs();
195 assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
196 assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
197 assertEquals("VGKA", seqs.get(0).getSequenceAsString());
198 assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
199 assertEquals("SA", seqs.get(1).getSequenceAsString());
200 assertEquals("SA", mcseqs.get(1).getSequenceAsString());
204 * Test parsing a chain with 'altloc' residues
208 @Test(groups = { "Functional" })
209 public void testParse_alternativeResidues() throws Exception
211 PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
212 AppletFormatAdapter.PASTE);
213 boolean annotFromStructure = false;
214 boolean localSecondaryStruct = false;
215 boolean serviceSecondaryStruct = false;
216 JmolParser jtest = new JmolParser(annotFromStructure,
217 localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
218 jalview.io.AppletFormatAdapter.PASTE);
219 Vector<SequenceI> seqs = jtest.getSeqs();
220 Vector<SequenceI> mcseqs = mctest.getSeqs();
222 assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
223 assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
224 assertEquals("ALC", seqs.get(0).getSequenceAsString());
225 assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
228 @Test(groups = "Functional")
229 public void testSetSecondaryStructure()
231 JmolParser testee = new JmolParser();
232 char[] struct = new char[10];
233 char[] structCode = new char[10];
237 testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
238 testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
239 testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
240 testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
241 testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
242 testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
244 assertEquals(0, struct[0]);
245 assertEquals('H', struct[1]);
246 assertEquals('3', struct[2]);
247 assertEquals('H', struct[3]);
248 assertEquals('P', struct[4]);
249 assertEquals('E', struct[5]);
251 assertEquals(0, structCode[0]);
252 assertEquals('H', structCode[1]);
253 assertEquals('H', structCode[2]);
254 assertEquals('H', structCode[3]);
255 assertEquals('H', structCode[4]);
256 assertEquals('E', structCode[5]);