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;
35 import java.util.Vector;
37 import org.jmol.c.STR;
38 import org.testng.annotations.BeforeMethod;
39 import org.testng.annotations.Test;
41 import MCview.PDBfile;
47 public class JmolParserTest
50 * 1GAQ has been reduced to alpha carbons only
51 * 1QCF is the full PDB file including headers, HETATM etc
53 String[] testFile = new String[] { "./examples/1GAQ.txt",
54 "./test/jalview/ext/jmol/1xyz.pdb",
55 "./test/jalview/ext/jmol/1qcf.pdb" };
58 // a modified and very cut-down extract of 4UJ4
59 String pastePDBDataWithChainBreak =
60 "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
61 // chain B has missing residues; these should all go in the same sequence:
62 "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
63 "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
64 "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
65 "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
66 // switch to chain C; should be a separate sequence
67 "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
68 "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
72 // a very cut-down extract of 1ejg
73 String pdbWithAltLoc =
74 "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
75 "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
76 "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
77 // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
78 "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
79 // including the next altloc causes the unit test to fail but it works with the full file
81 // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
82 "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
85 @BeforeMethod(alwaysRun = true)
88 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
89 Boolean.TRUE.toString());
90 Cache.applicationProperties.setProperty("ADD_SS_ANN",
91 Boolean.TRUE.toString());
92 StructureImportSettings.setDefaultStructureFileFormat("PDB");
95 @Test(groups = { "Functional" })
96 public void testAlignmentLoader() throws Exception
98 for (String f : testFile)
100 FileLoader fl = new jalview.io.FileLoader(false);
102 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
103 validateSecStrRows(af.getViewport().getAlignment());
107 @Test(groups = { "Functional" })
108 public void testFileParser() throws Exception
110 for (String pdbStr : testFile)
112 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
113 AppletFormatAdapter.FILE);
114 JmolParser jtest = new JmolParser(false, false, false, pdbStr,
115 jalview.io.AppletFormatAdapter.FILE);
116 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
119 "No sequences extracted from testfile\n"
120 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
121 : "(No warnings raised)"), seqs != null
123 for (SequenceI sq : seqs)
125 assertEquals("JMol didn't process " + pdbStr
126 + " to the same sequence as MCView",
127 sq.getSequenceAsString(), mcseqs.remove(0)
128 .getSequenceAsString());
129 AlignmentI al = new Alignment(new SequenceI[] { sq });
130 validateSecStrRows(al);
136 private void validateSecStrRows(AlignmentI al)
138 if (!al.isNucleotide())
140 for (SequenceI asq : al.getSequences())
143 boolean hasDs = false;
144 while (sq.getDatasetSequence() != null
145 && sq.getAnnotation() == null)
147 sq = sq.getDatasetSequence();
150 checkFirstAAIsAssoc(sq);
153 // also verify if alignment sequence has annotation on it
154 // that is correctly mapped
155 checkFirstAAIsAssoc(asq);
161 private void checkFirstAAIsAssoc(SequenceI sq)
163 assertTrue("No secondary structure assigned for protein sequence.",
164 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
165 && sq.getAnnotation()[0].hasIcons);
167 "Secondary structure not associated for sequence "
168 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
172 * Test parsing a chain with missing residues
176 @Test(groups = { "Functional" })
177 public void testParse_missingResidues() throws Exception
179 PDBfile mctest = new PDBfile(false, false, false,
180 pastePDBDataWithChainBreak,
181 AppletFormatAdapter.PASTE);
182 boolean annotFromStructure = false;
183 boolean localSecondaryStruct = false;
184 boolean serviceSecondaryStruct = false;
185 JmolParser jtest = new JmolParser(annotFromStructure,
186 localSecondaryStruct, serviceSecondaryStruct,
187 pastePDBDataWithChainBreak,
188 jalview.io.AppletFormatAdapter.PASTE);
189 Vector<SequenceI> seqs = jtest.getSeqs();
190 Vector<SequenceI> mcseqs = mctest.getSeqs();
192 assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
193 assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
194 assertEquals("VGKA", seqs.get(0).getSequenceAsString());
195 assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
196 assertEquals("SA", seqs.get(1).getSequenceAsString());
197 assertEquals("SA", mcseqs.get(1).getSequenceAsString());
201 * Test parsing a chain with 'altloc' residues
205 @Test(groups = { "Functional" })
206 public void testParse_alternativeResidues() throws Exception
208 PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
209 AppletFormatAdapter.PASTE);
210 boolean annotFromStructure = false;
211 boolean localSecondaryStruct = false;
212 boolean serviceSecondaryStruct = false;
213 JmolParser jtest = new JmolParser(annotFromStructure,
214 localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
215 jalview.io.AppletFormatAdapter.PASTE);
216 Vector<SequenceI> seqs = jtest.getSeqs();
217 Vector<SequenceI> mcseqs = mctest.getSeqs();
219 assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
220 assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
221 assertEquals("ALC", seqs.get(0).getSequenceAsString());
222 assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
225 @Test(groups = "Functional")
226 public void testSetSecondaryStructure()
228 JmolParser testee = new JmolParser();
229 char[] struct = new char[10];
230 char[] structCode = new char[10];
234 testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
235 testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
236 testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
237 testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
238 testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
239 testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
241 assertEquals(0, struct[0]);
242 assertEquals('H', struct[1]);
243 assertEquals('3', struct[2]);
244 assertEquals('H', struct[3]);
245 assertEquals('P', struct[4]);
246 assertEquals('E', struct[5]);
248 assertEquals(0, structCode[0]);
249 assertEquals('H', structCode[1]);
250 assertEquals('H', structCode[2]);
251 assertEquals('H', structCode[3]);
252 assertEquals('H', structCode[4]);
253 assertEquals('E', structCode[5]);