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.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
29 import jalview.bin.Cache;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceI;
36 import jalview.io.AppletFormatAdapter;
37 import jalview.structure.StructureImportSettings;
39 import java.io.IOException;
40 import java.util.List;
42 import org.testng.annotations.BeforeMethod;
43 import org.testng.annotations.Test;
45 public class PDBfileTest
47 @Test(groups = { "Functional" })
48 public void testIsRna()
50 SequenceI seq = new Sequence("Seq1", "CGAU");
51 assertTrue(PDBfile.isRNA(seq));
53 seq.setSequence("CGAu");
54 assertFalse(PDBfile.isRNA(seq));
56 seq.setSequence("CGAT");
57 assertFalse(PDBfile.isRNA(seq));
59 seq.setSequence("GRSWYFLAVM");
60 assertFalse(PDBfile.isRNA(seq));
64 * Test the 'high level' outputs of parsing. More detailed tests in
69 @Test(groups = { "Functional" })
70 public void testParse() throws IOException
73 * Constructor with file path performs parse()
75 PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
76 AppletFormatAdapter.FILE);
78 assertEquals("3W5V", pf.getId());
79 // verify no alignment annotations created
80 assertNull(getAlignmentAnnotations(pf));
82 assertEquals(4, pf.getChains().size());
83 assertEquals("A", pf.getChains().get(0).id);
84 assertEquals("B", pf.getChains().get(1).id);
85 assertEquals("C", pf.getChains().get(2).id);
86 assertEquals("D", pf.getChains().get(3).id);
88 PDBChain chainA = pf.getChains().get(0);
89 SequenceI seqA = pf.getSeqs().get(0);
91 assertEquals(0, chainA.seqstart); // not set
92 assertEquals(0, chainA.seqend); // not set
93 assertEquals(18, chainA.sequence.getStart());
94 assertEquals(314, chainA.sequence.getEnd());
95 assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
96 assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
97 assertEquals("3W5V|A", chainA.sequence.getName());
98 assertNull(chainA.sequence.getAnnotation());
99 assertEquals(1, seqA.getAllPDBEntries().size());
100 PDBEntry pdb = seqA.getAllPDBEntries().get(0);
101 assertEquals("A", pdb.getChainCode());
102 assertEquals("PDB", pdb.getType());
103 assertEquals("3W5V", pdb.getId());
105 PDBChain chainB = pf.getChains().get(1);
106 assertEquals(1, chainB.sequence.getStart());
107 assertEquals(96, chainB.sequence.getEnd());
108 assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK"));
109 assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT"));
110 assertEquals("3W5V|B", chainB.sequence.getName());
112 PDBChain chainC = pf.getChains().get(2);
113 assertEquals(18, chainC.sequence.getStart());
114 assertEquals(314, chainC.sequence.getEnd());
115 assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
116 assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
117 assertEquals("3W5V|C", chainC.sequence.getName());
119 PDBChain chainD = pf.getChains().get(3);
120 assertEquals(1, chainD.sequence.getStart());
121 assertEquals(96, chainD.sequence.getEnd());
122 assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
123 assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
124 assertEquals("3W5V|D", chainD.sequence.getName());
127 * verify PDB-related data in parsed sequences
129 List<SequenceI> seqs = pf.getSeqs();
130 assertEquals(4, seqs.size());
131 assertEquals("3W5V|A", seqs.get(0).getName());
132 assertEquals("3W5V|B", seqs.get(1).getName());
133 assertEquals("3W5V|C", seqs.get(2).getName());
134 assertEquals("3W5V|D", seqs.get(3).getName());
135 assertEquals(1, seqs.get(0).getAllPDBEntries().size());
136 PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
137 assertEquals("A", pdbe.getChainCode());
138 assertEquals("3W5V", pdbe.getId());
139 assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
143 * Test parsing, with annotations added to the alignment but no secondary
144 * structure prediction
146 * @throws IOException
148 @Test(groups = { "Functional" })
149 public void testParse_withAnnotations_noSS() throws IOException
151 PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
152 AppletFormatAdapter.FILE);
154 AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
155 assertEquals(4, anns.length);
158 * Inspect temp factor annotation for chain A
160 AlignmentAnnotation chainAnnotation = anns[0];
161 assertEquals("Temperature Factor", chainAnnotation.label);
162 // PDBChain constructor changes PDB id to lower case (why?)
163 assertEquals("Temperature Factor for 3w5vA",
164 chainAnnotation.description);
165 assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef);
166 assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph);
167 assertEquals(0f, chainAnnotation.graphMin, 0.001f);
168 assertEquals(40f, chainAnnotation.graphMax, 0.001f);
169 assertEquals(297, chainAnnotation.annotations.length);
170 assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f);
173 * Chain B temp factor
175 chainAnnotation = anns[1];
176 assertEquals("Temperature Factor for 3w5vB",
177 chainAnnotation.description);
178 assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef);
179 assertEquals(96, chainAnnotation.annotations.length);
182 * Chain C temp factor
184 chainAnnotation = anns[2];
185 assertEquals("Temperature Factor for 3w5vC",
186 chainAnnotation.description);
187 assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef);
188 assertEquals(297, chainAnnotation.annotations.length);
191 * Chain D temp factor
193 chainAnnotation = anns[3];
194 assertEquals("Temperature Factor for 3w5vD",
195 chainAnnotation.description);
196 assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef);
197 assertEquals(96, chainAnnotation.annotations.length);
201 * Test parsing including secondary structure annotation using JMol; this test
202 * for the case where flag to add annotations to alignment is set false
204 * @throws IOException
206 @Test(groups = { "Functional" })
207 public void testParse_withJmol_noAnnotations() throws IOException
209 PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
210 AppletFormatAdapter.FILE);
213 * alignment annotations _are_ created anyway (in
214 * AlignSeq.replaceMatchingSeqsWith())
216 final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
217 assertEquals(4, anns.length);
220 * no sequence annotations created - tempFactor annotation is not added
221 * unless the flag to 'addAlignmentAnnotations' is set true
223 for (PDBChain c : pf.getChains())
225 assertNull(c.sequence.getAnnotation());
230 * Test parsing including secondary structure prediction and annotation using
233 * @throws IOException
235 @Test(groups = { "Functional" })
236 public void testParse_withJmolAddAlignmentAnnotations()
239 PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
240 AppletFormatAdapter.FILE);
243 * Alignment annotations for TempFactor, SecStruct, per sequence (chain)
245 AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
246 assertEquals(8, anns.length);
249 * other tests have detailed assertions for Temp Factor annotations
251 assertEquals("Temperature Factor for 3w5vA", anns[1].description);
252 assertEquals("Temperature Factor for 3w5vB", anns[3].description);
253 assertEquals("Temperature Factor for 3w5vC", anns[5].description);
254 assertEquals("Temperature Factor for 3w5vD", anns[7].description);
257 * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
259 assertEquals("Secondary Structure for 3w5vA", anns[0].description);
260 assertEquals("Secondary Structure for 3w5vB", anns[2].description);
261 assertEquals("Secondary Structure for 3w5vC", anns[4].description);
262 assertEquals("Secondary Structure for 3w5vD", anns[6].description);
265 * Verify SS annotations are linked to respective sequences (chains)
267 assertSame(pf.getSeqs().get(0), anns[0].sequenceRef);
268 assertSame(pf.getSeqs().get(1), anns[2].sequenceRef);
269 assertSame(pf.getSeqs().get(2), anns[4].sequenceRef);
270 assertSame(pf.getSeqs().get(3), anns[6].sequenceRef);
273 * Verify a sample of SS predictions
275 for (int i = 0; i < 20; i++)
277 assertNull(anns[0].annotations[i]);
278 assertEquals("E", anns[0].annotations[20].displayCharacter);
279 assertEquals('E', anns[0].annotations[20].secondaryStructure);
280 assertEquals("E", anns[2].annotations[18].displayCharacter);
281 assertEquals("H", anns[2].annotations[23].displayCharacter);
286 * Placeholder for a test of parsing RNA structure with secondary structure
287 * prediction using the Annotate3D service
289 * @throws IOException
292 @Test(groups = { "Functional" }, enabled = false)
293 public void testParse_withAnnotate3D() throws IOException
295 // TODO requires a mock for Annotate3D processing
296 // and/or run as an integration test
297 PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
298 AppletFormatAdapter.FILE);
302 * Helper method to extract parsed annotations from the PDBfile
307 private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)
309 AlignmentI al = new Alignment(pf.getSeqsAsArray());
310 pf.addAnnotations(al);
311 return al.getAlignmentAnnotation();
316 @BeforeMethod(alwaysRun = true)
319 Cache.loadProperties("test/jalview/io/testProps.jvprops");
320 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
321 Boolean.TRUE.toString());
322 Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
323 Boolean.TRUE.toString());
324 Cache.applicationProperties.setProperty("ADD_SS_ANN",
325 Boolean.TRUE.toString());
326 StructureImportSettings.setDefaultStructureFileFormat("PDB");