Skip to content

Commit 266d835

Browse files
josemduartejosemduarte
committed
Fixing test
1 parent 1042a33 commit 266d835

File tree

1 file changed

+11
-55
lines changed

1 file changed

+11
-55
lines changed

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java‎

Lines changed: 11 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -31,8 +31,7 @@
3131
import java.util.List;
3232
import java.util.Map;
3333

34-
import static org.junit.Assert.assertEquals;
35-
import static org.junit.Assert.assertTrue;
34+
import static org.junit.Assert.*;
3635

3736
public class TestQuaternaryStructureProviders {
3837

@@ -51,35 +50,20 @@ public void test3FAD() throws IOException, StructureException{
5150
public void test5LDH() throws IOException, StructureException{
5251
comparePdbVsMmcif("5LDH",1, 4);
5352

54-
// the pdb file of 5ldh contains only 1 bioassembly, whilst the mmcif contains 2,
55-
// thus we can't test here the comparison between the 2
56-
//testID("5LDH",2, 2);
53+
// Note 1: since v5 remediation there's 4 bioassemblies with numerical ids for 5ldh, no more PAU and XAU
54+
// Note 2: before March 2024 remediation, this entry had 4 assemblies. Now only 1
5755

58-
// since v5 remediation there's 4 bioassemblies with numerical ids for 5ldh, no more PAU and XAU
56+
// bioassembly 1 does exist in mmcif file, let's check that
5957
boolean gotException = false;
6058
try {
6159
AtomCache cache = new AtomCache();
6260
cache.setFiletype(StructureFiletype.CIF);
6361
StructureIO.setAtomCache(cache);
64-
StructureIO.getBiologicalAssembly("5LDH",3);
62+
StructureIO.getBiologicalAssembly("5LDH",1);
6563
} catch (StructureException e) {
6664
gotException = true;
6765
}
68-
69-
assertTrue("Bioassembly 3 for PDB id 5LDH should fail with a StructureException!", !gotException);
70-
71-
// bioassembly 2 does exist in mmcif file, let's check that
72-
gotException = false;
73-
try {
74-
AtomCache cache = new AtomCache();
75-
cache.setFiletype(StructureFiletype.CIF);
76-
StructureIO.setAtomCache(cache);
77-
StructureIO.getBiologicalAssembly("5LDH",2);
78-
} catch (StructureException e) {
79-
gotException = true;
80-
}
81-
assertTrue("Bioassembly 2 for PDB id 5LDH should not fail with a StructureException!", !gotException);
82-
66+
assertFalse("Bioassembly 1 for PDB id 5LDH should exist and not fail with a StructureException!", gotException);
8367
}
8468

8569
@Test
@@ -94,17 +78,9 @@ public void test1A29() throws IOException, StructureException{
9478

9579
@Test
9680
public void test1EI7() throws IOException, StructureException {
97-
9881
comparePdbVsMmcif("1ei7",1, 68);
99-
10082
}
10183

102-
@Test
103-
public void testGetNrBioAssemblies5LDH() throws IOException, StructureException {
104-
assertEquals("There should be 4 bioassemblies for 5LDH, see github issue #230", 4, StructureIO.getBiologicalAssemblies("5LDH").size());
105-
}
106-
107-
10884
/**
10985
* Bioassembly tests for a single PDB entry
11086
* @param pdbId
@@ -115,9 +91,7 @@ public void testGetNrBioAssemblies5LDH() throws IOException, StructureException
11591
*/
11692
private void comparePdbVsMmcif(String pdbId, int bioMolecule, int mmSize) throws IOException, StructureException{
11793

118-
11994
Structure pdbS = getPdbBioAssembly(pdbId, bioMolecule, true);
120-
12195
Structure mmcifS = getMmcifBioAssembly(pdbId, bioMolecule, true);
12296

12397
PDBHeader pHeader = pdbS.getPDBHeader();
@@ -129,16 +103,13 @@ private void comparePdbVsMmcif(String pdbId, int bioMolecule, int mmSize) throws
129103
// mmcif files contain sometimes partial virus assemblies, so they can contain more info than pdb
130104
assertTrue(pHeader.getNrBioAssemblies() <= mHeader.getNrBioAssemblies());
131105

132-
133106
Map<Integer, BioAssemblyInfo> pMap = pHeader.getBioAssemblies();
134107
Map<Integer, BioAssemblyInfo> mMap = mHeader.getBioAssemblies();
135108

136-
137109
assertTrue(pMap.keySet().size()<= mMap.keySet().size());
138110

139111
assertEquals(mmSize, mMap.get(bioMolecule).getMacromolecularSize());
140112

141-
142113
for ( int k : pMap.keySet()) {
143114
assertTrue(mMap.containsKey(k));
144115

@@ -154,45 +125,32 @@ private void comparePdbVsMmcif(String pdbId, int bioMolecule, int mmSize) throws
154125

155126
//assertEquals(pL.size(), mL.size());
156127

157-
158-
for (BiologicalAssemblyTransformation m1 : pL){
159-
128+
for (BiologicalAssemblyTransformation m1 : pL) {
160129
boolean found = false;
161-
for ( BiologicalAssemblyTransformation m2 : mL){
162-
163-
if (! m1.getChainId().equals(m2.getChainId()))
130+
for (BiologicalAssemblyTransformation m2 : mL) {
131+
if (! m1.getChainId().equals(m2.getChainId()))
164132
continue;
165133

166-
if ( ! m1.getTransformationMatrix().epsilonEquals(m2.getTransformationMatrix(), 0.0001))
134+
if (! m1.getTransformationMatrix().epsilonEquals(m2.getTransformationMatrix(), 0.0001))
167135
continue;
168136

169137
found = true;
170-
171138
}
172-
173-
if ( ! found ){
139+
if (! found) {
174140
System.err.println("did not find matching matrix " + m1);
175141
System.err.println(mL);
176142
}
177143
assertTrue(found);
178-
179144
}
180145
}
181146

182-
183147
assertEquals("Not the same number of chains!" , pdbS.size(),mmcifS.size());
184148

185149
Atom[] pdbA = StructureTools.getAllAtomArray(pdbS);
186-
187150
Atom[] mmcifA = StructureTools.getAllAtomArray(mmcifS);
188151

189152
assertEquals(pdbA.length, mmcifA.length);
190-
191153
assertEquals(pdbA[0].toPDB(), mmcifA[0].toPDB());
192-
193-
194-
195-
196154
}
197155

198156
private Structure getPdbBioAssembly(String pdbId, int bioMolecule, boolean multiModel) throws IOException, StructureException {
@@ -213,6 +171,4 @@ private Structure getMmcifBioAssembly(String pdbId, int bioMolecule, boolean mul
213171
return mmcifS;
214172
}
215173

216-
217-
218174
}

0 commit comments

Comments
 (0)