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josemduartejosemduarte
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Fixed one more test
1 parent a10a81d commit f27e56a

1 file changed

Lines changed: 25 additions & 34 deletions

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  • biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopTest.java‎

Lines changed: 25 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -24,13 +24,15 @@
2424
import org.biojava.nbio.structure.Group;
2525
import org.biojava.nbio.structure.GroupIterator;
2626
import org.biojava.nbio.structure.Structure;
27+
import org.biojava.nbio.structure.StructureException;
2728
import org.biojava.nbio.structure.align.util.AtomCache;
2829
import org.biojava.nbio.structure.scop.ScopDatabase;
2930
import org.biojava.nbio.structure.scop.ScopDomain;
3031
import org.biojava.nbio.structure.scop.ScopFactory;
3132
import org.biojava.nbio.structure.scop.ScopInstallation;
3233
import org.junit.Test;
3334

35+
import java.io.IOException;
3436
import java.util.List;
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3638
import static org.junit.Assert.*;
@@ -44,7 +46,7 @@ public class ScopTest {
4446
boolean debug = false;
4547

4648
@Test
47-
public void testLocalScop(){
49+
public void testLocalScop() throws IOException, StructureException{
4850

4951
if ( debug ){
5052
System.out.println("local");
@@ -90,7 +92,7 @@ public void testRemoteScop(){
9092
}
9193

9294

93-
private void runSCOPTests(){
95+
private void runSCOPTests() throws IOException, StructureException {
9496

9597
ScopDatabase scop = ScopFactory.getSCOP(ScopFactory.VERSION_1_75);
9698

@@ -121,49 +123,42 @@ private void runSCOPTests(){
121123
ScopDomain d2 = domains1cdg.get(0);
122124
assertEquals("Wrong SCOP Id", "d1cdga1", d2.getScopId());
123125
AtomCache cache = new AtomCache();
124-
try {
125-
Structure s = cache.getStructureForDomain(d2);
126-
/*
126+
127+
Structure s = cache.getStructureForDomain(d2);
128+
/*
127129
The actual SCOP description is A:496-581.
128130
HET MAL A 688 23
129131
HET MAL A 689 23
130132
HET MAL A 690 23
131133
HET CA A 691 1
132134
HET CA A 692 1
133135
Thus, the two hetero-atoms are out of range.
134-
*/
135-
// t
136-
//checkRange(s,"A:496-581");
137-
// now with ligands!
138-
checkRange(s,"A:496-692");
136+
*/
137+
// t
138+
//checkRange(s,"A:496-581");
139+
// now with ligands!
140+
checkRange(s,"A:496-692");
141+
139142

140143

141144

142-
} catch (Exception e){
143-
e.printStackTrace();
144-
fail(e.getMessage());
145-
}
146145

147146

148147
// check a domain with multiple ranges
149148
List<ScopDomain> domains1xzp = scop.getDomainsForPDB("1xzp");
150149
assertTrue(domains1xzp.size() ==4 );
151150

152151

153-
try {
152+
154153

154+
s = cache.getStructureForDomain(domains1xzp.get(0));
155155

156-
Structure s = cache.getStructureForDomain(domains1xzp.get(0));
156+
Chain a = s.getPolyChainByPDB("A");
157157

158-
Chain a = s.getChainByPDB("A");
158+
// since biojava 5.0, there's no ligands in the polymer chains: thus we substract 3 SO4 molecules present in chain A
159+
assertEquals(176 -3,a.getAtomGroups().size());
159160

160-
// now with ligands...
161-
assertEquals(176,a.getAtomGroups().size());
162-
163-
}catch (Exception e){
164-
e.printStackTrace();
165-
fail(e.getMessage());
166-
}
161+
167162

168163
// check insertion codes
169164

@@ -172,17 +167,13 @@ private void runSCOPTests(){
172167
ScopDomain target = scop.getDomainByScopID("d2bq6a1");
173168

174169
assertNotNull(target);
175-
try {
176-
Structure s = cache.getStructureForDomain(target);
170+
171+
s = cache.getStructureForDomain(target);
177172

178-
Chain a = s.getChainByPDB("A");
179-
assertEquals(a.getAtomGroups().size(),52);
180-
checkRange(s,"A:1A-49");
173+
a = s.getPolyChainByPDB("A");
174+
assertEquals(a.getAtomGroups().size(),52);
175+
checkRange(s,"A:1A-49");
181176

182-
}catch (Exception e){
183-
e.printStackTrace();
184-
fail(e.getMessage());
185-
}
186177
}
187178

188179
private void checkRange(Structure s, String range) {
@@ -194,7 +185,7 @@ private void checkRange(Structure s, String range) {
194185
}
195186
assertNotNull(g1);
196187
assertNotNull(g2);
197-
String chainId = g1.getChain().getChainID();
188+
String chainId = g1.getChain().getName();
198189
String rangeTest = chainId + ":"+ g1.getResidueNumber().toString()+"-"+ g2.getResidueNumber().toString();
199190

200191
assertEquals("The expected range and the detected range don't match!", range, rangeTest);

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