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josemduartejosemduarte
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Asserting in right order
1 parent 9ebf1f0 commit 988dee7

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+24
-23
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  • biojava-structure/src/test/java/org/biojava/nbio/structure

1 file changed

+24
-23
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‎biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java‎

Lines changed: 24 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -165,13 +165,13 @@ public void testNucleotideBonds() throws IOException, StructureException {
165165
*/
166166
@Test
167167
public void testHeavyAtomBondMissing() throws IOException, StructureException {
168-
assertEquals(testMissingBonds("3jtm"),0);
169-
assertEquals(testMissingBonds("3jq8"),0);
170-
assertEquals(testMissingBonds("3jq9"),0);
171-
assertEquals(testMissingBonds("3i06"),0);
172-
assertEquals(testMissingBonds("3nu3"),0);
173-
assertEquals(testMissingBonds("3nu4"),0);
174-
assertEquals(testMissingBonds("3nvd"),0);
168+
assertEquals(0, countAtomsWithoutBonds("3jtm"));
169+
assertEquals(0, countAtomsWithoutBonds("3jq8"));
170+
assertEquals(0, countAtomsWithoutBonds("3jq9"));
171+
assertEquals(0, countAtomsWithoutBonds("3i06"));
172+
assertEquals(0, countAtomsWithoutBonds("3nu3"));
173+
assertEquals(0, countAtomsWithoutBonds("3nu4"));
174+
assertEquals(0, countAtomsWithoutBonds("3nvd"));
175175
}
176176

177177

@@ -182,8 +182,8 @@ public void testHeavyAtomBondMissing() throws IOException, StructureException {
182182
*/
183183
@Test
184184
public void testHydrogenToProteinBondMissing() throws IOException, StructureException {
185-
assertEquals(testMissingBonds("4txr"),0);
186-
assertEquals(testMissingBonds("3nvd"),0);
185+
assertEquals(0, countAtomsWithoutBonds("4txr"));
186+
assertEquals(0, countAtomsWithoutBonds("3nvd"));
187187
}
188188

189189
/**
@@ -193,18 +193,19 @@ public void testHydrogenToProteinBondMissing() throws IOException, StructureExce
193193
*/
194194
@Test
195195
public void testAltLocBondMissing() throws IOException, StructureException {
196-
assertEquals(testMissingBonds("4cup"),0);
196+
assertEquals(0, countAtomsWithoutBonds("4cup"));
197197
}
198198

199199
/**
200-
*
200+
* Loops through whole structure counting all atoms (in groups larger than 1 atom)
201+
* that have no bonds.
201202
* @throws IOException
202203
* @throws StructureException
203204
*/
204-
private int testMissingBonds(String pdbId) throws IOException, StructureException {
205+
private int countAtomsWithoutBonds(String pdbId) throws IOException, StructureException {
205206
Structure inputStructure = StructureIO.getStructure(pdbId);
206207
// Loop through the structure
207-
int nonBondedCounter =0;
208+
int nonBondedCounter = 0;
208209
for(int i=0;i<inputStructure.nrModels();i++){
209210
for(Chain c: inputStructure.getChains(i)){
210211
for(Group g: c.getAtomGroups()){
@@ -230,7 +231,7 @@ private int testMissingBonds(String pdbId) throws IOException, StructureExceptio
230231
return nonBondedCounter;
231232
}
232233

233-
private int testBondedToSelf(String pdbId) throws IOException, StructureException {
234+
private int countBondedToSelf(String pdbId) throws IOException, StructureException {
234235
Structure inputStructure = StructureIO.getStructure(pdbId);
235236
int bondedToSelf =0;
236237
for(int i=0;i<inputStructure.nrModels();i++){
@@ -248,12 +249,12 @@ private int testBondedToSelf(String pdbId) throws IOException, StructureExceptio
248249
// Check they all have bonds
249250
for(Atom a: atomsList){
250251
if(a.getBonds()!=null){
251-
for(Bond b: a.getBonds()){
252-
if(b.getAtomA().equals(b.getAtomB())){
253-
bondedToSelf+=1;
252+
for(Bond b: a.getBonds()){
253+
if(b.getAtomA().equals(b.getAtomB())){
254+
bondedToSelf+=1;
255+
}
254256
}
255257
}
256-
}
257258
}
258259
}
259260
}
@@ -299,10 +300,10 @@ public void test1BDX() throws IOException, StructureException {
299300
@Test
300301
public void testDeuterated() throws IOException, StructureException {
301302
// The terminal Hydrogen D3 - is missing (from the CCD)
302-
assertEquals(testMissingBonds("1GKT"),2);
303-
assertEquals(testMissingBonds("1IO5"),2);
303+
assertEquals(2, countAtomsWithoutBonds("1GKT"));
304+
assertEquals(2, countAtomsWithoutBonds("1IO5"));
304305
// All H/D2,H/D3 errors
305-
assertEquals(testMissingBonds("5E5J"),13);
306+
assertEquals(13, countAtomsWithoutBonds("5E5J"));
306307
}
307308

308309
/**
@@ -313,7 +314,7 @@ public void testDeuterated() throws IOException, StructureException {
313314
*/
314315
@Test
315316
public void testWeirdCase() throws IOException, StructureException {
316-
assertEquals(testMissingBonds("1IU6"),6);
317+
assertEquals(6, countAtomsWithoutBonds("1IU6"));
317318
}
318319

319320

@@ -325,7 +326,7 @@ public void testWeirdCase() throws IOException, StructureException {
325326
@Test
326327
public void testSSBonds() throws IOException, StructureException {
327328
for(String pdbCode : new String[]{"3ZXW","1NTY", "4H2I", "2K6D", "2MLM"}){
328-
assertEquals(testBondedToSelf(pdbCode),0);
329+
assertEquals(0, countBondedToSelf(pdbCode));
329330
}
330331
}
331332

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