Skip to content

Commit 0a68908

Browse files
josemduartejosemduarte
committed
Removing loadChemCompInfo, some tests don't pass yet
1 parent e64be0d commit 0a68908

File tree

22 files changed

+97
-303
lines changed

22 files changed

+97
-303
lines changed

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java‎

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,6 @@ public void testGetAtomsConsistency() throws IOException, StructureException{
9999

100100
AtomCache cache = new AtomCache();
101101
FileParsingParameters params = new FileParsingParameters();
102-
params.setLoadChemCompInfo(true);
103102
cache.setFileParsingParams(params);
104103

105104
Structure hivA = cache.getStructure("1hiv.A");
@@ -448,13 +447,11 @@ public void testCAmmCIF() throws StructureException {
448447
AtomCache pdbCache = new AtomCache();
449448
pdbCache.setUseMmCif(false);
450449
FileParsingParameters params = new FileParsingParameters();
451-
params.setLoadChemCompInfo(true);
452450
pdbCache.setFileParsingParams(params);
453451

454452
AtomCache mmcifCache = new AtomCache();
455453
mmcifCache.setUseMmCif(true);
456454
FileParsingParameters params2 = new FileParsingParameters();
457-
params2.setLoadChemCompInfo(true);
458455
mmcifCache.setFileParsingParams(params2);
459456

460457

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java‎

Lines changed: 22 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -49,26 +49,23 @@ protected void setUp() throws Exception {
4949

5050
if ( structure != null )
5151
return;
52-
try {
53-
InputStream inStream = this.getClass().getResourceAsStream("/1a4w.pdb");
54-
assertNotNull(inStream);
5552

56-
PDBFileParser pdbpars = new PDBFileParser();
57-
FileParsingParameters params = new FileParsingParameters();
58-
params.setLoadChemCompInfo(true);
59-
params.setAlignSeqRes(true);
60-
61-
pdbpars.setFileParsingParameters(params);
53+
InputStream inStream = this.getClass().getResourceAsStream("/1a4w.pdb");
54+
assertNotNull(inStream);
55+
56+
PDBFileParser pdbpars = new PDBFileParser();
57+
FileParsingParameters params = new FileParsingParameters();
58+
params.setAlignSeqRes(true);
59+
60+
pdbpars.setFileParsingParameters(params);
61+
62+
structure = pdbpars.parsePDBFile(inStream) ;
6263

63-
structure = pdbpars.parsePDBFile(inStream) ;
64-
} catch (IOException e) {
65-
e.printStackTrace();
66-
}
6764
}
6865

6966

7067

71-
public void test1a4wPDBFile()
68+
public void test1a4wPDBFile() throws IOException
7269
{
7370

7471
// structure = null;
@@ -83,25 +80,21 @@ public void test1a4wPDBFile()
8380

8481

8582
Structure structure2 = null;
86-
try {
87-
InputStream inStream = this.getClass().getResourceAsStream("/1a4w.cif");
88-
assertNotNull(inStream);
8983

90-
MMcifParser pdbpars = new SimpleMMcifParser();
91-
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
92-
FileParsingParameters params = new FileParsingParameters();
93-
params.setLoadChemCompInfo(true);
94-
params.setAlignSeqRes(true);
95-
consumer.setFileParsingParameters(params);
96-
pdbpars.addMMcifConsumer(consumer);
84+
InputStream inStream = this.getClass().getResourceAsStream("/1a4w.cif");
85+
assertNotNull(inStream);
9786

98-
pdbpars.parse(inStream) ;
99-
structure2 = consumer.getStructure();
87+
MMcifParser pdbpars = new SimpleMMcifParser();
88+
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
89+
FileParsingParameters params = new FileParsingParameters();
90+
params.setAlignSeqRes(true);
91+
consumer.setFileParsingParameters(params);
92+
pdbpars.addMMcifConsumer(consumer);
93+
94+
pdbpars.parse(inStream) ;
95+
structure2 = consumer.getStructure();
10096

10197

102-
} catch (IOException e) {
103-
e.printStackTrace();
104-
}
10598

10699
assertNotNull(structure2);
107100

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,6 @@ protected void setUp() throws Exception {
2121
cache.setUseMmCif(true);
2222
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
2323
FileParsingParameters params = cache.getFileParsingParams();
24-
params.setLoadChemCompInfo(true);
2524
params.setUseInternalChainId(true);
2625
cache.setFileParsingParams(params);
2726
StructureIO.setAtomCache(cache);

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,6 @@ public static String compareAlignment(String pdb1, String chain1, String pdb2, S
4949

5050
FileParsingParameters params = new FileParsingParameters();
5151
params.setAlignSeqRes(true);
52-
params.setLoadChemCompInfo(false);
5352
params.setParseCAOnly(true);
5453
pdbpars.setFileParsingParameters(params);
5554

‎biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,6 @@ public class TmpAtomCache
3434
public static AtomCache cache = new AtomCache(tmpDir, tmpDir);
3535
static {
3636
FileParsingParameters params = new FileParsingParameters();
37-
params.setLoadChemCompInfo(true);
3837
params.setAlignSeqRes(true);
3938
params.setParseSecStruc(false);
4039
cache.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);

‎biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -222,7 +222,6 @@ private static Structure readStructure(String pdbId, int bioAssemblyId) {
222222

223223
FileParsingParameters params = new FileParsingParameters();
224224
params.setParseCAOnly(true);
225-
params.setLoadChemCompInfo(true);
226225
params.setAtomCaThreshold(Integer.MAX_VALUE);
227226
cache.setFileParsingParams(params);
228227

‎biojava-structure/src/main/java/demo/DemoAtomCache.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -60,7 +60,6 @@ private static void demoAtomCache() {
6060

6161
FileParsingParameters params = cache.getFileParsingParams();
6262

63-
params.setLoadChemCompInfo(false);
6463
params.setAlignSeqRes(true);
6564
params.setHeaderOnly(false);
6665
params.setParseCAOnly(false);

‎biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -98,7 +98,6 @@ public void basicLoad(PDBFileReader reader, boolean loadChemComp, String pdbId){
9898
params.setAlignSeqRes(true);
9999

100100
//
101-
params.setLoadChemCompInfo(loadChemComp);
102101
// should secondary structure get parsed from the file
103102
params.setParseSecStruc(false);
104103

‎biojava-structure/src/main/java/demo/DemoDomainsplit.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -57,7 +57,6 @@ public void basicLoad(String pdbId){
5757

5858
// should the ATOM and SEQRES residues be aligned when creating the internal data model?
5959
params.setAlignSeqRes(true);
60-
params.setLoadChemCompInfo(true);
6160
// should secondary structure get parsed from the file
6261
params.setParseSecStruc(false);
6362

‎biojava-structure/src/main/java/demo/DemoSCOP.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -118,7 +118,6 @@ public void alignSuperfamily(){
118118
AtomCache cache = new AtomCache();
119119
FileParsingParameters fileparams = new FileParsingParameters() ;
120120
fileparams.setAlignSeqRes(false);
121-
fileparams.setLoadChemCompInfo(true);
122121
fileparams.setParseSecStruc(false);
123122
cache.setFileParsingParams(fileparams);
124123

0 commit comments

Comments
 (0)