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Updating to latest RCSB URLs for 4.2.x #683

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Merged
josemduarte merged 5 commits into from
Jul 6, 2017
Merged

Updating to latest RCSB URLs for 4.2.x #683

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4bdd304
Updating dssp urls to latest RCSB convention
josemduarte Jul 5, 2017
541b61c
Updating to latest RCSB URL
josemduarte Jul 5, 2017
42d628d
Fixing test after remediation
josemduarte Jul 5, 2017
dc7f3ea
Updating ligand URLs to latest RCSB convention
josemduarte Jul 6, 2017
a38c8c8
Better http than https
josemduarte Jul 6, 2017
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Fixing test after remediation
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@josemduarte
josemduarte committed Jul 5, 2017
commit 42d628d2dc3d07582782ecdf983e9ab57e9991ab
10 changes: 5 additions & 5 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,9 @@
*/
package org.biojava.nbio.structure;

import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.assertEquals;

import java.io.IOException;

Expand Down Expand Up @@ -55,7 +55,7 @@ public void test2JA5() throws IOException, StructureException {
// assertTrue(StructureTools.getNrAtoms(s1) == 0);

// SeqRes contains 15 chains, but since we cannot align Chain N to AtomGroups => 14.
assertTrue(s1.getChains().size() == 14);
assertEquals(14, s1.getChains().size());

Chain nChain = null;
try {
Expand Down Expand Up @@ -84,15 +84,15 @@ public void test2JA5noHeader() throws IOException, StructureException {
// This is not applicable anymore, we need to parse atoms to have chains to match.
assertTrue(StructureTools.getNrAtoms(s1) == 0);

// All 15 seqres chains will be store.
assertTrue(s1.getChains().size() == 15);
// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
assertEquals(14, s1.getChains().size());

Chain nChain = null;
try {
nChain = s1.getChainByPDB("N");
} catch (StructureException e){
// this is expected here, since there is no chain N
}
assertNotNull(nChain);
assertNull(nChain);
}
}