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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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2 changes: 1 addition & 1 deletion ...structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
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Expand Up @@ -67,7 +67,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {

public static final String CHEM_COMP_CACHE_DIRECTORY = "chemcomp";

public static final String SERVER_LOCATION = "http://www.rcsb.org/pdb/files/ligand/";
public static final String SERVER_LOCATION = "http://files.rcsb.org/ligands/download/";


private static File path;
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8 changes: 6 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
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Expand Up @@ -31,6 +31,7 @@
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.GZIPInputStream;

import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.ResidueNumber;
Expand Down Expand Up @@ -95,8 +96,11 @@ public static List<SecStrucState> fetch(String pdb,
Structure structure, boolean assign)
throws IOException, StructureException {

InputStream in = new URL("http://www.rcsb.org/pdb/files/"+
pdb+".dssp").openStream();
URL url = new URL("http://files.rcsb.org/dssp/" +
pdb.toLowerCase().substring(1, 3) + "/" +
pdb.toLowerCase() + "/" +
pdb + ".dssp.gz");
InputStream in = new GZIPInputStream(url.openStream());
Reader read = new InputStreamReader(in);
BufferedReader reader = new BufferedReader(read);
return generalParse(reader, structure, assign);
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10 changes: 5 additions & 5 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
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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);
}
}
2 changes: 1 addition & 1 deletion biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
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Expand Up @@ -101,7 +101,7 @@ public void testURLParameters() throws StructureException, IOException {
assertEquals("wrong length for chainId=A", 94, StructureTools.getRepresentativeAtomArray(reduced).length);

try {
url = new URL("http://www.rcsb.org/pdb/files/1B8G.pdb.gz");
url = new URL("http://files.rcsb.org/download/1B8G.pdb.gz");
id = new URLIdentifier(url);

full = id.loadStructure(cache);
Expand Down