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Merge remote-tracking branch 'origin/master' into flaky_test_fixed
2 parents 2cbb6c6 + 65ad15f commit 3a40972

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‎CHANGELOG.md

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@@ -12,6 +12,7 @@ BioJava 6.0.0 (future release)
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* The whole `org.biojava.nbio.structure.rcsb` package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020)
1313
* The whole `org.biojava.nbio.structure.validation` package
1414
* The `org.biojava.nbio.structure.domain.PDBDomainProvider` class to pull domain definitions from legacy RCSB PDB APIs
15+
* Support for automatically fetching dssp files from RCSB (`org.biojava.nbio.structure.secstruc.DSSPParser.fetch()`)
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BioJava 5.4.0
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=============

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

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@@ -27,7 +27,6 @@
2727
import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.util.AtomCache;
2929
import org.biojava.nbio.structure.io.FileParsingParameters;
30-
import org.biojava.nbio.structure.secstruc.DSSPParser;
3130
import org.biojava.nbio.structure.secstruc.SecStrucCalc;
3231
import org.biojava.nbio.structure.secstruc.SecStrucInfo;
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import org.biojava.nbio.structure.secstruc.SecStrucTools;
@@ -64,13 +63,6 @@ public static void main(String[] args) throws IOException,
6463
System.out.println("Author's assignment: ");
6564
printSecStruc(s);
6665

67-
// If the more detailed DSSP prediction is required call this
68-
DSSPParser.fetch(pdbID, s, true);
69-
70-
// Print the assignment residue by residue
71-
System.out.println("DSSP assignment: ");
72-
printSecStruc(s);
73-
7466
// finally use BioJava's built in DSSP-like secondary structure assigner
7567
SecStrucCalc secStrucCalc = new SecStrucCalc();
7668

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java

Lines changed: 1 addition & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -164,13 +164,7 @@ public static void calculateDsspSecondaryStructure(Structure bioJavaStruct) {
164164
ssp.calculate(bioJavaStruct, true);
165165
}
166166
catch(StructureException e) {
167-
LOGGER.warn("Could not calculate secondary structure (error {}). Will try to get a DSSP file from the RCSB web server instead.", e.getMessage());
168-
169-
try {
170-
DSSPParser.fetch(bioJavaStruct.getPDBCode(), bioJavaStruct, true); //download from PDB the DSSP result
171-
} catch(Exception bige){
172-
LOGGER.warn("Could not get a DSSP file from RCSB web server. There will not be secondary structure assignment for this structure ({}). Error: {}", bioJavaStruct.getPDBCode(), bige.getMessage());
173-
}
167+
LOGGER.warn("Could not calculate secondary structure (error {}). Secondary structure annotation will be missing.", e.getMessage());
174168
}
175169
}
176170

‎biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java

Lines changed: 9 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -28,10 +28,8 @@
2828
import java.io.InputStreamReader;
2929
import java.io.Reader;
3030
import java.io.StringReader;
31-
import java.net.URL;
3231
import java.util.ArrayList;
3332
import java.util.List;
34-
import java.util.zip.GZIPInputStream;
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3634
import org.biojava.nbio.structure.Group;
3735
import org.biojava.nbio.structure.ResidueNumber;
@@ -99,32 +97,6 @@ public static List<SecStrucState> parseFile(String dsspPath,
9997
return generalParse(reader, structure, assign);
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}
10199

102-
/**
103-
* Fetch and parse the DSSP file of the specified pdb code
104-
* from the PDB web server and return the secondary structure
105-
* annotation as a List of {@link SecStrucState} objects.
106-
*
107-
* @param pdb path to the DSSP file to parse
108-
* @param structure Structure object associated to the dssp
109-
* @param assign assigns the SS to the structure if true
110-
* @return a List of SS annotation objects
111-
* @throws StructureException
112-
* @throws IOException
113-
*/
114-
public static List<SecStrucState> fetch(String pdb,
115-
Structure structure, boolean assign)
116-
throws IOException, StructureException {
117-
118-
URL url = new URL("http://files.rcsb.org/dssp/" +
119-
pdb.toLowerCase().substring(1, 3) + "/" +
120-
pdb.toLowerCase() + "/" +
121-
pdb.toLowerCase() + ".dssp.gz");
122-
InputStream in = new GZIPInputStream(url.openStream());
123-
Reader read = new InputStreamReader(in);
124-
BufferedReader reader = new BufferedReader(read);
125-
return generalParse(reader, structure, assign);
126-
}
127-
128100
/**
129101
* Parse a DSSP format String and return the secondary structure
130102
* annotation as a List of {@link SecStrucState} objects.
@@ -183,16 +155,16 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
183155

184156
//Parse the Bridge partners - TODO parallel or antiparallel?
185157
String bp = line.substring(25,29).trim();
186-
if (bp != "") {
158+
if (!bp.equals("")) {
187159
BetaBridge bb = new BetaBridge(
188-
index, Integer.valueOf(bp), BridgeType.parallel);
160+
index, Integer.parseInt(bp), BridgeType.parallel);
189161
ss.addBridge(bb);
190162
} else logger.warn("Unable to parse beta Bridge for resn "+index);
191163

192164
bp = line.substring(29,33).trim();
193-
if (bp != "") {
165+
if (!bp.equals("")) {
194166
BetaBridge bb = new BetaBridge(
195-
index, Integer.valueOf(bp), BridgeType.parallel);
167+
index, Integer.parseInt(bp), BridgeType.parallel);
196168
ss.addBridge(bb);
197169
} else logger.warn("Unable to parse beta Bridge for resn "+index);
198170

@@ -203,7 +175,7 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
203175
int b = a + 8;
204176

205177
String val = line.substring(a,b).trim();
206-
if (val == "") {
178+
if (val.equals("")) {
207179
logger.warn("Unable to parse energy for resn "+index);
208180
continue;
209181
}
@@ -212,7 +184,7 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
212184

213185
int partner = Integer.parseInt(p[0]);
214186
if (partner != 0) partner += index;
215-
double energy = Double.valueOf(p[1]) * 1000.0;
187+
double energy = Double.parseDouble(p[1]) * 1000.0;
216188

217189
switch(i){
218190
case 0:
@@ -236,15 +208,15 @@ private static List<SecStrucState> generalParse(BufferedReader reader,
236208

237209
//Angle properties
238210
String val = line.substring(91,97).trim();
239-
if (val != "") ss.setKappa(Float.valueOf(val));
211+
if (!val.equals("")) ss.setKappa(Float.parseFloat(val));
240212
else logger.warn("Unable to parse kappa for resn "+index);
241213

242214
val = line.substring(103,109).trim();
243-
if (val != "") ss.setPhi(Float.valueOf(val));
215+
if (!val.equals("")) ss.setPhi(Float.parseFloat(val));
244216
else logger.warn("Unable to parse phi for resn "+index);
245217

246218
val = line.substring(109,116).trim();
247-
if (val != "") ss.setPsi(Float.valueOf(val));
219+
if (!val.equals("")) ss.setPsi(Float.parseFloat(val));
248220
else logger.warn("Unable to parse psi for resn "+index);
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250222
if (assign) parent.setProperty(Group.SEC_STRUC, ss);

‎biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java

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@@ -21,7 +21,6 @@
2121
package org.biojava.nbio.structure;
2222

2323
import org.biojava.nbio.core.util.FlatFileCache;
24-
import org.biojava.nbio.structure.io.LocalPDBDirectory;
2524
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
2625
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
2726
import org.junit.Test;
@@ -47,39 +46,6 @@ public void testProtectedIDs(){
4746
assertEquals(cc.getId(), id);
4847
}
4948

50-
@Test
51-
public void testRedirectWorks() {
52-
// since August 2017, RCSB is redirecting:
53-
// http://rcsb.org/pdb/files/ligand/HEM.cif ----> http://files.org/ligands/HEM.cif
54-
// see #703
55-
56-
File file = new File(DownloadChemCompProvider.getLocalFileName("HEM"));
57-
file.delete();
58-
59-
DownloadChemCompProvider prov = new DownloadChemCompProvider();
60-
61-
DownloadChemCompProvider.serverBaseUrl = "http://www.rcsb.org/pdb/files/ligand/";
62-
63-
ChemComp cc = prov.getChemComp("HEM");
64-
65-
//System.out.println(file.toString());
66-
67-
assertTrue(file.exists());
68-
69-
// just in case the we did get garbage, let's clean up
70-
file.delete();
71-
72-
// very important: we have a memory cache of files, we need to reset it not to pollute the cache for later tests
73-
FlatFileCache.clear();
74-
75-
assertNotNull(cc);
76-
77-
assertNotNull(cc.getName());
78-
79-
// reset to default URL or otherwise we could affect other tests
80-
DownloadChemCompProvider.serverBaseUrl = DownloadChemCompProvider.DEFAULT_SERVER_URL;
81-
}
82-
8349
@Test
8450
public void testWeDontCacheGarbage() {
8551
// see #703

‎biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java

Lines changed: 2 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -56,10 +56,7 @@ public void testDSSPParser() throws IOException, StructureException {
5656
List<SecStrucState> file = DSSPParser.parseInputStream(new GZIPInputStream(
5757
this.getClass().getResourceAsStream("/org/biojava/nbio/structure/secstruc/"+name+".dssp.gz")), s, false);
5858

59-
// Test fetching from PDB
60-
List<SecStrucState> pdb = DSSPParser.fetch(name, s, false);
61-
62-
// Test predicting, writting and parsing back
59+
// Test predicting, writing and parsing back
6360
SecStrucCalc sec = new SecStrucCalc();
6461
List<SecStrucState> pred = sec.calculate(s, false);
6562

@@ -68,13 +65,10 @@ public void testDSSPParser() throws IOException, StructureException {
6865

6966
assertTrue(
7067
"SS assignment lengths do not match",
71-
file.size() == pdb.size()
72-
&& pred.size() == parseBack.size()
68+
pred.size() == parseBack.size()
7369
&& pred.size() == file.size());
7470

7571
for (int i = 0; i < file.size(); i++) {
76-
assertEquals("SS assignment position " + (i + 1)
77-
+ " does not match", file.get(i), pdb.get(i));
7872
assertEquals("SS assignment position " + (i + 1)
7973
+ " does not match", pred.get(i), parseBack.get(i));
8074
assertEquals("SS assignment position " + (i + 1)

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