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GeezerVison is showing github.com — Merge remote-tracking branch 'upstream/master' into bcif-integration · biojava/biojava@16792bd

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  • CHANGELOG.md
  • biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry
    • TestQuatSymmetryDetectorExamples.java
  • biojava-structure/src
    • main/java
      • demo
        • DemoLoadSecStruc.java
      • org/biojava/nbio/structure
        • PDBStatus.java
        • io
          • LocalPDBDirectory.java
          • mmtf
            • MmtfStructureReader.java
            • MmtfUtils.java
        • secstruc
          • DSSPParser.java
    • test/java/org/biojava/nbio/structure
      • PDBStatusTest.java
      • TestDownloadChemCompProvider.java
      • secstruc
        • TestDSSPParser.java
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‎CHANGELOG.md‎

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+3Lines changed: 3 additions & 0 deletions
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Original file line numberDiff line numberDiff line change
@@ -12,6 +12,9 @@ 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)
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* The whole `org.biojava.nbio.structure.validation` package
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* 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()`)
16+
* `org.biojava.nbio.structure.PDBStatus`: simplified `Status` enum to 3 states, with OBSOLETE now called REMOVED
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* `org.biojava.nbio.structure.PDBStatus`: removed `getReplacement` and `getReplaces`
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BioJava 5.4.0
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=============
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java‎

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+2-2Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -241,7 +241,7 @@ public void testLocal() throws IOException, StructureException {
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testIds.add("BIO:3JC9:1");
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testStoichiometries.add("A12B12C12D12E12F12G5H2");
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localSymmetries = new HashMap<>();
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localSymmetries.put("A12C12D12E12F12H2","C2");
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localSymmetries.put("A12B12C12D12E12H2","C2");
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localSymmetries.put("A12B12C12D12E12F12","C12");
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localSymmetries.put("G5","H");
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testLocalSymmetries.add(localSymmetries);
@@ -269,7 +269,7 @@ public void testLocal() throws IOException, StructureException {
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for (QuatSymmetryResults local:foundLocal) {
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logger.info("Found stoichiometry "+local.getStoichiometry().toString()+" with symmetry "+local.getSymmetry());
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assertTrue("Stoichiometry "+local.getStoichiometry().toString()+" not expected for "+testIds.get(iTest),
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refLocal.keySet().contains(local.getStoichiometry().toString()));
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refLocal.containsKey(local.getStoichiometry().toString()));
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assertEquals("Symmetry "+local.getSymmetry()+" with stoichiometry "+local.getStoichiometry().toString()+
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" not expected for "+testIds.get(iTest),
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‎biojava-structure/src/main/java/demo/DemoLoadSecStruc.java‎

Copy file name to clipboardExpand all lines: biojava-structure/src/main/java/demo/DemoLoadSecStruc.java
-8Lines changed: 0 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,6 @@
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import org.biojava.nbio.structure.StructureFiletype;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.secstruc.DSSPParser;
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import org.biojava.nbio.structure.secstruc.SecStrucCalc;
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import org.biojava.nbio.structure.secstruc.SecStrucInfo;
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import org.biojava.nbio.structure.secstruc.SecStrucTools;
@@ -65,13 +64,6 @@ public static void main(String[] args) throws IOException,
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System.out.println("Author's assignment: ");
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printSecStruc(s);
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// If the more detailed DSSP prediction is required call this
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DSSPParser.fetch(pdbID, s, true);
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// Print the assignment residue by residue
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System.out.println("DSSP assignment: ");
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printSecStruc(s);
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// finally use BioJava's built in DSSP-like secondary structure assigner
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SecStrucCalc secStrucCalc = new SecStrucCalc();
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