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josemduartejosemduarte
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Adding some more non-deposited files tests, #305.
Also reverting mmcif parser to not remove purely non-poly chains. Like that it matches what the pdb parser does.
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+69
-6
lines changed

5 files changed

+69
-6
lines changed

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java‎

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -753,11 +753,6 @@ public void documentEnd() {
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logger.warn("Chain with chain id {} (asym id {}) and {} residues, contains only waters. Will ignore the chain because it doesn't fit into the BioJava structure data model.",
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chain.getChainID(),chain.getInternalChainID(),chain.getAtomGroups().size());
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}
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else if (StructureTools.isChainPureNonPolymer(chain) ) {
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logger.warn("Chain with chain id {} (asym id {}) and {} residues, does not seem to be polymeric. Will ignore the chain because it doesn't fit into the BioJava structure data model.",
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chain.getChainID(),chain.getInternalChainID(),chain.getAtomGroups().size());
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it.remove();
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}
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}
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}
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}

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java‎

Lines changed: 69 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -195,7 +195,7 @@ private void checkChains(Structure s) {
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* @throws IOException
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*/
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@Test
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public void testPhenixFile() throws IOException {
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public void testPhenixCifFile() throws IOException {
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InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/4lup_phenix_output.cif.gz"));
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MMcifParser parser = new SimpleMMcifParser();
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@@ -215,6 +215,74 @@ public void testPhenixFile() throws IOException {
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assertNotNull(s);
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assertTrue(s.isCrystallographic());
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// all ligands are into their own chains, so we have 2 proteins, 2 nucleotide chains and 1 ligand chain
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assertEquals(5, s.getChains().size());
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assertEquals(2, s.getCompounds().size());
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}
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@Test
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public void testPhenixPdbFile() throws IOException {
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InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/4lup_phenix_output.pdb.gz"));
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PDBFileParser pdbpars = new PDBFileParser();
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FileParsingParameters params = new FileParsingParameters();
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params.setAlignSeqRes(true);
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pdbpars.setFileParsingParameters(params);
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Structure s = pdbpars.parsePDBFile(inStream) ;
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assertNotNull(s);
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assertTrue(s.isCrystallographic());
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// all ligands are into their own chains, so we have 2 proteins, 2 nucleotide chains and 1 ligand chain
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assertEquals(5, s.getChains().size());
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assertEquals(2, s.getCompounds().size());
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}
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@Test
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public void testPhaserPdbFile() throws IOException {
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InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/4lup_phaser_output.pdb.gz"));
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PDBFileParser pdbpars = new PDBFileParser();
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FileParsingParameters params = new FileParsingParameters();
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params.setAlignSeqRes(true);
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pdbpars.setFileParsingParameters(params);
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Structure s = pdbpars.parsePDBFile(inStream) ;
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assertNotNull(s);
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assertTrue(s.isCrystallographic());
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assertEquals(2, s.getChains().size());
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assertEquals(1, s.getCompounds().size());
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}
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@Test
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public void testRefmacPdbFile() throws IOException {
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InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/rnase_refmac_output.pdb.gz"));
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PDBFileParser pdbpars = new PDBFileParser();
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FileParsingParameters params = new FileParsingParameters();
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params.setAlignSeqRes(true);
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pdbpars.setFileParsingParameters(params);
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Structure s = pdbpars.parsePDBFile(inStream) ;
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assertNotNull(s);
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assertTrue(s.isCrystallographic());
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assertEquals(2, s.getChains().size());
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assertEquals(1, s.getCompounds().size());
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}
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}

‎biojava-structure/src/test/resources/org/biojava/nbio/structure/io/4lup_phaser_output.pdb.gz‎

39.6 KB
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‎biojava-structure/src/test/resources/org/biojava/nbio/structure/io/4lup_phenix_output.pdb.gz‎

116 KB
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‎biojava-structure/src/test/resources/org/biojava/nbio/structure/io/rnase_refmac_output.pdb.gz‎

35.9 KB
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