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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java‎

Lines changed: 0 additions & 295 deletions
This file was deleted.

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -24,11 +24,11 @@
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
27+
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
28+
import org.biojava.nbio.structure.chem.ChemCompProvider;
29+
import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.PDBFileParser;
29-
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
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import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
31-
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
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import org.junit.Before;
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import org.junit.Test;
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java‎

Lines changed: 5 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -26,14 +26,13 @@
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
29+
import org.biojava.nbio.structure.io.CifFileReader;
2930
import org.biojava.nbio.structure.io.FileParsingParameters;
3031
import org.biojava.nbio.structure.io.PDBFileParser;
31-
import org.biojava.nbio.structure.io.mmcif.MMcifParser;
32-
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
33-
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
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import org.junit.Assert;
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import org.junit.Before;
3634
import org.junit.Test;
35+
import org.rcsb.cif.model.CifFile;
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import java.io.IOException;
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import java.io.InputStream;
@@ -87,17 +86,11 @@ public void test1a4wPDBFile() throws IOException
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InputStream inStream = this.getClass().getResourceAsStream("/1a4w.cif");
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Assert.assertNotNull(inStream);
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90-
MMcifParser pdbpars = new SimpleMMcifParser();
91-
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
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FileParsingParameters params = new FileParsingParameters();
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params.setAlignSeqRes(true);
94-
consumer.setFileParsingParameters(params);
95-
pdbpars.addMMcifConsumer(consumer);
96-
97-
pdbpars.parse(inStream) ;
98-
structure2 = consumer.getStructure();
99-
100-
91+
CifFileReader reader = new CifFileReader();
92+
reader.setFileParsingParameters(params);
93+
structure2 = reader.getStructure(inStream);
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Assert.assertNotNull(structure2);
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierIntegrationTest.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212
import org.biojava.nbio.structure.Structure;
1313
import org.biojava.nbio.structure.StructureImpl;
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import org.biojava.nbio.structure.StructureTools;
15-
import org.biojava.nbio.structure.io.cif.CifFileConverter;
15+
import org.biojava.nbio.structure.io.cif.StructureConverter;
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import org.junit.Test;
1717

1818
import java.io.ByteArrayInputStream;
@@ -49,10 +49,10 @@ public void test1A2C() throws IOException {
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private static void testRoundTrip(String pdbId) throws IOException {
5151
URL url = new URL("https://files.rcsb.org/download/" + pdbId + ".cif");
52-
Structure originalStruct = CifFileConverter.fromURL(url);
52+
Structure originalStruct = StructureConverter.fromURL(url);
5353

54-
InputStream inputStream = new ByteArrayInputStream(CifFileConverter.toText(originalStruct).getBytes());
55-
Structure readStruct = CifFileConverter.fromInputStream(inputStream);
54+
InputStream inputStream = new ByteArrayInputStream(StructureConverter.toText(originalStruct).getBytes());
55+
Structure readStruct = StructureConverter.fromInputStream(inputStream);
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5757
assertNotNull(readStruct);
5858
assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
@@ -113,7 +113,7 @@ private static void testRoundTrip(String pdbId) throws IOException {
113113
@Test
114114
public void testBiounitWriting() throws IOException {
115115
Structure s = createDummyStructure();
116-
String mmcif = CifFileConverter.toText(s);
116+
String mmcif = StructureConverter.toText(s);
117117
String[] lines = mmcif.split("\n");
118118
long atomLines = Arrays.stream(lines).filter(l -> l.startsWith("ATOM")).count();
119119
assertNotNull(mmcif);

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