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josemduartejosemduarte
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Now considering branched entities as non-polymeric. Ends up in a more consistent state. Can be mmtf-encoded.
1 parent 41c36ae commit ab76f92

4 files changed

Lines changed: 66 additions & 13 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -110,6 +110,10 @@ public void addChain(Chain c) {
110110
logger.warn("Chain with asym id {} (author id {}) has entity type 'macrolide', considering it non-polymeric", c.getId(), c.getName());
111111
nonPolyChains.add(c);
112112

113+
} else if (info.getType() == EntityType.BRANCHED) {
114+
logger.warn("Chain with asym id {} (author id {}) has entity type 'branched', considering it non-polymeric", c.getId(), c.getName());
115+
nonPolyChains.add(c);
116+
113117
} else {
114118
logger.warn("Chain with asym id {} (author id {}) has unsupported entity type '{}'. Will not add it to the Structure.", c.getId(), c.getName(), info.getType().toString());
115119
// ignore it

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

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,8 @@
3737
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
3838
import org.rcsb.mmtf.api.StructureAdapterInterface;
3939
import org.rcsb.mmtf.dataholders.MmtfStructure;
40+
import org.slf4j.Logger;
41+
import org.slf4j.LoggerFactory;
4042

4143
/**
4244
* Class to take Biojava structure data and covert to the DataApi for encoding.
@@ -48,7 +50,9 @@
4850
*/
4951
public class MmtfStructureWriter {
5052

51-
private StructureAdapterInterface mmtfDecoderInterface;
53+
private static final Logger logger = LoggerFactory.getLogger(MmtfStructureWriter.class);
54+
55+
private final StructureAdapterInterface mmtfDecoderInterface;
5256

5357
/**
5458
* Pass data from Biojava structure to another generic output type. Loops through the data
@@ -179,9 +183,8 @@ private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> enti
179183
List<Chain> entityChains = entityInfo.getChains();
180184
if (entityChains.isEmpty()){
181185
// Error mapping chain to entity
182-
System.err.println("ERROR MAPPING CHAIN TO ENTITY: "+description);
186+
logger.error("ERROR MAPPING CHAIN TO ENTITY: "+description);
183187
mmtfDecoderInterface.setEntityInfo(new int[0], "", description, type);
184-
continue;
185188
}
186189
else{
187190
int[] chainIndices = new int[entityChains.size()];
@@ -194,7 +197,7 @@ private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> enti
194197
chainImpl = (ChainImpl) entityChains.get(0);
195198
}
196199
else{
197-
throw new RuntimeException();
200+
throw new RuntimeException("Encountered Chain of unexpected type");
198201
}
199202
String sequence = chainImpl.getSeqResOneLetterSeq();
200203
mmtfDecoderInterface.setEntityInfo(chainIndices, sequence, description, type);
@@ -205,8 +208,7 @@ private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> enti
205208

206209
/**
207210
* Generate the bioassembly information on in the desired form.
208-
* @param bioJavaStruct the Biojava structure
209-
* @param header the header
211+
*
210212
*/
211213
private void storeBioassemblyInformation(Map<String, Integer> chainIdToIndexMap, Map<Integer, BioAssemblyInfo> inputBioAss) {
212214
int bioAssemblyIndex = 0;

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

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -446,7 +446,7 @@ private static int[] countEntityTypes(List<EntityInfo> entities) {
446446
}
447447

448448
@Test
449-
public void testCarbohydrates() throws IOException {
449+
public void testStructureWithBranchedEntities() throws IOException {
450450
// Example carbohydrate remediation file to be released in July 2020
451451
URL url = new URL("https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/examples/models/1B5F-carb.cif");
452452
InputStream inStream = url.openStream();
@@ -464,8 +464,15 @@ public void testCarbohydrates() throws IOException {
464464
assertEquals(2, structure.getEntityById(1).getChains().size());
465465
assertEquals(2, structure.getEntityById(2).getChains().size());
466466

467-
assertEquals(0, structure.getNonPolyChains().size());
467+
// we consider the branched chains non-poly chains
468+
assertEquals(4, structure.getNonPolyChains().size());
468469
assertEquals(4, structure.getPolyChains().size());
469470

471+
assertEquals(1, structure.getEntityById(3).getChains().size());
472+
473+
// chain asym_id="E" is from entity 3
474+
assertSame(structure.getNonPolyChain("E"), structure.getEntityById(3).getChains().get(0));
475+
476+
assertEquals(5, structure.getNonPolyChain("E").getAtomGroups().size());
470477
}
471478
}

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java‎

Lines changed: 45 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -20,12 +20,11 @@
2020
*/
2121
package org.biojava.nbio.structure.io.mmtf;
2222

23-
import static org.junit.Assert.assertArrayEquals;
24-
import static org.junit.Assert.assertEquals;
25-
import static org.junit.Assert.assertNotNull;
26-
import static org.junit.Assert.assertTrue;
27-
23+
import java.io.BufferedReader;
2824
import java.io.IOException;
25+
import java.io.InputStream;
26+
import java.io.InputStreamReader;
27+
import java.net.URL;
2928
import java.util.ArrayList;
3029
import java.util.Collections;
3130
import java.util.Comparator;
@@ -43,12 +42,17 @@
4342
import org.biojava.nbio.structure.io.FileParsingParameters;
4443
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
4544
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
45+
import org.biojava.nbio.structure.io.mmcif.MMcifParser;
46+
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
47+
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
4648
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
4749
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
4850
import org.junit.Test;
4951
import org.rcsb.mmtf.decoder.StructureDataToAdapter;
5052
import org.rcsb.mmtf.encoder.AdapterToStructureData;
5153

54+
import static org.junit.Assert.*;
55+
5256
/**
5357
* Tests to see if roundtripping of MMTF can be done.
5458
*
@@ -350,4 +354,40 @@ private void checkBioAssemblies1(Structure structOne, Structure structTwo) throw
350354
}
351355
}
352356
}
357+
358+
@Test
359+
public void testStructWithBranchedEntitiesRoundTrip() throws IOException {
360+
// Example carbohydrate remediation file to be released in July 2020
361+
URL url = new URL("https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/examples/models/1B5F-carb.cif");
362+
InputStream inStream = url.openStream();
363+
364+
MMcifParser parser = new SimpleMMcifParser();
365+
366+
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
367+
parser.addMMcifConsumer(consumer);
368+
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
369+
370+
Structure structure = consumer.getStructure();
371+
372+
AdapterToStructureData writerToEncoder = new AdapterToStructureData();
373+
new MmtfStructureWriter(structure, writerToEncoder);
374+
MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
375+
new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
376+
Structure structure2 = mmtfStructureReader.getStructure();
377+
378+
assertEquals(7, structure2.getEntityInfos().size());
379+
380+
assertEquals(2, structure2.getEntityById(1).getChains().size());
381+
assertEquals(2, structure2.getEntityById(2).getChains().size());
382+
383+
assertEquals(4, structure2.getNonPolyChains().size());
384+
assertEquals(4, structure2.getPolyChains().size());
385+
386+
assertEquals(1, structure2.getEntityById(3).getChains().size());
387+
388+
// chain asym_id="E" is from entity 3
389+
assertSame(structure2.getNonPolyChain("E"), structure2.getEntityById(3).getChains().get(0));
390+
391+
assertEquals(5, structure2.getNonPolyChain("E").getAtomGroups().size());
392+
}
353393
}

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