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Merged
josemduarte merged 2 commits into from
Apr 18, 2020
Merged

Minimal read support for files with 'branched' entities #868

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41c36ae
Now biojava can parse mmcif files with carbohydrates, though it ignor…
josemduarte Apr 13, 2020
ab76f92
Now considering branched entities as non-polymeric. Ends up in a more…
josemduarte Apr 13, 2020
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12 changes: 12 additions & 0 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,18 @@ public enum EntityType {
*/
POLYMER("polymer"),

/**
* The 'branched' type use mainly to represent carbohydrates.
* The type was introduced in these versions of the mmcif dictionary:
* 5.101 2012-08-22
* 5.291 2017-09-10
* 5.304 2018-08-01
* The type will only be used for PDB-deposited files from July 2020, as part of
* the carbohydrate remediation project.
* @since 5.4.0
*/
BRANCHED("branched"),

/**
* Non-polymeric entities: ligands, metal ions, buffer molecules, etc
*/
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4 changes: 4 additions & 0 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
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Expand Up @@ -110,6 +110,10 @@ public void addChain(Chain c) {
logger.warn("Chain with asym id {} (author id {}) has entity type 'macrolide', considering it non-polymeric", c.getId(), c.getName());
nonPolyChains.add(c);

} else if (info.getType() == EntityType.BRANCHED) {
logger.warn("Chain with asym id {} (author id {}) has entity type 'branched', considering it non-polymeric", c.getId(), c.getName());
nonPolyChains.add(c);

} else {
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());
// ignore it
Expand Down
14 changes: 8 additions & 6 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java
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Expand Up @@ -37,6 +37,8 @@
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
import org.rcsb.mmtf.api.StructureAdapterInterface;
import org.rcsb.mmtf.dataholders.MmtfStructure;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
* Class to take Biojava structure data and covert to the DataApi for encoding.
Expand All @@ -48,7 +50,9 @@
*/
public class MmtfStructureWriter {

private StructureAdapterInterface mmtfDecoderInterface;
private static final Logger logger = LoggerFactory.getLogger(MmtfStructureWriter.class);

private final StructureAdapterInterface mmtfDecoderInterface;

/**
* Pass data from Biojava structure to another generic output type. Loops through the data
Expand Down Expand Up @@ -179,9 +183,8 @@ private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> enti
List<Chain> entityChains = entityInfo.getChains();
if (entityChains.isEmpty()){
// Error mapping chain to entity
System.err.println("ERROR MAPPING CHAIN TO ENTITY: "+description);
logger.error("ERROR MAPPING CHAIN TO ENTITY: "+description);
mmtfDecoderInterface.setEntityInfo(new int[0], "", description, type);
continue;
}
else{
int[] chainIndices = new int[entityChains.size()];
Expand All @@ -194,7 +197,7 @@ private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> enti
chainImpl = (ChainImpl) entityChains.get(0);
}
else{
throw new RuntimeException();
throw new RuntimeException("Encountered Chain of unexpected type");
}
String sequence = chainImpl.getSeqResOneLetterSeq();
mmtfDecoderInterface.setEntityInfo(chainIndices, sequence, description, type);
Expand All @@ -205,8 +208,7 @@ private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> enti

/**
* Generate the bioassembly information on in the desired form.
* @param bioJavaStruct the Biojava structure
* @param header the header
*
*/
private void storeBioassemblyInformation(Map<String, Integer> chainIdToIndexMap, Map<Integer, BioAssemblyInfo> inputBioAss) {
int bioAssemblyIndex = 0;
Expand Down
32 changes: 32 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java
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Expand Up @@ -27,6 +27,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.List;
import java.util.zip.GZIPInputStream;

Expand Down Expand Up @@ -443,4 +444,35 @@ private static int[] countEntityTypes(List<EntityInfo> entities) {
return counts;

}

@Test
public void testStructureWithBranchedEntities() throws IOException {
// Example carbohydrate remediation file to be released in July 2020
URL url = new URL("https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/examples/models/1B5F-carb.cif");
InputStream inStream = url.openStream();

MMcifParser parser = new SimpleMMcifParser();

SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
parser.addMMcifConsumer(consumer);
parser.parse(new BufferedReader(new InputStreamReader(inStream)));

Structure structure = consumer.getStructure();

assertEquals(7, structure.getEntityInfos().size());

assertEquals(2, structure.getEntityById(1).getChains().size());
assertEquals(2, structure.getEntityById(2).getChains().size());

// we consider the branched chains non-poly chains
assertEquals(4, structure.getNonPolyChains().size());
assertEquals(4, structure.getPolyChains().size());

assertEquals(1, structure.getEntityById(3).getChains().size());

// chain asym_id="E" is from entity 3
assertSame(structure.getNonPolyChain("E"), structure.getEntityById(3).getChains().get(0));

assertEquals(5, structure.getNonPolyChain("E").getAtomGroups().size());
}
}
50 changes: 45 additions & 5 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,11 @@
*/
package org.biojava.nbio.structure.io.mmtf;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
Expand All @@ -43,12 +42,17 @@
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
import org.biojava.nbio.structure.io.mmcif.MMcifParser;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
import org.junit.Test;
import org.rcsb.mmtf.decoder.StructureDataToAdapter;
import org.rcsb.mmtf.encoder.AdapterToStructureData;

import static org.junit.Assert.*;

/**
* Tests to see if roundtripping of MMTF can be done.
*
Expand Down Expand Up @@ -350,4 +354,40 @@ private void checkBioAssemblies1(Structure structOne, Structure structTwo) throw
}
}
}

@Test
public void testStructWithBranchedEntitiesRoundTrip() throws IOException {
// Example carbohydrate remediation file to be released in July 2020
URL url = new URL("https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/examples/models/1B5F-carb.cif");
InputStream inStream = url.openStream();

MMcifParser parser = new SimpleMMcifParser();

SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
parser.addMMcifConsumer(consumer);
parser.parse(new BufferedReader(new InputStreamReader(inStream)));

Structure structure = consumer.getStructure();

AdapterToStructureData writerToEncoder = new AdapterToStructureData();
new MmtfStructureWriter(structure, writerToEncoder);
MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
Structure structure2 = mmtfStructureReader.getStructure();

assertEquals(7, structure2.getEntityInfos().size());

assertEquals(2, structure2.getEntityById(1).getChains().size());
assertEquals(2, structure2.getEntityById(2).getChains().size());

assertEquals(4, structure2.getNonPolyChains().size());
assertEquals(4, structure2.getPolyChains().size());

assertEquals(1, structure2.getEntityById(3).getChains().size());

// chain asym_id="E" is from entity 3
assertSame(structure2.getNonPolyChain("E"), structure2.getEntityById(3).getChains().get(0));

assertEquals(5, structure2.getNonPolyChain("E").getAtomGroups().size());
}
}