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Some more categories written out to CIF #1063

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Merged
josemduarte merged 7 commits into from
Jun 1, 2023
Merged

Some more categories written out to CIF #1063

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615a570
Writing out entity info in CIF
josemduarte May 10, 2023
3543eb9
New test
josemduarte May 11, 2023
a8a96ec
Handling nulls in descriptions
josemduarte May 11, 2023
12137bf
Fixing empty seqres groups for pdb files with not seqres
josemduarte May 12, 2023
6431114
Fixing empty seqres groups for cif files with no _entity
josemduarte May 12, 2023
a06ac88
Latest ciftools
josemduarte May 18, 2023
4d146e1
Improvements from review comments
josemduarte May 24, 2023
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Handling nulls in descriptions
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@josemduarte
josemduarte committed May 11, 2023
commit a8a96ec122133b10cf5b4faf0cd6d79d65b7dbbe
6 changes: 3 additions & 3 deletions ...va-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
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Original file line number Diff line number Diff line change
Expand Up @@ -100,11 +100,11 @@ protected CifFile getInternal(Structure structure, List<WrappedAtom> wrappedAtom
EntityInfo e = entityInfos.get(i);
entityIds[i] = Integer.toString(e.getMolId());
entityTypes[i] = e.getType().getEntityType();
entityDescriptions[i] = e.getDescription();
entityDescriptions[i] = e.getDescription() == null? "?" : e.getDescription();
}

String[] polyEntityIds = entityInfos.stream().filter(e -> e.getType() == EntityType.POLYMER).map(e -> Integer.toString(e.getMolId())).collect(Collectors.toList()).toArray(new String[]{});
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@sbittrich sbittrich May 24, 2023

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Streams have a toArray method as well. .collect(Collectors.toList()).toArray(new String[]{}) can be simplified to .toArray(String[]::new), effectively skipping the creation of a List.

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@josemduarte josemduarte May 24, 2023

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Nice one, thanks. Added a commit.

And shame to IntelliJ for not suggesting this!

String[] entitySeqs = entityInfos.stream().filter(e -> e.getType() == EntityType.POLYMER).map(e -> e.getChains().get(0).getSeqResSequence()).collect(Collectors.toList()).toArray(new String[]{});
String[] polyEntitySeqs = entityInfos.stream().filter(e -> e.getType() == EntityType.POLYMER).map(e -> e.getChains().get(0).getSeqResSequence()).collect(Collectors.toList()).toArray(new String[]{});
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@sbittrich sbittrich May 24, 2023

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Same as above.


blockBuilder.enterEntity()
.enterId()
Expand All @@ -127,7 +127,7 @@ protected CifFile getInternal(Structure structure, List<WrappedAtom> wrappedAtom
.leaveColumn()

.enterPdbxSeqOneLetterCodeCan()
.add(entitySeqs)
.add(polyEntitySeqs)
.leaveColumn()

.leaveCategory();
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4 changes: 2 additions & 2 deletions ...va-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java
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Expand Up @@ -10,8 +10,7 @@
import java.io.InputStream;
import java.util.zip.GZIPInputStream;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.*;

public class CifFileSupplierImplTest {

Expand All @@ -29,6 +28,7 @@ public void shouldReadRawPdbOutputtingCifWithEntity() throws IOException {
String cifText = CifStructureConverter.toText(s);
assertTrue(cifText.contains("_entity.type"));
assertTrue(cifText.contains("_entity_poly.pdbx_seq_one_letter_code_can"));
assertFalse(cifText.contains("null"));

InputStream inputStream = new ByteArrayInputStream(cifText.getBytes());
Structure readStruct = CifStructureConverter.fromInputStream(inputStream);
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