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updates to ciftools from maven · biojava/biojava@4824817 · GitHub

/ biojava Public

Commit 4824817

Browse files
Sebastian Bittrich
committed
updates to ciftools from maven
1 parent 2c90336 commit 4824817

7 files changed

Lines changed: 102 additions & 145 deletions

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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerImplTest.java‎

Lines changed: 49 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -2,26 +2,65 @@
22

33
import org.biojava.nbio.structure.*;
44
import org.biojava.nbio.structure.io.*;
5+
import org.biojava.nbio.structure.io.cif.CifFileConverter;
6+
import org.junit.Ignore;
57
import org.junit.Test;
68
import org.rcsb.cif.CifReader;
7-
import org.rcsb.cif.model.CifFile;
8-
import org.rcsb.cif.model.Column;
9-
import org.rcsb.cif.model.ValueKind;
109

11-
import java.io.ByteArrayInputStream;
1210
import java.io.IOException;
1311
import java.io.InputStream;
14-
import java.text.ParseException;
15-
import java.text.SimpleDateFormat;
16-
import java.util.Date;
12+
import java.nio.file.Files;
13+
import java.nio.file.Paths;
1714
import java.util.List;
18-
import java.util.Locale;
19-
import java.util.Objects;
20-
import java.util.zip.GZIPInputStream;
15+
import java.util.concurrent.atomic.AtomicInteger;
2116

2217
import static org.junit.Assert.*;
2318

2419
public class CifFileConsumerImplTest {
20+
@Test
21+
public void test2z4j() {
22+
23+
}
24+
25+
@Test
26+
@Ignore
27+
public void parseEntireArchive() throws IOException {
28+
AtomicInteger counter = new AtomicInteger(0);
29+
AtomicInteger failed = new AtomicInteger(0);
30+
long start = System.nanoTime();
31+
int chunkSize = 250;
32+
33+
Files.walk(Paths.get(
34+
// change to your own paths
35+
// "/var/pdb/" // cif
36+
"/var/bcif/" // bcif
37+
))
38+
.parallel()
39+
.filter(path -> !Files.isDirectory(path))
40+
.forEach(path -> {
41+
int count = counter.incrementAndGet();
42+
if (count % chunkSize == 0) {
43+
long end_chunk = System.nanoTime();
44+
System.out.println("[" + count + "] @ " + (((end_chunk - start) /
45+
1_000 / count) + " µs per structure"));
46+
}
47+
48+
try {
49+
// the work is to obtain the CifFile instance and convert into a BioJava structure
50+
// CifFileConverter.convert(CifReader.readText(Files.newInputStream(path))); // cif
51+
CifFileConverter.convert(CifReader.readBinary(Files.newInputStream(path))); // bcif
52+
} catch (Exception e) {
53+
System.err.println("failed for " + path.toFile().getAbsolutePath());
54+
e.printStackTrace();
55+
failed.incrementAndGet();
56+
}
57+
});
58+
59+
long end = System.nanoTime();
60+
System.out.println((end - start) / 1_000_000_000 + " s");
61+
System.out.println("failed for " + failed.intValue() + " structures");
62+
}
63+
2564
private static boolean headerOnly;
2665
private static boolean binary;
2766

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierImplTest.java‎

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,6 @@
11
package org.biojava.nbio.structure.test.io.cif;
22

33
import org.biojava.nbio.structure.*;
4-
import org.biojava.nbio.structure.align.util.AtomCache;
5-
import org.biojava.nbio.structure.io.FileParsingParameters;
64
import org.biojava.nbio.structure.io.cif.CifFileConverter;
75
import org.junit.Test;
86
import org.rcsb.cif.CifReader;
@@ -15,11 +13,12 @@
1513
import java.nio.file.Files;
1614
import java.util.Arrays;
1715

18-
import static org.junit.Assert.*;
16+
import static org.junit.Assert.assertEquals;
17+
import static org.junit.Assert.assertNotNull;
1918

2019
public class CifFileSupplierImplTest {
2120
@Test
22-
public void test1SMT() throws IOException, StructureException {
21+
public void test1SMT() throws IOException {
2322
// an x-ray structure
2423
testRoundTrip("1SMT");
2524
}
@@ -29,18 +28,18 @@ public void test1SMT() throws IOException, StructureException {
2928
* @throws IOException propagated
3029
*/
3130
@Test
32-
public void test2N3J() throws IOException, StructureException {
31+
public void test2N3J() throws IOException {
3332
// an NMR structure (multimodel) with 2 chains
3433
testRoundTrip("2N3J");
3534
}
3635

3736
@Test
38-
public void test1A2C() throws IOException, StructureException {
37+
public void test1A2C() throws IOException {
3938
// a structure with insertion codes
4039
testRoundTrip("1A2C");
4140
}
4241

43-
private static void testRoundTrip(String pdbId) throws IOException, StructureException {
42+
private static void testRoundTrip(String pdbId) throws IOException {
4443
Structure originalStruct = CifFileConverter.convert(CifReader.readText(new URL("https://files.rcsb.org/download/" + pdbId
4544
+ ".cif").openStream()));
4645

‎biojava-structure/pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@
2121
<dependency>
2222
<groupId>org.rcsb</groupId>
2323
<artifactId>ciftools-java</artifactId>
24-
<version>1.0-SNAPSHOT</version>
24+
<version>0.3.0</version>
2525
</dependency>
2626
<dependency>
2727
<groupId>org.rcsb</groupId>

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java‎

Lines changed: 1 addition & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -1,50 +1,6 @@
11
package org.biojava.nbio.structure.io.cif;
22

3-
import org.rcsb.cif.model.generated.atomsite.AtomSite;
4-
import org.rcsb.cif.model.generated.atomsites.AtomSites;
5-
import org.rcsb.cif.model.generated.auditauthor.AuditAuthor;
6-
import org.rcsb.cif.model.generated.cell.Cell;
7-
import org.rcsb.cif.model.generated.chemcomp.ChemComp;
8-
import org.rcsb.cif.model.generated.chemcompbond.ChemCompBond;
9-
import org.rcsb.cif.model.generated.databasepdbremark.DatabasePDBRemark;
10-
import org.rcsb.cif.model.generated.databasepdbrev.DatabasePDBRev;
11-
import org.rcsb.cif.model.generated.databasepdbrevrecord.DatabasePDBRevRecord;
12-
import org.rcsb.cif.model.generated.entity.Entity;
13-
import org.rcsb.cif.model.generated.entitypoly.EntityPoly;
14-
import org.rcsb.cif.model.generated.entitypolyseq.EntityPolySeq;
15-
import org.rcsb.cif.model.generated.entitysrcgen.EntitySrcGen;
16-
import org.rcsb.cif.model.generated.entitysrcnat.EntitySrcNat;
17-
import org.rcsb.cif.model.generated.exptl.Exptl;
18-
import org.rcsb.cif.model.generated.pdbxauditrevisionhistory.PdbxAuditRevisionHistory;
19-
import org.rcsb.cif.model.generated.pdbxchemcompidentifier.PdbxChemCompIdentifier;
20-
import org.rcsb.cif.model.generated.pdbxdatabasestatus.PdbxDatabaseStatus;
21-
import org.rcsb.cif.model.generated.pdbxentitydescriptor.PdbxEntityDescriptor;
22-
import org.rcsb.cif.model.generated.pdbxentitysrcsyn.PdbxEntitySrcSyn;
23-
import org.rcsb.cif.model.generated.pdbxmolecule.PdbxMolecule;
24-
import org.rcsb.cif.model.generated.pdbxmoleculefeatures.PdbxMoleculeFeatures;
25-
import org.rcsb.cif.model.generated.pdbxnonpolyscheme.PdbxNonpolyScheme;
26-
import org.rcsb.cif.model.generated.pdbxreferenceentitylink.PdbxReferenceEntityLink;
27-
import org.rcsb.cif.model.generated.pdbxreferenceentitylist.PdbxReferenceEntityList;
28-
import org.rcsb.cif.model.generated.pdbxreferenceentitypolylink.PdbxReferenceEntityPolyLink;
29-
import org.rcsb.cif.model.generated.pdbxstructassembly.PdbxStructAssembly;
30-
import org.rcsb.cif.model.generated.pdbxstructassemblygen.PdbxStructAssemblyGen;
31-
import org.rcsb.cif.model.generated.pdbxstructmodresidue.PdbxStructModResidue;
32-
import org.rcsb.cif.model.generated.pdbxstructoperlist.PdbxStructOperList;
33-
import org.rcsb.cif.model.generated.refine.Refine;
34-
import org.rcsb.cif.model.generated.struct.Struct;
35-
import org.rcsb.cif.model.generated.structasym.StructAsym;
36-
import org.rcsb.cif.model.generated.structconf.StructConf;
37-
import org.rcsb.cif.model.generated.structconn.StructConn;
38-
import org.rcsb.cif.model.generated.structconntype.StructConnType;
39-
import org.rcsb.cif.model.generated.structkeywords.StructKeywords;
40-
import org.rcsb.cif.model.generated.structncsoper.StructNcsOper;
41-
import org.rcsb.cif.model.generated.structref.StructRef;
42-
import org.rcsb.cif.model.generated.structrefseq.StructRefSeq;
43-
import org.rcsb.cif.model.generated.structrefseqdif.StructRefSeqDif;
44-
import org.rcsb.cif.model.generated.structsheetrange.StructSheetRange;
45-
import org.rcsb.cif.model.generated.structsite.StructSite;
46-
import org.rcsb.cif.model.generated.structsitegen.StructSiteGen;
47-
import org.rcsb.cif.model.generated.symmetry.Symmetry;
3+
import org.rcsb.cif.model.generated.*;
484

495
/**
506
* Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java‎

Lines changed: 31 additions & 78 deletions
Original file line numberDiff line numberDiff line change
@@ -12,59 +12,8 @@
1212
import org.biojava.nbio.structure.xtal.CrystalCell;
1313
import org.biojava.nbio.structure.xtal.SpaceGroup;
1414
import org.biojava.nbio.structure.xtal.SymoplibParser;
15-
import org.rcsb.cif.model.Category;
16-
import org.rcsb.cif.model.Column;
17-
import org.rcsb.cif.model.generated.atomsite.*;
18-
import org.rcsb.cif.model.generated.atomsites.AtomSites;
19-
import org.rcsb.cif.model.generated.auditauthor.AuditAuthor;
20-
import org.rcsb.cif.model.generated.cell.Cell;
21-
import org.rcsb.cif.model.generated.chemcomp.ChemComp;
22-
import org.rcsb.cif.model.generated.chemcompbond.ChemCompBond;
23-
import org.rcsb.cif.model.generated.databasepdbremark.DatabasePDBRemark;
24-
import org.rcsb.cif.model.generated.databasepdbrev.DatabasePDBRev;
25-
import org.rcsb.cif.model.generated.databasepdbrevrecord.DatabasePDBRevRecord;
26-
import org.rcsb.cif.model.generated.entity.Entity;
27-
import org.rcsb.cif.model.generated.entitypoly.EntityPoly;
28-
import org.rcsb.cif.model.generated.entitypolyseq.EntityPolySeq;
29-
import org.rcsb.cif.model.generated.entitysrcgen.EntitySrcGen;
30-
import org.rcsb.cif.model.generated.entitysrcnat.EntitySrcNat;
31-
import org.rcsb.cif.model.generated.exptl.Exptl;
32-
import org.rcsb.cif.model.generated.pdbxauditrevisionhistory.PdbxAuditRevisionHistory;
33-
import org.rcsb.cif.model.generated.pdbxchemcompidentifier.PdbxChemCompIdentifier;
34-
import org.rcsb.cif.model.generated.pdbxdatabasestatus.PdbxDatabaseStatus;
35-
import org.rcsb.cif.model.generated.pdbxdatabasestatus.RecvdInitialDepositionDate;
36-
import org.rcsb.cif.model.generated.pdbxentitydescriptor.PdbxEntityDescriptor;
37-
import org.rcsb.cif.model.generated.pdbxentitysrcsyn.PdbxEntitySrcSyn;
38-
import org.rcsb.cif.model.generated.pdbxmolecule.PdbxMolecule;
39-
import org.rcsb.cif.model.generated.pdbxmoleculefeatures.PdbxMoleculeFeatures;
40-
import org.rcsb.cif.model.generated.pdbxnonpolyscheme.PdbxNonpolyScheme;
41-
import org.rcsb.cif.model.generated.pdbxreferenceentitylink.PdbxReferenceEntityLink;
42-
import org.rcsb.cif.model.generated.pdbxreferenceentitylist.PdbxReferenceEntityList;
43-
import org.rcsb.cif.model.generated.pdbxreferenceentitypolylink.PdbxReferenceEntityPolyLink;
44-
import org.rcsb.cif.model.generated.pdbxstructassembly.PdbxStructAssembly;
45-
import org.rcsb.cif.model.generated.pdbxstructassemblygen.PdbxStructAssemblyGen;
46-
import org.rcsb.cif.model.generated.pdbxstructmodresidue.PdbxStructModResidue;
47-
import org.rcsb.cif.model.generated.pdbxstructoperlist.PdbxStructOperList;
48-
import org.rcsb.cif.model.generated.refine.LsRFactorRFree;
49-
import org.rcsb.cif.model.generated.refine.LsRFactorRWork;
50-
import org.rcsb.cif.model.generated.refine.Refine;
51-
import org.rcsb.cif.model.generated.struct.Struct;
52-
import org.rcsb.cif.model.generated.structasym.StructAsym;
53-
import org.rcsb.cif.model.generated.structconf.StructConf;
54-
import org.rcsb.cif.model.generated.structconn.StructConn;
55-
import org.rcsb.cif.model.generated.structconntype.StructConnType;
56-
import org.rcsb.cif.model.generated.structkeywords.PdbxKeywords;
57-
import org.rcsb.cif.model.generated.structkeywords.StructKeywords;
58-
import org.rcsb.cif.model.generated.structncsoper.StructNcsOper;
59-
import org.rcsb.cif.model.generated.structref.StructRef;
60-
import org.rcsb.cif.model.generated.structrefseq.PdbxDbAlignBegInsCode;
61-
import org.rcsb.cif.model.generated.structrefseq.PdbxDbAlignEndInsCode;
62-
import org.rcsb.cif.model.generated.structrefseq.StructRefSeq;
63-
import org.rcsb.cif.model.generated.structrefseqdif.StructRefSeqDif;
64-
import org.rcsb.cif.model.generated.structsheetrange.StructSheetRange;
65-
import org.rcsb.cif.model.generated.structsite.StructSite;
66-
import org.rcsb.cif.model.generated.structsitegen.StructSiteGen;
67-
import org.rcsb.cif.model.generated.symmetry.Symmetry;
15+
import org.rcsb.cif.model.*;
16+
import org.rcsb.cif.model.generated.*;
6817
import org.slf4j.Logger;
6918
import org.slf4j.LoggerFactory;
7019

@@ -145,30 +94,30 @@ public void consumeAtomSite(AtomSite atomSite) {
14594
return;
14695
}
14796

148-
LabelAsymId labelAsymId = atomSite.getLabelAsymId();
149-
AuthAsymId authAsymId = atomSite.getAuthAsymId();
97+
StrColumn labelAsymId = atomSite.getLabelAsymId();
98+
StrColumn authAsymId = atomSite.getAuthAsymId();
15099

151-
GroupPDB groupPDB = atomSite.getGroupPDB();
152-
AuthSeqId authSeqId = atomSite.getAuthSeqId();
100+
StrColumn groupPDB = atomSite.getGroupPDB();
101+
IntColumn authSeqId = atomSite.getAuthSeqId();
153102

154-
LabelCompId labelCompId = atomSite.getLabelCompId();
103+
StrColumn labelCompId = atomSite.getLabelCompId();
155104

156-
Id id = atomSite.getId();
157-
LabelAtomId labelAtomId = atomSite.getLabelAtomId();
105+
IntColumn id = atomSite.getId();
106+
StrColumn labelAtomId = atomSite.getLabelAtomId();
158107

159-
CartnX cartnX = atomSite.getCartnX();
160-
CartnY cartnY = atomSite.getCartnY();
161-
CartnZ cartnZ = atomSite.getCartnZ();
108+
FloatColumn cartnX = atomSite.getCartnX();
109+
FloatColumn cartnY = atomSite.getCartnY();
110+
FloatColumn cartnZ = atomSite.getCartnZ();
162111

163-
Occupancy occupancy = atomSite.getOccupancy();
164-
BIsoOrEquiv bIsoOrEquiv = atomSite.getBIsoOrEquiv();
112+
FloatColumn occupancy = atomSite.getOccupancy();
113+
FloatColumn bIsoOrEquiv = atomSite.getBIsoOrEquiv();
165114

166-
LabelAltId labelAltId = atomSite.getLabelAltId();
167-
TypeSymbol typeSymbol = atomSite.getTypeSymbol();
115+
StrColumn labelAltId = atomSite.getLabelAltId();
116+
StrColumn typeSymbol = atomSite.getTypeSymbol();
168117

169-
PdbxPDBInsCode pdbxPDBInsCode = atomSite.getPdbxPDBInsCode();
170-
LabelSeqId labelSeqId = atomSite.getLabelSeqId();
171-
PdbxPDBModelNum pdbx_pdb_model_num = atomSite.getPdbxPDBModelNum();
118+
StrColumn pdbxPDBInsCode = atomSite.getPdbxPDBInsCode();
119+
IntColumn labelSeqId = atomSite.getLabelSeqId();
120+
IntColumn pdbx_pdb_model_num = atomSite.getPdbxPDBModelNum();
172121

173122
for (int atomIndex = 0; atomIndex < atomSite.getRowCount(); atomIndex++) {
174123
boolean startOfNewChain = false;
@@ -726,6 +675,7 @@ public void consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory pdbxAuditRe
726675
if (pdbxAuditRevisionHistory.getOrdinal().get(rowIndex) == 1) {
727676
String release = pdbxAuditRevisionHistory.getRevisionDate().get(rowIndex);
728677
try {
678+
// TODO java.lang.NumberFormatException: multiple points - failed for /var/bcif/z4/1z4s.bcif, failed for /var/bcif/he/4hec.bcif
729679
Date releaseDate = DATE_FORMAT.parse(release);
730680
pdbHeader.setRelDate(releaseDate);
731681
} catch (ParseException e) {
@@ -737,6 +687,7 @@ public void consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory pdbxAuditRe
737687
// the last revision date will "stick"
738688
String revision = pdbxAuditRevisionHistory.getRevisionDate().get(rowIndex);
739689
try {
690+
// TODO java.lang.NumberFormatException: multiple points - failed for /var/bcif/dz/1dzw.bcif, failed for /var/bcif/y2/2y28.bcif
740691
Date revisionDate = DATE_FORMAT.parse(revision);
741692
pdbHeader.setModDate(revisionDate);
742693
} catch (ParseException e) {
@@ -755,11 +706,12 @@ public void consumePdbxChemCompIdentifier(PdbxChemCompIdentifier pdbxChemCompIde
755706
public void consumePdbxDatabaseStatus(PdbxDatabaseStatus pdbxDatabaseStatus) {
756707
for (int rowIndex = 0; rowIndex < pdbxDatabaseStatus.getRowCount(); rowIndex++) {
757708
// the deposition date field is only available in mmCIF 5.0
758-
RecvdInitialDepositionDate col = pdbxDatabaseStatus.getRecvdInitialDepositionDate();
759-
if (col.isDefined()) {
760-
String deposition = col.get(rowIndex);
709+
StrColumn recvdInitialDepositionDate = pdbxDatabaseStatus.getRecvdInitialDepositionDate();
710+
if (recvdInitialDepositionDate.isDefined()) {
711+
String deposition = recvdInitialDepositionDate.get(rowIndex);
761712

762713
try {
714+
// TODO failed for /var/bcif/z4/2z4j.bcif java.lang.NumberFormatException: For input string: ".202717E4202717E4"
763715
Date depositionDate = DATE_FORMAT.parse(deposition);
764716
pdbHeader.setDepDate(depositionDate);
765717
} catch (ParseException e) {
@@ -838,7 +790,7 @@ public void consumeRefine(Refine refine) {
838790
}
839791
pdbHeader.setResolution((float) lsDResHigh);
840792

841-
LsRFactorRFree lsRFactorRFree = refine.getLsRFactorRFree();
793+
FloatColumn lsRFactorRFree = refine.getLsRFactorRFree();
842794
// RFREE
843795
if (pdbHeader.getRfree() != PDBHeader.DEFAULT_RFREE) {
844796
logger.warn("More than 1 Rfree value present, will use last one {} and discard previous {}",
@@ -852,7 +804,7 @@ public void consumeRefine(Refine refine) {
852804
}
853805

854806
// RWORK
855-
LsRFactorRWork lsRFactorRWork = refine.getLsRFactorRWork();
807+
FloatColumn lsRFactorRWork = refine.getLsRFactorRWork();
856808
if(pdbHeader.getRwork() != PDBHeader.DEFAULT_RFREE) {
857809
logger.warn("More than 1 R work value present, will use last one {} and discard previous {} ",
858810
lsRFactorRWork, String.format("%4.2f",pdbHeader.getRwork()));
@@ -898,7 +850,7 @@ public void consumeStructConnType(StructConnType structConnType) {
898850

899851
@Override
900852
public void consumeStructKeywords(StructKeywords structKeywords) {
901-
PdbxKeywords pdbxKeywords = structKeywords.getPdbxKeywords();
853+
StrColumn pdbxKeywords = structKeywords.getPdbxKeywords();
902854
// TODO what is the correct format for these?
903855
pdbHeader.setDescription(pdbxKeywords.values().collect(Collectors.joining(", ")));
904856
pdbHeader.setClassification(pdbxKeywords.values().collect(Collectors.joining(", ")));
@@ -978,7 +930,7 @@ public void consumeStructRefSeq(StructRefSeq structRefSeq) {
978930
int dbSeqEnd = structRefSeq.getDbAlignEnd().get(rowIndex);
979931

980932
char dbBeginInsCode = ' ';
981-
PdbxDbAlignBegInsCode pdbxDbAlignBegInsCodeCol = structRefSeq.getPdbxDbAlignBegInsCode();
933+
StrColumn pdbxDbAlignBegInsCodeCol = structRefSeq.getPdbxDbAlignBegInsCode();
982934
if (pdbxDbAlignBegInsCodeCol.isDefined()) {
983935
String pdbxDbAlignBegInsCode = pdbxDbAlignBegInsCodeCol.get(rowIndex);
984936
if (pdbxDbAlignBegInsCode.length() > 0) {
@@ -987,7 +939,7 @@ public void consumeStructRefSeq(StructRefSeq structRefSeq) {
987939
}
988940

989941
char dbEndInsCode = ' ';
990-
PdbxDbAlignEndInsCode pdbxDbAlignEndInsCodeCol = structRefSeq.getPdbxDbAlignEndInsCode();
942+
StrColumn pdbxDbAlignEndInsCodeCol = structRefSeq.getPdbxDbAlignEndInsCode();
991943
if (pdbxDbAlignEndInsCodeCol.isDefined()) {
992944
String pdbxDbAlignEndInsCode = pdbxDbAlignEndInsCodeCol.get(rowIndex);
993945
if (pdbxDbAlignEndInsCode.length() > 0) {
@@ -1157,6 +1109,7 @@ public void finish() {
11571109
SeqRes2AtomAligner.storeUnAlignedSeqRes(structure, seqResChains, params.isHeaderOnly());
11581110
}
11591111

1112+
// TODO java.lang.NullPointerException - failed for /var/bcif/hm/2hmz.bcif
11601113
// Now make sure all altlocgroups have all the atoms in all the groups
11611114
StructureTools.cleanUpAltLocs(structure);
11621115

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -276,8 +276,7 @@ public void accept(WrappedAtom wrappedAtom) {
276276
AtomSiteCollector combine(AtomSiteCollector other) {
277277
throw new UnsupportedOperationException("impl by calling addAll for all collection - not feeling like writing that code");
278278
}
279-
280-
@SuppressWarnings("Duplicates")
279+
281280
Category get() {
282281
return new CategoryBuilder("atom_site", null)
283282
.addColumn(groupPDB.build())

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