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removes modifications to AtomCache again · biojava/biojava@2c90336 · GitHub

/ biojava Public

Commit 2c90336

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Sebastian Bittrich
committed
removes modifications to AtomCache again
1 parent 6d8e3e7 commit 2c90336

2 files changed

Lines changed: 44 additions & 127 deletions

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

Lines changed: 3 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
1111
import java.io.File;
1212
import java.io.FileWriter;
1313
import java.io.IOException;
14+
import java.net.URL;
1415
import java.nio.file.Files;
1516
import java.util.Arrays;
1617

@@ -40,18 +41,8 @@ public void test1A2C() throws IOException, StructureException {
4041
}
4142

4243
private static void testRoundTrip(String pdbId) throws IOException, StructureException {
43-
AtomCache cache = new AtomCache();
44-
45-
StructureIO.setAtomCache(cache);
46-
47-
cache.setUseCif(true);
48-
49-
FileParsingParameters params = new FileParsingParameters();
50-
params.setAlignSeqRes(true);
51-
cache.setFileParsingParams(params);
52-
53-
assertTrue(StructureIO.getAtomCache().isUseCif());
54-
Structure originalStruct = StructureIO.getStructure(pdbId);
44+
Structure originalStruct = CifFileConverter.convert(CifReader.readText(new URL("https://files.rcsb.org/download/" + pdbId
45+
+ ".cif").openStream()));
5546

5647
File outputFile = File.createTempFile("biojava_testing_", ".cif");
5748
outputFile.deleteOnExit();

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java‎

Lines changed: 41 additions & 115 deletions
Original file line numberDiff line numberDiff line change
@@ -35,9 +35,12 @@
3535
import org.biojava.nbio.structure.cath.CathFactory;
3636
import org.biojava.nbio.structure.domain.PDPProvider;
3737
import org.biojava.nbio.structure.domain.RemotePDPProvider;
38-
import org.biojava.nbio.structure.io.*;
38+
import org.biojava.nbio.structure.io.FileParsingParameters;
3939
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
4040
import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
41+
import org.biojava.nbio.structure.io.MMCIFFileReader;
42+
import org.biojava.nbio.structure.io.MMTFFileReader;
43+
import org.biojava.nbio.structure.io.PDBFileReader;
4144
import org.biojava.nbio.core.util.FileDownloadUtils;
4245
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder;
4346
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
@@ -93,17 +96,8 @@ public class AtomCache {
9396

9497
private String path;
9598

96-
/**
97-
* The format for structure data to use.
98-
*/
99-
private Format format;
100-
enum Format {
101-
PDB,
102-
MMCIF,
103-
MMTF,
104-
CIF,
105-
BCIF
106-
}
99+
private boolean useMmCif;
100+
private boolean useMmtf;
107101

108102
/**
109103
* Default AtomCache constructor.
@@ -156,7 +150,9 @@ public AtomCache(String pdbFilePath, String cachePath) {
156150
currentlyLoading.clear();
157151
params = new FileParsingParameters();
158152

153+
setUseMmCif(false);
159154
setUseMmtf(true);
155+
160156
}
161157

162158
/**
@@ -169,10 +165,11 @@ public AtomCache(UserConfiguration config) {
169165
this(config.getPdbFilePath(), config.getCacheFilePath());
170166
fetchBehavior = config.getFetchBehavior();
171167
obsoleteBehavior = config.getObsoleteBehavior();
168+
useMmCif = config.getFileFormat().equals( UserConfiguration.MMCIF_FORMAT );
169+
170+
if ( useMmCif)
171+
useMmtf = false;
172172

173-
if (config.getFileFormat().equals(UserConfiguration.MMCIF_FORMAT)) {
174-
format = Format.MMCIF;
175-
}
176173
}
177174

178175
/**
@@ -300,7 +297,8 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
300297

301298
// if we use mmcif or mmtf, then we need to pass useAsymIds=true
302299
boolean useAsymIds = false;
303-
if (format != Format.PDB) useAsymIds = true;
300+
if (useMmCif) useAsymIds = true;
301+
if (useMmtf) useAsymIds = true;
304302
return builder.rebuildQuaternaryStructure(asymUnit, transformations, useAsymIds, multiModel);
305303

306304
}
@@ -358,7 +356,8 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws
358356

359357
// if we use mmcif or mmtf, then we need to pass useAsymIds=true
360358
boolean useAsymIds = false;
361-
if (format != Format.PDB) useAsymIds = true;
359+
if (useMmCif) useAsymIds = true;
360+
if (useMmtf) useAsymIds = true;
362361
return builder.rebuildQuaternaryStructure(asymUnit, transformations, useAsymIds, multiModel);
363362

364363
}
@@ -410,7 +409,8 @@ public List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel)
410409

411410
// if we use mmcif or mmtf, then we need to pass useAsymIds=true
412411
boolean useAsymIds = false;
413-
if (format != Format.PDB) useAsymIds = true;
412+
if (useMmCif) useAsymIds = true;
413+
if (useMmtf) useAsymIds = true;
414414
Structure s = builder.rebuildQuaternaryStructure(asymUnit, transformations, useAsymIds, multiModel);
415415
assemblies.add(s);
416416
}
@@ -606,7 +606,7 @@ public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatab
606606
}
607607
}
608608
boolean alreadyContains = newChain.getAtomGroups().contains(group); // we don't want to add duplicate
609-
// ligands
609+
// ligands
610610
if (shouldContain && !alreadyContains) {
611611

612612
newChain.addGroup(group);
@@ -772,89 +772,37 @@ public void setPdpprovider(PDPProvider pdpprovider) {
772772
* @return the useMmCif
773773
*/
774774
public boolean isUseMmCif() {
775-
return format == Format.MMCIF;
775+
return useMmCif;
776776
}
777777

778778
/**
779779
* @param useMmCif
780780
* the useMmCif to set
781781
*/
782782
public void setUseMmCif(boolean useMmCif) {
783-
if (useMmCif) {
784-
this.format = Format.MMCIF;
785-
}
783+
this.useMmCif = useMmCif;
784+
// Either way the user wants to use PDB or MMCIF
785+
this.useMmtf = false;
786786
}
787787

788788
/**
789789
* Set whether to use mmtf.
790790
* @param useMmtf the input boolean to set
791791
*/
792792
public void setUseMmtf(boolean useMmtf) {
793-
if (useMmtf) {
794-
this.format = Format.MMTF;
793+
this.useMmtf = useMmtf;
794+
if(useMmtf){
795+
useMmCif=false;
795796
}
797+
796798
}
797799

798800
/** Returns useMmtf flag
799801
*
800802
* @return true if will load data via mmtf file format
801803
*/
802804
public boolean isUseMmtf(){
803-
return this.format == Format.MMTF;
804-
}
805-
806-
/**
807-
* The PDB flag.
808-
* @return true if legacy PDB parsing will be employed
809-
*/
810-
public boolean isUsePdb() {
811-
return this.format == Format.PDB;
812-
}
813-
814-
/**
815-
* The experimental Bcif flag.
816-
* @return true if experimental Bcif parsing will be employed
817-
*/
818-
public boolean isUseBcif() {
819-
return this.format == Format.BCIF;
820-
}
821-
822-
/**
823-
* The experimental Cif flag.
824-
* @return true if experimental Cif parsing will be employed
825-
*/
826-
public boolean isUseCif() {
827-
return this.format == Format.CIF;
828-
}
829-
830-
/**
831-
* Use the experimental Bcif parser to acquire structure data.
832-
* @param useBcif use?
833-
*/
834-
public void setUseBcif(boolean useBcif) {
835-
if (useBcif) {
836-
this.format = Format.BCIF;
837-
}
838-
}
839-
840-
/**
841-
* Use the experimental Cif parser to acquire structure data.
842-
* @param useCif use?
843-
*/
844-
public void setUseCif(boolean useCif) {
845-
if (useCif) {
846-
this.format = Format.CIF;
847-
}
848-
}
849-
850-
/**
851-
* Use the legacy PDB format to acquire structure data.
852-
* @param usePdb use?
853-
*/
854-
public void usePdb(boolean usePdb) {
855-
if (usePdb) {
856-
this.format = Format.PDB;
857-
}
805+
return this.useMmtf;
858806
}
859807

860808
private boolean checkLoading(String name) {
@@ -933,25 +881,19 @@ public Structure getStructureForPdbId(String pdbId) throws IOException, Structur
933881

934882
}
935883

936-
switch (format) {
937-
case MMTF:
938-
logger.debug("loading from mmtf");
939-
return loadStructureFromMmtfByPdbId(pdbId);
940-
case MMCIF:
941-
logger.debug("loading from mmcif");
942-
return loadStructureFromCifByPdbId(pdbId);
943-
case CIF:
944-
logger.debug("loading from experimental cif");
945-
return loadStructureFromExperimentalCifByPdbId(pdbId);
946-
case PDB:
947-
logger.debug("loading from pdb");
948-
return loadStructureFromPdbByPdbId(pdbId);
949-
case BCIF:
950-
logger.debug("loading from bcif");
951-
return loadStructureFromBcifByPdbId(pdbId);
952-
default:
953-
throw new IllegalArgumentException("no strategy implemented for format " + format);
884+
Structure s;
885+
if (useMmtf) {
886+
logger.debug("loading from mmtf");
887+
s = loadStructureFromMmtfByPdbId(pdbId);
888+
}
889+
else if (useMmCif) {
890+
logger.debug("loading from mmcif");
891+
s = loadStructureFromCifByPdbId(pdbId);
892+
} else {
893+
logger.debug("loading from pdb");
894+
s = loadStructureFromPdbByPdbId(pdbId);
954895
}
896+
return s;
955897
}
956898

957899
/**
@@ -969,22 +911,6 @@ private Structure loadStructureFromMmtfByPdbId(String pdbId) throws IOException
969911
return structure;
970912
}
971913

972-
private Structure loadStructureFromBcifByPdbId(String pdbId) throws IOException {
973-
logger.debug("Loading structure {} from Bcif file.", pdbId);
974-
BcifFileReader reader = new BcifFileReader();
975-
reader.setFetchBehavior(fetchBehavior);
976-
reader.setObsoleteBehavior(obsoleteBehavior);
977-
return reader.getStructureById(pdbId.toLowerCase());
978-
}
979-
980-
private Structure loadStructureFromExperimentalCifByPdbId(String pdbId) throws IOException {
981-
logger.debug("Loading structure {} experimentally from Cif file.", pdbId);
982-
CifFileReader reader = new CifFileReader();
983-
reader.setFetchBehavior(fetchBehavior);
984-
reader.setObsoleteBehavior(obsoleteBehavior);
985-
return reader.getStructureById(pdbId.toLowerCase());
986-
}
987-
988914
protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException, StructureException {
989915

990916
logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
@@ -1025,4 +951,4 @@ protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException
1025951
return s;
1026952
}
1027953

1028-
}
954+
}

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