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josemduartejosemduarte
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Now getting mmSize from num operators and chains.
The oligomeric size annotation in file is now ignored (often inconsistent, sometimes not even present)
1 parent 38edbb7 commit 5c39b20

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7 files changed

+77
-95
lines changed

7 files changed

+77
-95
lines changed

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -126,7 +126,7 @@ public void testVeryLongPdbVsMmCif() throws IOException, StructureException {
126126

127127
@Test
128128
public void testSingle() throws IOException, StructureException {
129-
testAll(Arrays.asList("4a10"));
129+
testAll(Arrays.asList("4kro"));
130130
}
131131

132132
@After
@@ -394,7 +394,7 @@ private void testHeader(Structure sPdb, Structure sCif) {
394394
// there's an inconsistency in 4amh pdb vs mmCIF in mmSize
395395
if (sPdb.getPDBCode().equalsIgnoreCase("4amh")) continue;
396396

397-
assertEquals("Macromolecular size of assemblies doesn't coincide",
397+
assertEquals("Macromolecular size of assembly "+id+" doesn't coincide",
398398
batPdb.get(id).getMacromolecularSize(), batCif.get(id).getMacromolecularSize());
399399
}
400400
}

‎biojava-structure/src/main/java/demo/DemoMMCIFReader.java‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ public static void main(String[] args){
4545

4646
demo.loadSimple();
4747

48-
//demo.loadFromDirectAccess();
48+
demo.loadFromDirectAccess();
4949

5050
}
5151

@@ -84,6 +84,8 @@ public void loadFromDirectAccess(){
8484

8585
try {
8686
Structure s = pdbreader.getStructureById(pdbId);
87+
88+
System.out.println("Getting chain H of 1A4W");
8789

8890
List<Chain> hs = s.getNonPolyChainsByPDB("H");
8991

@@ -97,7 +99,7 @@ public void loadFromDirectAccess(){
9799
}
98100

99101
System.out.println("Accessing QWE directly: ");
100-
Group qwe = h.getGroupByPDB(new ResidueNumber("H",373,null));
102+
Group qwe = s.getNonPolyChainsByPDB("H").get(2).getGroupByPDB(new ResidueNumber("H",373,null));
101103

102104
System.out.println(qwe.getChemComp());
103105

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java‎

Lines changed: 31 additions & 75 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@
2323
import org.biojava.nbio.structure.jama.Matrix;
2424
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
2525
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
26-
import org.slf4j.Logger;
27-
import org.slf4j.LoggerFactory;
26+
//import org.slf4j.Logger;
27+
//import org.slf4j.LoggerFactory;
2828

2929
import java.util.*;
3030

@@ -38,15 +38,14 @@
3838
*/
3939
public class PDBBioAssemblyParser {
4040

41-
private static final Logger logger = LoggerFactory.getLogger(PDBBioAssemblyParser.class);
41+
//private static final Logger logger = LoggerFactory.getLogger(PDBBioAssemblyParser.class);
4242

4343
private Integer currentBioMolecule = null;
4444
private List<String> currentChainIDs = new ArrayList<String>();
4545
private Matrix currentMatrix = null;
4646
private double[] shift = null;
4747
private Map<Integer,BioAssemblyInfo> transformationMap = new HashMap<Integer, BioAssemblyInfo>();
4848
private int modelNumber = 1;
49-
private int currentMmSize;
5049

5150
private List<BiologicalAssemblyTransformation> transformations;
5251

@@ -62,13 +61,17 @@ public void pdb_REMARK_350_Handler(String line) {
6261
initialize();
6362
currentBioMolecule = Integer.parseInt(line.substring(24).trim());
6463

65-
} else if ( line.matches("REMARK 350 \\w+ DETERMINED BIOLOGICAL UNIT:.*" ) ||
66-
line.matches("REMARK 350 \\w+ DETERMINED QUATERNARY STRUCTURE:.*" )) {
64+
}
65+
// not parsing anymore the size (from biojava 5.0), thus this is not needed anymore
66+
// eventually if needed this could be used to
67+
// infer if bioassembly is author or software determined
68+
//else if ( line.matches("REMARK 350 \\w+ DETERMINED BIOLOGICAL UNIT:.*" ) ||
69+
// line.matches("REMARK 350 \\w+ DETERMINED QUATERNARY STRUCTURE:.*" )) {
6770
// text can be :
6871
// author determined biological unit
6972
// software determined quaternary structure
70-
currentMmSize = getMmSize(line);
71-
} else if ( line.startsWith("REMARK 350 APPLY THE FOLLOWING TO CHAINS:")) {
73+
//}
74+
else if ( line.startsWith("REMARK 350 APPLY THE FOLLOWING TO CHAINS:")) {
7275
currentChainIDs.clear();
7376
addToCurrentChainList(line);
7477

@@ -80,10 +83,10 @@ public void pdb_REMARK_350_Handler(String line) {
8083
addToCurrentChainList(line);
8184

8285
} else if ( line.startsWith("REMARK 350 BIOMT")) {
83-
if (readMatrix(line)) {
84-
saveMatrix();
85-
modelNumber++;
86-
}
86+
if (readMatrix(line)) {
87+
saveMatrix();
88+
modelNumber++;
89+
}
8790
}
8891
}
8992

@@ -139,79 +142,18 @@ private void saveMatrix() {
139142
if (!transformationMap.containsKey(currentBioMolecule)) {
140143
BioAssemblyInfo bioAssembly = new BioAssemblyInfo();
141144
bioAssembly.setId(currentBioMolecule);
142-
if (currentMmSize==0) {
143-
logger.warn("No macromolecular size could be parsed for biological assembly {}",currentBioMolecule);
144-
}
145-
bioAssembly.setMacromolecularSize(currentMmSize);
146145
bioAssembly.setTransforms(transformations);
147146
transformationMap.put(currentBioMolecule,bioAssembly);
148147
}
149148
}
150149

151-
private int getMmSize(String line) {
152-
int index = line.indexOf(':');
153-
String mmString = line.substring(index+1,line.length()-1).trim().toLowerCase();
154-
return getSizefromString(mmString);
155-
}
156-
157-
private static int getSizefromString(String oligomer){
158-
int size=0;
159-
160-
oligomer = oligomer.toLowerCase();
161-
162-
if (oligomer.equals("monomeric")) {
163-
size = 1;
164-
} else if (oligomer.equals("dimeric")) {
165-
size = 2;
166-
} else if (oligomer.equals("trimeric")) {
167-
size = 3;
168-
} else if (oligomer.equals("tetrameric")) {
169-
size = 4;
170-
} else if (oligomer.equals("pentameric")) {
171-
size = 5;
172-
} else if (oligomer.equals("hexameric")) {
173-
size = 6;
174-
} else if (oligomer.equals("heptameric")) {
175-
size = 7;
176-
} else if (oligomer.equals("octameric")) {
177-
size = 8;
178-
} else if (oligomer.equals("nonameric")) {
179-
size = 9;
180-
} else if (oligomer.equals("decameric")) {
181-
size = 10;
182-
} else if (oligomer.equals("undecameric")) {
183-
size = 11;
184-
} else if (oligomer.equals("dodecameric")) {
185-
size = 12;
186-
} else if (oligomer.equals("tridecameric")) {
187-
size = 13;
188-
} else if (oligomer.equals("tetradecameric")) {
189-
size = 14;
190-
} else if (oligomer.equals("pentadecameric")) {
191-
size = 15;
192-
} else if (oligomer.equals("hexadecameric")) {
193-
size = 16;
194-
} else if (oligomer.equals("heptadecameric")) {
195-
size = 17;
196-
} else if (oligomer.equals("octadecameric")) {
197-
size = 18;
198-
} else if (oligomer.equals("nonadecameric")) {
199-
size = 19;
200-
} else if (oligomer.equals("eicosameric")) {
201-
size = 20;
202-
} else if( oligomer.matches("(\\d+).*")) {
203-
size = Integer.parseInt((oligomer.replaceAll("(\\d+).*", "$1")));
204-
}
205-
return size;
206-
}
207-
208150
/**
209151
* Parses list of chain ids (A, B, C, etc.)
210152
*/
211153
private void addToCurrentChainList(String line) {
212154
int index = line.indexOf(":");
213155
String chainList = line.substring(index+1).trim();
214-
// split by spaces or commas
156+
// split by spaces or commas
215157
String[] chainIds = chainList.split("[ ,]+");
216158
currentChainIDs.addAll(Arrays.asList(chainIds));
217159
}
@@ -222,6 +164,20 @@ private void initialize() {
222164
currentBioMolecule = null;
223165
shift = new double[3];
224166
modelNumber = 1;
225-
currentMmSize = 0;
167+
}
168+
169+
/**
170+
* Set the macromolecularSize fields of the parsed bioassemblies.
171+
* This can only be called after the full PDB file has been read so that
172+
* all the info for all bioassemblies has been gathered.
173+
* Note that an explicit method to set the field is necessary here because
174+
* in PDB files the transformations contain only the author chain ids, corresponding
175+
* to polymeric chains, whilst in mmCIF files the transformations
176+
* contain all asym ids of both polymers and non-polymers.
177+
*/
178+
public void setMacromolecularSizes() {
179+
for (BioAssemblyInfo bioAssembly : transformationMap.values()) {
180+
bioAssembly.setMacromolecularSize(bioAssembly.getTransforms().size());
181+
}
226182
}
227183
}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2726,6 +2726,7 @@ private void triggerEndFileChecks(){
27262726
}
27272727

27282728
if ( bioAssemblyParser != null){
2729+
bioAssemblyParser.setMacromolecularSizes();
27292730
pdbHeader.setBioAssemblies(bioAssemblyParser.getTransformationMap());
27302731
}
27312732

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java‎

Lines changed: 18 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -804,30 +804,35 @@ public void documentEnd() {
804804
// these are the transformations that need to be applied to our model
805805
List<BiologicalAssemblyTransformation> transformations = builder.getBioUnitTransformationList(psa, psags, structOpers);
806806

807-
int mmSize = 0;
808807
int bioAssemblyId = -1;
809808
try {
810809
bioAssemblyId = Integer.parseInt(psa.getId());
811810
} catch (NumberFormatException e) {
812811
logger.info("Could not parse a numerical bio assembly id from '{}'",psa.getId());
813812
}
814-
try {
815-
mmSize = Integer.parseInt(psa.getOligomeric_count());
816-
} catch (NumberFormatException e) {
817-
if (bioAssemblyId!=-1)
818-
// if we have a numerical id, then it's unusual to have no oligomeric size: we warn about it
819-
logger.warn("Could not parse oligomeric count from '{}' for biological assembly id {}",
820-
psa.getOligomeric_count(),psa.getId());
821-
else
822-
// no numerical id (PAU,XAU in virus entries), it's normal to have no oligomeric size
823-
logger.info("Could not parse oligomeric count from '{}' for biological assembly id {}",
824-
psa.getOligomeric_count(),psa.getId());
825-
}
826813

827814
// if bioassembly id is not numerical we throw it away
828815
// this happens usually for viral capsid entries, like 1ei7
829816
// see issue #230 in github
830817
if (bioAssemblyId!=-1) {
818+
int mmSize = 0;
819+
// note that the transforms contain asym ids of both polymers and non-polymers
820+
// For the mmsize, we are only interested in the polymers
821+
for (BiologicalAssemblyTransformation transf:transformations) {
822+
Chain c = structure.getChain(transf.getChainId());
823+
if (c==null) {
824+
logger.warn("Could not find asym id {} specified in struct_assembly_gen", transf.getChainId());
825+
continue;
826+
}
827+
if (c.getEntityType() == EntityType.POLYMER &&
828+
// for entries like 4kro, sugars are annotated as polymers but we
829+
// don't want them in the macromolecularSize count
830+
!c.getEntityInfo().getDescription().contains("SUGAR") ) {
831+
832+
mmSize++;
833+
}
834+
}
835+
831836
BioAssemblyInfo bioAssembly = new BioAssemblyInfo();
832837
bioAssembly.setId(bioAssemblyId);
833838
bioAssembly.setMacromolecularSize(mmSize);

‎biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyInfo.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -75,8 +75,8 @@ public void setTransforms(List<BiologicalAssemblyTransformation> transforms) {
7575

7676
/**
7777
* Returns the macromolecular size of this biological assembly, i.e.
78-
* the number of polymeric chains (protein or nucleotide chains) in the biological
79-
* assembly.
78+
* the number of polymeric chains (protein or nucleotide chains, not sugars)
79+
* in the biological assembly.
8080
* @return
8181
*/
8282
public int getMacromolecularSize() {

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

Lines changed: 19 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -50,19 +50,37 @@ public void test3FAD() throws IOException, StructureException{
5050
@Test
5151
public void test5LDH() throws IOException, StructureException{
5252
testID("5LDH",1, 4);
53-
testID("5LDH",2, 0); // bioassembly 2 has 2 as mmsize, but at the moment the parsed value from mmcif files says 0
53+
54+
// the pdb file of 5ldh contains only 1 bioassembly, whilst the mmcif contains 2,
55+
// thus we can't test here the comparison between the 2
56+
//testID("5LDH",2, 2);
5457

5558
// in 5ldh there's also PAU and XAU but those are ignored, see github issue #230
5659

5760
boolean gotException = false;
5861
try {
62+
AtomCache cache = new AtomCache();
63+
cache.setUseMmCif(true);
64+
StructureIO.setAtomCache(cache);
5965
StructureIO.getBiologicalAssembly("5LDH",3);
6066
} catch (StructureException e) {
6167
gotException = true;
6268
}
6369

6470
assertTrue("Bioassembly 3 for PDB id 5LDH should fail with a StructureException!", gotException);
6571

72+
// bioassembly 2 does exist in mmcif file, let's check that
73+
gotException = false;
74+
try {
75+
AtomCache cache = new AtomCache();
76+
cache.setUseMmCif(true);
77+
StructureIO.setAtomCache(cache);
78+
StructureIO.getBiologicalAssembly("5LDH",2);
79+
} catch (StructureException e) {
80+
gotException = true;
81+
}
82+
assertTrue("Bioassembly 2 for PDB id 5LDH should not fail with a StructureException!", !gotException);
83+
6684
}
6785

6886
@Test

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