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emckee2006emckee2006
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Merge pull request #2 from biojava/master
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2 parents 66a4f0d + 0754f43 commit 9ba724a

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Lines changed: 480 additions & 621 deletions

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‎biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBBioAssemblyParser.java‎

Lines changed: 160 additions & 275 deletions
Large diffs are not rendered by default.

‎biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileParser.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3026,7 +3026,6 @@ private void triggerEndFileChecks(){
30263026
}
30273027

30283028
if ( bioAssemblyParser != null){
3029-
bioAssemblyParser.finalizeCurrentBioMolecule();
30303029
pdbHeader.setBioUnitTranformationMap(bioAssemblyParser.getTransformationMap());
30313030
pdbHeader.setNrBioAssemblies(bioAssemblyParser.getNrBioAssemblies());
30323031
//System.out.println("setting nr bioAssemblies: " + pdbHeader.getNrBioAssemblies());

‎biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/BioAssemblyTools.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -138,7 +138,7 @@ public static double[][] getBiologicalMoleculeBounds(Structure asymStructure,Li
138138
intChainID = c.getChainID();
139139

140140
for (ModelTransformationMatrix m: transformations) {
141-
if ( ! m.ndbChainId.equals(intChainID))
141+
if ( ! m.getChainId().equals(intChainID))
142142
continue;
143143
Atom na = (Atom)a.clone();
144144
//m.transformPoint(atom.coordinate, transformedCoordinate);
@@ -293,7 +293,7 @@ public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,L
293293

294294

295295
for (ModelTransformationMatrix m: transformations) {
296-
if (! m.ndbChainId.equals(intChainID))
296+
if (! m.getChainId().equals(intChainID))
297297
continue;
298298

299299
m.transformPoint(atom.getCoords(), transformedCoordinate);

‎biojava3-structure/src/main/java/org/biojava/bio/structure/quaternary/BiologicalAssemblyBuilder.java‎

Lines changed: 99 additions & 111 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,30 @@
1+
/*
2+
* BioJava development code
3+
*
4+
* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
19+
*
20+
*/
21+
122
package org.biojava.bio.structure.quaternary;
223

324
import java.util.ArrayList;
425
import java.util.Arrays;
26+
import java.util.Collections;
27+
import java.util.Comparator;
528
import java.util.List;
629

730
import org.biojava.bio.structure.Atom;
@@ -15,134 +38,108 @@
1538
import org.biojava.bio.structure.io.mmcif.model.PdbxStructOperList;
1639
import org.biojava.bio.structure.jama.Matrix;
1740

18-
19-
20-
/** Reconstructs the quaternary structure of a protein from an asymmetric unit
41+
/**
42+
* Reconstructs the quaternary structure of a protein from an asymmetric unit
2143
*
2244
* @author Peter Rose
2345
* @author Andreas Prlic
2446
*
2547
*/
2648
public class BiologicalAssemblyBuilder {
49+
private OperatorResolver operatorResolver;
50+
private List<PdbxStructAssemblyGen> psags;
2751

28-
OperatorResolver operatorResolver;
29-
30-
String asymId ;
31-
32-
PdbxStructAssembly psa;
33-
List<PdbxStructAssemblyGen> psags;
34-
//List<PdbxStructOperList> operators;
52+
private List<ModelTransformationMatrix> modelTransformations;
3553

36-
List<ModelTransformationMatrix> modelTransformations;
37-
38-
//List<String> asymIds;
3954
public BiologicalAssemblyBuilder(){
4055
init();
4156
}
4257

43-
private void init(){
44-
operatorResolver= new OperatorResolver();
45-
modelTransformations = new ArrayList<ModelTransformationMatrix>(1);
46-
47-
}
48-
49-
50-
51-
5258
public Structure rebuildQuaternaryStructure(Structure asymUnit, List<ModelTransformationMatrix> transformations){
53-
59+
// ensure that new chains are build in the same order as they appear in the asymmetric unit
60+
orderTransformationsByChainId(asymUnit, transformations);
61+
5462
Structure s = asymUnit.clone();
5563
List<Chain> transformedChains = new ArrayList<Chain>();
5664
s.setChains(transformedChains);
57-
//System.out.print("rebuilding " + s.getPDBCode() + " ");
58-
//for (Chain c : s.getChains()) {
59-
//System.out.print(c.getChainID());
60-
//if ( c.getInternalChainID() != null) {
61-
//System.out.print("("+c.getInternalChainID()+")");
62-
//}
63-
64-
//}
65-
66-
//asymUnit.getPDBHeader().setBioUnitTranformations(transformations);
67-
6865

69-
//double[] tmpcoords = new double[3];
7066
for (ModelTransformationMatrix max : transformations){
71-
boolean foundChain = false;
72-
for ( Chain c : asymUnit.getChains()){
73-
67+
for (Chain c : asymUnit.getChains()){
68+
7469
String intChainID = c.getInternalChainID();
7570
if ( intChainID == null) {
7671
//System.err.println("no internal chain ID found, using " + c.getChainID() + " ( while looking for " + max.ndbChainId+")");
7772
intChainID = c.getChainID();
7873
}
7974

80-
if ( max.ndbChainId.equals(intChainID)){
81-
82-
/*System.out.println("transforming " + max.ndbChainId + " " + c.getChainID());
83-
System.out.println(max );
84-
System.out.println();
85-
*/
86-
foundChain = true;
87-
Chain newChain = (Chain)c.clone();
75+
if (max.getChainId().equals(intChainID)){
76+
Chain chain = (Chain)c.clone();
8877
Matrix m = max.getMatrix();
89-
//m = m.transpose();
9078
double[] vector = max.getVector();
9179
Atom v = new AtomImpl();
9280
v.setCoords(vector);
93-
for ( Group g :newChain.getAtomGroups()) {
94-
for ( Atom a : g.getAtoms()) {
95-
//max.transformPoint(a.getCoords(), tmpcoords);
96-
//a.setX(tmpcoords[0]);
97-
//a.setY(tmpcoords[1]);
98-
//a.setZ(tmpcoords[2]);
99-
Calc.rotate(a, m);
100-
Calc.shift(a, v);
101-
}
81+
for (Group g : chain.getAtomGroups()) {
82+
Calc.rotate(g, m);
83+
Calc.shift(g, v);
10284
}
10385

104-
105-
addCheckChainModel(s,newChain);
106-
86+
int modelNumber = Integer.parseInt(max.getId());
87+
addChainAndModel(s, chain, modelNumber);
10788
}
10889
}
109-
if (! foundChain){
110-
//System.err.println("could not transform chain: " + max.ndbChainId);
111-
}
11290
}
11391

114-
//s.setChains(transformedChains);
11592
s.setBiologicalAssembly(true);
11693
return s;
117-
118-
11994
}
120-
121-
122-
private void addCheckChainModel(Structure s, Chain newChain) {
123-
for ( int i = 0 ; i < s.nrModels() ; i ++){
124-
List<Chain> model = s.getModel(i);
125-
boolean found = false;
126-
for ( Chain c : model){
127-
if ( c.getChainID().equals(newChain.getChainID())) {
128-
found = true;
129-
break;
95+
96+
/**
97+
* Orders model transformations by chain ids in the same order as in the asymmetric unit
98+
* @param asymUnit
99+
* @param transformations
100+
*/
101+
private void orderTransformationsByChainId(Structure asymUnit, List<ModelTransformationMatrix> transformations) {
102+
final List<String> chainIds = getChainIds(asymUnit);
103+
Collections.sort(transformations, new Comparator<ModelTransformationMatrix>() {
104+
public int compare(ModelTransformationMatrix t1, ModelTransformationMatrix t2) {
105+
// set sort order only if the two ids are identical
106+
if (t1.getId().equals(t2.getId())) {
107+
return chainIds.indexOf(t1.getChainId()) - chainIds.indexOf(t2.getChainId());
130108
}
109+
return 0;
110+
}
111+
});
112+
}
113+
114+
/**
115+
* Returns a list of chain ids in the order they are specified in the ATOM
116+
* records in the asymmetric unit
117+
* @param asymUnit
118+
* @return
119+
*/
120+
private List<String> getChainIds(Structure asymUnit) {
121+
List<String> chainIds = new ArrayList<String>();
122+
for ( Chain c : asymUnit.getChains()){
123+
String intChainID = c.getInternalChainID();
124+
if ( intChainID == null) {
125+
//System.err.println("no internal chain ID found, using " + c.getChainID() + " ( while looking for " + max.ndbChainId+")");
126+
intChainID = c.getChainID();
131127
}
132-
if ( ! found){
133-
134-
model.add(newChain);
135-
return;
136-
}
137-
128+
chainIds.add(intChainID);
129+
}
130+
return chainIds;
131+
}
132+
133+
private void addChainAndModel(Structure s, Chain newChain, int modelCount) {
134+
if (modelCount == 0) {
135+
s.addChain(newChain);
136+
} else if (modelCount > s.nrModels()) {
137+
List<Chain> newModel = new ArrayList<Chain>();
138+
newModel.add(newChain);
139+
s.addModel(newModel);
140+
} else {
141+
s.addChain(newChain, modelCount-1);
138142
}
139-
140-
// all existing models contain already a chain with the same ID. add a new model
141-
List<Chain> newModel = new ArrayList<Chain>();
142-
newModel.add(newChain);
143-
s.addModel(newModel);
144-
145-
146143
}
147144

148145
/**
@@ -153,26 +150,20 @@ private void addCheckChainModel(Structure s, Chain newChain) {
153150
* @return list of transformation matrices to generate macromolecular assembly
154151
*/
155152
public ArrayList<ModelTransformationMatrix> getBioUnitTransformationList(PdbxStructAssembly psa, List<PdbxStructAssemblyGen> psags, List<PdbxStructOperList> operators) {
156-
157153
//System.out.println("Rebuilding " + psa.getDetails() + " | " + psa.getOligomeric_details() + " | " + psa.getOligomeric_count());
158154
//System.out.println(psag);
159155
init();
160-
this.psa=psa;
161156
this.psags = psags;
162157

163-
//this.operators = operators;
164-
165-
asymId = psa.getId();
158+
psa.getId();
166159

167160
for (PdbxStructOperList oper: operators){
168161
ModelTransformationMatrix transform = new ModelTransformationMatrix();
169-
transform.id = oper.getId();
162+
transform.setId(oper.getId());
170163
transform.setTransformationMatrix(oper.getMatrix(), oper.getVector());
171164
modelTransformations.add(transform);
172165
}
173166

174-
///
175-
176167
ArrayList<ModelTransformationMatrix> transformations = getBioUnitTransformationsListUnaryOperators(psa.getId());
177168
transformations.addAll(getBioUnitTransformationsListBinaryOperators(psa.getId()));
178169
transformations.trimToSize();
@@ -193,7 +184,6 @@ private ArrayList<ModelTransformationMatrix> getBioUnitTransformationsListBinary
193184

194185
operatorResolver.parseOperatorExpressionString(psag.getOper_expression());
195186

196-
197187
// apply binary operators to the specified chains
198188
// Example 1M4X: generates all products of transformation matrices (1-60)(61-88)
199189
for (String chainId : asymIds) {
@@ -202,36 +192,29 @@ private ArrayList<ModelTransformationMatrix> getBioUnitTransformationsListBinary
202192
ModelTransformationMatrix original1 = getModelTransformationMatrix(operator.getElement1());
203193
ModelTransformationMatrix original2 = getModelTransformationMatrix(operator.getElement2());
204194
ModelTransformationMatrix transform = ModelTransformationMatrix.multiply4square_x_4square2(original1, original2);
205-
transform.ndbChainId = chainId;
206-
transform.id = original1.id + "x" + original2.id;
195+
transform.setChainId(chainId);
196+
transform.setId(original1.getId() + "x" + original2.getId());
207197
transformations.add(transform);
208198
}
209199
}
210-
211200
}
212201

213202
}
214203

215-
// apply binary operators to the specified chains
216-
// Example 1M4X: generates all products of transformation matrices (1-60)(61-88)
217-
218-
//System.out.println("BioUnitTrasnformListBinaryOperators " + assemblyId + " " + transformations.size());
219204
return transformations;
220205
}
221206

222207
private ModelTransformationMatrix getModelTransformationMatrix(String operator) {
223208
for (ModelTransformationMatrix transform: modelTransformations) {
224-
if (transform.id.equals(operator)) {
209+
if (transform.getId().equals(operator)) {
225210
return transform;
226211
}
227212
}
228213
System.err.println("Could not find modelTransformationmatrix for " + operator);
229214
return new ModelTransformationMatrix();
230215
}
231216

232-
private ArrayList<ModelTransformationMatrix> getBioUnitTransformationsListUnaryOperators(String assemblyId) {
233-
234-
217+
private ArrayList<ModelTransformationMatrix> getBioUnitTransformationsListUnaryOperators(String assemblyId) {
235218
ArrayList<ModelTransformationMatrix> transformations = new ArrayList<ModelTransformationMatrix>();
236219

237220

@@ -249,14 +232,19 @@ private ArrayList<ModelTransformationMatrix> getBioUnitTransformationsListUnaryO
249232
//System.out.println("transforming " + chainId + " " + operator);
250233
ModelTransformationMatrix original = getModelTransformationMatrix(operator);
251234
ModelTransformationMatrix transform = new ModelTransformationMatrix(original);
252-
transform.ndbChainId = chainId;
253-
transform.id = operator;
235+
transform.setChainId(chainId);
236+
transform.setId(operator);
254237
transformations.add(transform);
255238
}
256239
}
257240
}
258241
}
259-
//System.out.println("BioUnitTrasnformListUnary " + assemblyId + " " + transformations.size());
242+
260243
return transformations;
261244
}
245+
246+
private void init(){
247+
operatorResolver= new OperatorResolver();
248+
modelTransformations = new ArrayList<ModelTransformationMatrix>(1);
249+
}
262250
}

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