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Updates for the MMTF structure reader for the new data structure. #483

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Merged
andreasprlic merged 1 commit into from
May 13, 2016
Merged

Updates for the MMTF structure reader for the new data structure. #483

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42 changes: 25 additions & 17 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

Expand Down Expand Up @@ -70,6 +71,9 @@ public class MmtfStructureReader implements StructureAdapterInterface, Serializa
/** All the chains */
private List<Chain> chainList;

/** All the chains as a list of maps */
private List<Map<String,Chain>> chainMap;

/**
* Instantiates a new bio java structure decoder.
*/
Expand All @@ -78,6 +82,7 @@ public MmtfStructureReader() {
modelNumber = 0;
entityInfoList = new ArrayList<>();
chainList = new ArrayList<>();
chainMap = new ArrayList<>();
}

/**
Expand All @@ -91,15 +96,25 @@ public Structure getStructure() {

@Override
public void finalizeStructure() {
// Ensure all altlocs have all atoms
StructureTools.cleanUpAltLocs(structure);

// Number the remaining ones
int counter =0;
// Add the entity info
for (EntityInfo entityInfo : entityInfoList) {
counter++;
entityInfo.setMolId(counter);
}
structure.setEntityInfos(entityInfoList);
// Add the actual chains
for(int i=0; i<chainMap.size(); i++) {
// Now add the chain information
Map<String, Chain> modelChainMap = chainMap.get(i);
for(Chain modelChain : modelChainMap.values()){
structure.addChain(modelChain, i);
}
}
// Ensure all altlocs have all atoms
StructureTools.cleanUpAltLocs(structure);
}

@Override
Expand All @@ -118,6 +133,7 @@ public void setModelInfo(int inputModelNumber,
int chainCount) {
modelNumber = inputModelNumber;
structure.addModel(new ArrayList<Chain>(chainCount));
chainMap.add(new HashMap<>());
}

/* (non-Javadoc)
Expand All @@ -127,20 +143,17 @@ public void setModelInfo(int inputModelNumber,
@Override
public void setChainInfo(String chainId, String chainName, int groupCount) {
// First check to see if the chain exists
boolean newChain = true;
for (Chain c: structure.getChains(modelNumber)) {
if (c.getId().equals(chainId)) {
newChain = false;
chain = c;
break;
}
Map<String, Chain> modelChainMap = chainMap.get(modelNumber);
if(modelChainMap.containsKey(chainId)){
chain = modelChainMap.get(chainId);
}
// If we need to set a new chain do this
if (newChain){
else{
chain = new ChainImpl();
chain.setId(chainId.trim());
chain.setName(chainName);
structure.addChain(chain, modelNumber);
chain.setAtomGroups(new ArrayList<>(groupCount));
modelChainMap.put(chainId, chain);
chainList.add(chain);
}
}
Expand Down Expand Up @@ -283,7 +296,6 @@ public void setInterGroupBond(int indOne,
// set the new bond
@SuppressWarnings("unused")
BondImpl bond = new BondImpl(atomOne, atomTwo, bondOrder);

}


Expand Down Expand Up @@ -383,10 +395,6 @@ private int getGroupTypIndicator(String currentGroupType) {
@Override
public void setBioAssemblyTrans(int bioAssemblyId, int[] inputChainIndices, double[] inputTransform) {
PDBHeader pdbHeader = structure.getPDBHeader();
List<Chain> totChainList = new ArrayList<>();
for (int i=0; i<structure.nrModels(); i++) {
totChainList.addAll(structure.getChains(i));
}
// Get the bioassembly data
Map<Integer, BioAssemblyInfo> bioAssemblies = pdbHeader.getBioAssemblies();
// Get the bioassembly itself (if it exists
Expand All @@ -407,7 +415,7 @@ public void setBioAssemblyTrans(int bioAssemblyId, int[] inputChainIndices, doub
bioAssTrans.setId(transId.toString());
// If it actually has an index - if it doesn't it is because the chain has no density.
if (currChainIndex!=-1){
bioAssTrans.setChainId(totChainList.get(currChainIndex).getId());
bioAssTrans.setChainId(chainList.get(currChainIndex).getId());
}
else {
continue;
Expand Down