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Fix #929 #1023

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Merged
josemduarte merged 2 commits into from
Feb 25, 2022
Merged

Fix #929 #1023

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4186eed
Fix NullPointerException
zedomel Feb 15, 2022
2124007
Merge pull request #1 from zedomel/issue929
zedomel Feb 15, 2022
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16 changes: 8 additions & 8 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
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Original file line number Diff line number Diff line change
Expand Up @@ -296,15 +296,15 @@ private void formDisulfideBond(SSBondImpl disulfideBond) {
// The PDB format uses author chain ids to reference chains. But one author chain id corresponds to multiple asym ids,
// thus we need to grab all the possible asym ids (poly and nonpoly) and then try to find the atoms
// See issue https://github.com/biojava/biojava/issues/929
String polyChainId1 = structure.getPolyChainByPDB(disulfideBond.getChainID1()).getId();
String polyChainId2 = structure.getPolyChainByPDB(disulfideBond.getChainID2()).getId();
Chain polyChain1 = structure.getPolyChainByPDB(disulfideBond.getChainID1());
Chain polyChain2 = structure.getPolyChainByPDB(disulfideBond.getChainID2());
List<Chain> nonpolyChains1 = structure.getNonPolyChainsByPDB(disulfideBond.getChainID1());
List<Chain> nonpolyChains2 = structure.getNonPolyChainsByPDB(disulfideBond.getChainID2());

List<String> allChainIds1 = new ArrayList<>();
List<String> allChainIds2 = new ArrayList<>();
if (polyChainId1!=null) allChainIds1.add(polyChainId1);
if (polyChainId2!=null) allChainIds2.add(polyChainId2);
if (polyChain1!=null) allChainIds1.add(polyChain1.getId());
if (polyChain2!=null) allChainIds2.add(polyChain2.getId());
if (nonpolyChains1!=null) nonpolyChains1.forEach(npc -> allChainIds1.add(npc.getId()));
if (nonpolyChains2!=null) nonpolyChains2.forEach(npc -> allChainIds2.add(npc.getId()));

Expand Down Expand Up @@ -348,17 +348,17 @@ public void formLinkRecordBond(LinkRecord linkRecord) {
// The PDB format uses author chain ids to reference chains. But one author chain id corresponds to multiple asym ids,
// thus we need to grab all the possible asym ids (poly and nonpoly) and then try to find the atoms
// See issue https://github.com/biojava/biojava/issues/943
String polyChainId1 = structure.getPolyChainByPDB(linkRecord.getChainID1()).getId();
String polyChainId2 = structure.getPolyChainByPDB(linkRecord.getChainID2()).getId();
Chain polyChain1 = structure.getPolyChainByPDB(linkRecord.getChainID1());
Chain polyChain2 = structure.getPolyChainByPDB(linkRecord.getChainID2());
List<Chain> nonpolyChains1 = structure.getNonPolyChainsByPDB(linkRecord.getChainID1());
List<Chain> nonpolyChains2 = structure.getNonPolyChainsByPDB(linkRecord.getChainID2());
Chain waterChain1 = structure.getWaterChainByPDB(linkRecord.getChainID1());
Chain waterChain2 = structure.getWaterChainByPDB(linkRecord.getChainID2());

List<String> allChainIds1 = new ArrayList<>();
List<String> allChainIds2 = new ArrayList<>();
if (polyChainId1!=null) allChainIds1.add(polyChainId1);
if (polyChainId2!=null) allChainIds2.add(polyChainId2);
if (polyChain1!=null) allChainIds1.add(polyChain1.getId());
if (polyChain2!=null) allChainIds2.add(polyChain2.getId());
if (nonpolyChains1!=null) nonpolyChains1.forEach(npc -> allChainIds1.add(npc.getId()));
if (nonpolyChains2!=null) nonpolyChains2.forEach(npc -> allChainIds2.add(npc.getId()));
if (waterChain1!=null && linkRecord.getResName1().equals("HOH")) allChainIds1.add(waterChain1.getId());
Expand Down