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Bioassembly fails for a structure with null seqres groups (MMTF only) #792

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Bioassembly fails for a structure with null seqres groups (MMTF only)#792
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@biocryst

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@biocryst
biocryst
opened on Aug 21, 2018

StructureIO.getStructure("BIO:2X3T:1") causes exception when cloning the asymmetric unit, if MMTF is used (cache.setUseMmtf(true)). The reason is null seqres groups.

There are two issues here: difference in the data between MMTF and MMCIF, and "safe" code.

I can make the code a bit safer, i.e. take this test:

biojava/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java

Lines 190 to 193 in 8a7b651

if (seqResGroup==null) {
tmpSeqRes.add(null);
continue;
}

and put a similar one here:

biojava/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java

Lines 638 to 643 in 8a7b651

public void setSeqResGroups(List<Group> groups){
for (Group g: groups){
g.setChain(this);
}
this.seqResGroups = groups;
}

I am not sure what to do with the difference in the data at this point.

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