.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- StructureMapping mapping;
+ StructureMapping siftsMapping;
try
{
- mapping = getStructureMapping(seq, pdbFile, targetChainId, pdb,
- maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ pdb, maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(siftsMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
} catch (SiftsException e)
{
- // e.printStackTrace();
// fall back to NW alignment
System.err.println(e.getMessage());
- seqToStrucMapping.add(getNWMappings(seq, pdbFile,
- targetChainId,
- maxChain, pdb, maxAlignseq));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ targetChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
}
}
else
{
- try
+ ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
{
- ArrayList<StructureMapping> tempMapping = new ArrayList<StructureMapping>();
- for (PDBChain chain : pdb.getChains())
+ try
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile,
chain.id, pdb, chain, sqmpping, maxAlignseq);
- tempMapping.add(mapping);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
}
- seqToStrucMapping.addAll(tempMapping);
- } catch (SiftsException e)
+ }
+ if (!foundSiftsMappings.isEmpty())
{
- // e.printStackTrace();
- // fall back to NW alignment
- System.err.println(e.getMessage());
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+ sqmpping);
+ }
+ else
+ {
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
}
}
}