{
if (targetChainId.trim().length() == 0)
{
- targetChainId = " ";
+ targetChainId = StructureMapping.NO_CHAIN;
}
else
{
*/
int max = -10;
AlignSeq maxAlignseq = null;
- String maxChainId = " ";
+ String maxChainId = StructureMapping.NO_CHAIN; // space
PDBChain maxChain = null;
boolean first = true;
for (PDBChain chain : pdb.getChains())
.getString("status.obtaining_mapping_with_phyre2_template_alignment"));
String fastaFile = getPhyre2FastaFileFor(pdbFile);
StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
- .getStructureMapping(seq, pdbFile, fastaFile, " ");
+ .getStructureMapping(seq, pdbFile, fastaFile,
+ StructureMapping.NO_CHAIN);
seqToStrucMapping.add(phyre2ModelMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
maxChain.transferRESNUMFeatures(seq, null);
&& sm.pdbchain.equals(atom.getChain()))
{
int indexpos = sm.getSeqPos(atom.getPdbResNum());
- if (lastipos != indexpos && lastseq != sm.sequence)
+ if (lastipos != indexpos || lastseq != sm.sequence)
{
results.addResult(sm.sequence, indexpos, indexpos);
lastipos = indexpos;