try
{
- if (pdbFile != null && isCIFFile(pdbFile))
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
{
pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
secStructServices, pdbFile, protocol);
}
ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
+ if (isMapUsingSIFTs && seq.isProtein())
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with SIFTS");
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"));
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
else
{
setProgressBar(null);
- setProgressBar("Obtaining mapping with NW alignment");
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"));
seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
maxChain, pdb, maxAlignseq));
}
return "cif".equalsIgnoreCase(fileExt);
}
+ /**
+ * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+ * uniprot or PDB
+ *
+ * @param seq
+ * @param pdbFile
+ * @param targetChainId
+ * @param pdb
+ * @param maxChain
+ * @param sqmpping
+ * @param maxAlignseq
+ * @return
+ * @throws SiftsException
+ */
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,