+ if (isAlphafoldModel())
+ {
+ // TODO - work out how to handle different ways that pAE is provided
+ //
+ try
+ {
+ Console.info("retrieving pAE for " + pdbId);
+ Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+ EBIAlfaFold.retrieve_AlphaFold_pAE(pdbId, al, null);
+ if (al.getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ {
+ annotations.add(alann);
+ }
+ }
+ ;
+ } catch (Throwable t)
+ {
+ Console.error("Couldn't get the pAE for " + pdbId, t);
+ }
+ }