Update to v 1.9.0 - Fixed to PDB Downloader nodes


Following the discovery of a bug in these nodes as a result of files changing URLs on the RCSB website, we have updated our code.  The old nodes have been deprecated (they do now work though!), and new versions introduced.

The changes are:

  • More file type options (NMR shifts & constraints)
  • The new versions dont fail on missing data (because not all structures have data for every type!)
  • URLs for PDB downloads fixed following changes on RCSB website for both old and new versions
  • FileHelper readURLToString method attempts to follow 301 return type redirects (i.e. any of the nodes loading text files from remote urls will now act in this manner)
  • https: protocol now accepted for URLs in any of the downloader nodes (in addition to file:, knime:, http:, ftp:)

At the moment, it looks like more files are becoming available progressively (we had a test case fail today which passed yesterday as more files had become availalbe for the NMR constraints), so if you are wanting anything other than PDB, mmCIF or FASTA it might be worth giving it a few more days...

The new node has a new dialog to select the output formats:

(That was why we had to deprecate - but it allows us to add further new options relatively simply in the future)

Thanks to forum users @Emilie Pihan and @Laura_C for reporting this at https://tech.knime.org/forum/vernalis/pdb-downloader-and-pdb-downloader-source

Finally, whilst this hasnt needed any changes to our nodes, we draw attention also to some other changes in the RCSB webservices which might affect users with routine queries using the PDBConnector family of nodes - see the post here for details

As always, any questions/comments, then please get in touch.