Update to v 1.12.7

We have released on Friday an number of updates to our community contribution detailed below. This is an update to v1.12.7 (the previous released version was 1.12.0), fixing a number of bugs and introducing some improvements to existing nodes. The details provided below show all the intermediate (unreleased) versions and cumulative changes now available.

This update is currently only available in the 3.5 stable release update site due to an ongoing problem with a plugin dependency in the nightly builds release which we hope to resolve within the next week or so.

Update to 1.12.7

  • Efficiency improvements in RCSB Heterogen Details and SMILES Query nodes
  • ePMC Advanced Query node now uses required https: protocol
  • PDB Connector
    • New fields added to EM Report (EM Diffraction Resolution (A), EM Point Symmetry, EM Embedding, EM Staining, EM Vitrification, EM Additional Map)
    • Field emdbId replaced with new name (emdbMap), retaining old ‘EMDB ID’ column name for backwards compatibility
    • Field ‘Specimen Type’ removed in line with its removal at RCSB
    • Optional parameter ‘new’ added in report field XML definition DTD, which is parsed in class ReportField2. If this flag is set, InvalidSettingsExceptions during node settings load/validate are ignored

Update to 1.12.6

  • Fixed version constraint and resolved code issues for RDKit drawing API change

Update to v1.12.5

  • Fixed bug in PDB Heterogen details webservice causing failure when molecular formula XML tag is empty
  • Improved efficiency by making webservice result lazy-parse most fields

Update to v1.12.3

  • Fixes bug in MMP Pair generation resulting in non-canonical transform generation (https://www.knime.com/forum/vernalis/mmpa-reverse-direction-transform-issue)
  • Fixes bug in MMP fragmentation which counts [H] at end of a fragment SMILES as a heavy atom
  • Fixes bug in SpeedySMILES counting [H] at end of fragment SMILES as heavy atom in HAC Count node
  • Fixes bug in SpeedySMILES HAC Count in which attachment point (SMILES ‘*’) atoms where counted as heavy atoms
  • Enhances SpeedySMILES HAC count to correctly handle isotopically labelled and charged explicit H atoms
  • Fixed error in rendering of 1-cut ‘reverse’ fragmentations which flipped the key/value colours

Update to v1.12.2

  • Updated SMARTSviewer node to point to new URL
  • Fixed bugs in PMI calculations leading to symmetrical Discs being categorised as Spheres, and then in incorrect position
    • Incorporated a tolerance in Cubic for comparison of D with 0
    • Corrected error in D=0 roots

Update to v1.12.1

  • Fixed bug in string comparison of Flow Variable Value If Switch nodes

As always, any questions, problems or suggestions, please let us know.