Vernalis Release Notes / Changelog

Current build versions

Update Site Version Last Modified
Nightly 1.12.0 21-Jul-2017
Stable (v3.4) 1.12.0 14-Sep-2017
Stable (v 3.3) 1.12.0 14-Sep-2017
Stable (v 3.2) 1.12.0 14-Sep-2017
Stable (v 3.1) 1.8.1 02-Nov-2016
Stable (v 3.0) 1.6.0 25-Nov-2015
Stable (v 2.12) 1.5.0 11-Nov-2015
Stable (v 2.11) 1.5.0 11-Nov-2015
Stable (v 2.10) 1.4.0 18-May-2015
Stable (v 2.9) 1.1.5 04-Nov-2014
Stable (v 2.8) 1.1.2 25-Mar-2014

Changelog

14-Sep-2017 - v1.12.0 (v3.4, v3.3, and v3.2)

21-Jul-2017 - v1.12.0 (Nightly only)

  • Added 29 new fingerprint manipulation nodes
  • Added new Aggregation operators for fingerprint manipulations in GroupBy and related nodes
  • Deprecated original Vernalis Fingerprint Properties node

13-Jul-2017 - v1.11.2 (v3.2)

12-Jul-2017 - v1.11.2 (Nightly, v3.4, v3.3)

Minor bug fixes:

  • Output Smiles Adapter Cells for all molecule outputs
  • Output Types set to SmilesAdapterCell.RAW_TYPE via new constants in MMPConstants for all molecule outputs (makes compatible with Molecule Type Cast output)
  • All nodes now recognise either SmilesValue or SmilesAdapterCells for SMILES input columns

11-Jul-2017 - v1.11.1 (Nightly, v3.2, v3.3, v3.4)

Minor bug fixes:

  • Require JavaSE1.8 RTE for all plugins
  • MMP ProgressTableModel made threadsafe
  • Apply Transform node has correct regex for selecting the 'Left' AP fingerprint column
  • Apply Transform node handles, via warning, the situation when no fingerprint column properties are present (uses default settings and shows node warning)

07-Jul-2017 - v1.11.0 (Nightly only)

This is a major overhaul of the MMP Nodes which has been described at recent Cheminformatics SIGs and the Berlin Spring 2017 UGM.  Many of the original nodes have been deprecated, a number of new nodes and features added, and many of the new nodes are now streamable.

  • All Nodes
    • Performance improvements
    •  New predefined fragmentation patterns ('MATSY', 'Peptide Sidechains', 'Nucleic Acid Sidechains')
    • Improved rSMARTS validation
      • Now requires the bond between the two atoms to be both single and acyclic
      • Allows more complex SMARTS atoms matches (including recursive SMARTS)
      • No longer requires the SMARTS to be provided as an rSMARTS - although this is still supported for backwards compatibility
      • No longer requires atoms to be numbers in the SMARTS match 
  • Filtering (Updated)
    • Updated faster implementation
    • Streamable
    • Previous versions deprecated
  • Fragmentation nodes (UPDATED)
    • Performance improvements
    • Memory leaks fixed
    • AP Fingerprint columns have properties describing creation settings to avoid mismatch
    • Graph Distance AP fingerprint vectos added
    • ID can now be the RowID
    • HiLite mapping optionally implemented
    • New Progress View
    • Pass-through of data columns
    • Rendering of fragmentation
    • Complexity filter
    • Behavioural change to remove explicit H's for 1 cut option
    • Additional option regarding incoming explicit H's
    • Streamable
    • '3rd Gen' version deprecated
  • Pair Generation (UPDATED & NEW)
    • Performance improvements including parallelisation
    • HiLite mapping optionally implemented
    • Transforms can be filtered by
      • Heavy-Atom-Count change
      • Graph distance similarity
    • Remove explicit H's from pair output no longer available as an option
    • Added option to require attachment points to be attached by single, acyclic bonds in SMARTS pattern
    • Pass-through, difference (L-R or R-L) and ratio (L/R or R/L) of data columns from left or right of transform pair
    • New 'Reference Table' version of pair generation node implemented, only returning transforms between the rows of the two input tables
    • Deprecated older version
  • Apply Transforms (NEW)
    • New node to apply table of rSMARTS transforms
    • Allows AP-fingerprint environment filtering
    • Node Views showing progress, including currently processed transform(s)
    • Limited stereochemistry generation handling at present time
  • Rendering Nodes (NEW)
    • Show matching bonds (also calculates number of matching bonds)
    • Show cuttable bonds (also calculates number of cuttable bonds)
    • Streamable

23-Jun-2017 - v1.10.0 (Nightly, v3.3, v3.2)

  • Added new Generic Run-for/to-time Loop Start nodes
  • Fixed Timed Loop End nodes to show correct last iteration count in flow variables
  • Added possibility for user cancellation during all Timed Loop Start nodes

22-Jun-2017 - v1.9.0 (Nightly, v3.3, v3.2)

  • Existing PDB Downloader nodes deprecated
  • New PDB Downloader nodes introduced
    • More file type options (NMR shifts & constraints)
    • New versions dont fail on missing data
  • 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:)

06-Jun-2017 - v1.8.5 (Nightly)

  • Fixed undesired node execution failure when SpeedySMILES de-salt node encounters empty or missing input cell

01-Jun-2017 - v1.8.4 (Nightly, v 3.3, v 3.2)

  • Fixed bugs introduced into Matched Molecular Pairs plugin double bond stereochemistry handling by latest updates to RDKit

25-Jan-2017 - v1.8.3 (Nightly, v 3.3, v 3.2)

  • Fixed bug in Speedy SMILES row filter/splitters which cause missing cells to throw NullPointerException

16-Nov-2016 - v1.8.2 (Nightly)

  • Addreses loop end feature request from forum  for the multiple port loop ends (3 port, upto 4 port, upto 6 ports) and the timed loop ends (1 port, 2 port, 3 port, upto 4 ports)
  • All settings are now applied on a per-port basis
  • Added options to allow changing column types and changing table specs, in line with the KNIME core loop end nodes
  • Implemented the 'Row Key Policy' option (this was a bug in which the change from the 'Generate unique row IDs' check box meant that this was unimplemented)
  • Settings for non-connected optional input ports are disabled in the node configuration dialog

02-Nov-2016 - v1.8.1 (Nightly, v3.2, v3.1)

  • Fixed change in behaviour of European PMC Advanced query node due to remote webservice changes
    • Added options for page size and email address to register to remote service
  • Made further existing nodes streamable
  • Fixed dependency issues preventing installation to KNIME 3.1

31-Oct-2016 - v1.8.0 (v3.2)

  • 'Speedy SMILES' nodes (16 nodes) added for fast high-throughput pre-processing of SMILES strings (see slidesfrom 5th Cheminformatics SIG for details)
  • Benchmarking nodes with memory monitoring (6 nodes) added to Testing -> Benchmarking
  • Memory Use node added to Testing
  • Empty Column Checker node added to Testing - node ensures table columns have at least one non-missing cell in test cases
  • Multi-file reader source nodes added to IO folder (Load Local ... Files - currently 7 nodes - CDXML, Mol, Mol2, PDB, RXN XML and text)  NB These nodes will accept a single flow variable for multiple files. From the node documentation, "Alternatively, a flow variable can be specified, containing one or more filenames separated by ';'"
  • Many existing nodes are now streamable (more will become streamable in due course)

21-Oct-2016 - v1.8.0 (Nightly)

  • 'Speedy SMILES' nodes (16 nodes) added for fast high-throughput pre-processing of SMILES strings (see slidesfrom 5th Cheminformatics SIG for details)
  • Benchmarking nodes with memory monitoring (6 nodes) added to Testing -> Benchmarking
  • Memory Use node added to Testing
  • Empty Column Checker node added to Testing - node ensures table columns have at least one non-missing cell in test cases
  • Multi-file reader source nodes added to IO folder (Load Local ... Files - currently 7 nodes - CDXML, Mol, Mol2, PDB, RXN XML and text)  NB These nodes will accept a single flow variable for multiple files. From the node documentation, "Alternatively, a flow variable can be specified, containing one or more filenames separated by ';'"
  • Many existing nodes are now streamable (more will become streamable in due course)

09-Aug-2016 - v1.7.0 (v 3.1, v 3.2)

  • New versions of PDB Connector / PDB Connector (XML Query) nodes
  • Made up the complete set of optional query builder/query execution/report generation nodes:
    • PDB Connector (Query Only)
    • PDB Connector (XML Query) (Query Only)
    • Query Builder (returns the XML query as a flow var, does nothing else - although you can still run the test query button!)
    • Custom Reporter (Takes an input table and a column selection and runs custom report)
    • Query Combiner node (takes two XML advanced queries in flow variables and combines with AND or OR logic)
    • All Query generator or executor nodes now have 2 views:
      • 'Logical' query view
      • XML query view
    • POST and GET methods now allow chunking of report table, resolving strange behaviour for large result sets
      • Execution can now be cancelled at any point during the service request
    • Dialogs have option to change variable name of XML Query and to copy query to clipboard
    • Data parsing problems are now added to a column at the end of the report table in addition to the console
    • When both a query and a report are run, the exectution balance has been adjusted from 30/70 to 10/90
    • Query results are parsed directly to a BufferedDataContainer, reducing memory overhead for large result  sets
  • New manipulator node to access the PDB 'Describe Heterogens' webservice
  • New source node to access the PDB SMILES Query webservice

26-Jul-2016 - v.1.7.0 (Nightly)

  • New versions of PDB Connector / PDB Connector (XML Query) nodes
  • Made up the complete set of optional query builder/query execution/report generation nodes:
    • PDB Connector (Query Only)
    • PDB Connector (XML Query) (Query Only)
    • Query Builder (returns the XML query as a flow var, does nothing else - although you can still run the test query button!)
    • Custom Reporter (Takes an input table and a column selection and runs custom report)
    • Query Combiner node (takes two XML advanced queries in flow variables and combines with AND or OR logic)
    • All Query generator or executor nodes now have 2 views:
      • 'Logical' query view
      • XML query view
    • POST and GET methods now allow chunking of report table, resolving strange behaviour for large result sets
      • Execution can now be cancelled at any point during the service request
    • Dialogs have option to change variable name of XML Query and to copy query to clipboard
    • Data parsing problems are now added to a column at the end of the report table in addition to the console
    • When both a query and a report are run, the exectution balance has been adjusted from 30/70 to 10/90
    • Query results are parsed directly to a BufferedDataContainer, reducing memory overhead for large result  sets
  • New manipulator node to access the PDB 'Describe Heterogens' webservice
  • New source node to access the PDB SMILES Query webservice

30-Jun-2016 - v.1.6.5 (All builds)

  • Fixed bug introduced to PDB Connector nodes due to changes in RCSB webservices

10-May-2016 - v.1.6.5 (Nightly Only)

  • Fixed bug introduced to PDB Connector nodes due to changes in RCSB webservices

13-Apr-2016 - v1.6.4 (Nightly Only)

  • Added PMI Nodes plugin - nodes for calculating Principal Moments of Inertia, and aligning molecules to Inertial Reference Framge
  • Added support for knime:// protocol to List Folders node

17-Feb-2016 - v1.6.3 (Nightly Only)

  • Moved filtering of fragmentations forwards in process, resulting in significant performance improvements for filtered fragmentations (Unchanging HAC and Changing/Unchanging HAC ratio)
  • Improvements to H-removal algorithm
  • Moved all H-removal handling to fragmentation factory, and removed subsequent duplicate calls to H-removal (further performance improvement)
  • Added check for presence of unassigned double bonds before trying to do any assignment (upto 25% performance improvement)
  • Filter/Splitter nodes no longer pass multicomponent structures
  • Fragmentor nodes no longer fail with multicomponent structures
  • Fixed bug in which certain double bond geometries to near-symmetrical aromatic rings became corrupted causing crashes
  • Fixed bug causing multi-fragment node to only perform two cuts to a bond ([2*]-[1*] value) when the maximum number of cuts was 2
  • Improved garbage collector class to remove possible references to deleted native objexts

12-Feb-2016 - v1.6.2 (Nightly only)

  • Fixed loss of stereointegrity issue in MMP fragmentation
  • Fixed canonicalisation issue resulting from above fix (NB 'Values' will not be differently canonicalised to previously)
  • Fixed graceless failures for some salted forms and apparent successful failures of other salted forms

02-Feb-2016 - v1.6.1 (Nightly only)

  • RCSB PDB Loader nodes make 5 attempts to load each file before failing if unable to load (previously only a single attempt was made, resulting in a missing value in the output)
  • Local PDB Loader now makes 5 attempts to load each, but continues with a WARN to the console and a missing value cell if it fails to load a file
  • Bug fixes to MMP nodes which resulted in loss of double bond geometry (Change in RDKit toolkit behaviour), scrambling of attachment point labels and node failures in certain circumstances
  • Nodes transferred to the KNIME core product (Wait for time, Wait to time, Flow variable Case switch) deprecated

23-Nov-2015 - v1.6.0

  • This is a significant update.  No new functionality is provided, but the contribution is fully KNIME 3.0-ready.  See a full detailed list of changes here
  • MMP canonicalisation is modified to deal with duplicate components in the 'Key'

11-Nov-2015 - v1.5.0 (v 2.11, 2.12)

  • Major re-release of the MMP nodes.  The first generation nodes have been retired, and a new faster, more efficient implementation released

23-Oct-2015 - v1.5.0 (nightly only)

  • Major re-release of the MMP nodes.  The first generation nodes have been retired, and a new faster, more efficient implementation released

07-Sep-2015 - v1.4.1

  • Fixed intermittant problem with nodes ending in uncategorised folder

18-May-2014 - v1.4.0 (2.11, 2.10)

  • Updated stable builds to v 1.4.0

12-May-2015 - v1.4.0 (Nightly)

10-Apr-2015 - v1.3.5 (2.11, 2.10)

  • Updated stable builds to v 1.3.5

30-Mar-2015 - v1.3.5 (Nightly)

  • Fixed issues with RDKit conversion errors causing MMP node execution to fail
  • Added optional Attachment point context fingerprints to the MMP Node and MMP Molecule Fragment Node

12-Mar-2015 - v1.3.4 (Nightly, 2.11, 2.10)

  • Added Jameed Hussain's MMP Fragmentation rSMARTS from original JCIM paper
  • Added User Defined rSMARTS option
  • Added Include Reverse Transform option
  • Added Include rSMARTS for transform in output
  • Improved memory management (Explicit deleting or RDKit objects)
  • Enhanced node-cancelling capabality during fragmentation process

10-Mar-2015 - v1.3.3 (Nightly)

  • Added 'knime:' protocol support to Load Text-based files and Load local PDB files nodes

22-Jan-2015 - v1.3.2 (Nightly, 2.11, 2.10)

  • Corrected bug in Load Text-Based files node for non-'Guess' options

05-Jan-2015 - v1.3.1 (Nightly, 2.11, 2.10)

  • Removed erroneous reference to SMILES in MMP node dialogues

22-Dec-2014 - v1.3.0 (Nightly, 2.11, 2.10)

  • Added Matched Molecular Pairs nodes

10-Dec-2014 - v1.2.0 (Nightly, 2.11, 2.10)

  • Upgraded existing If/Case flow variable switch nodes
  • Added Database Port If/Case switch nodes
  • Added 3, upto 4 and upto 6 port loop ends
  • Added Timed loop nodes
  • Added delay nodes
  • Added Read/Write flow variable nodes

04-Nov-2014 - v1.1.5 (All Builds)

  • Added dialog option to set file encoding in load local text files node
  • Provided enhanced file encoding detection in the load local text/pdb files nodes (UTF-8, UTF-16 BE/LE, UTF-32 BE/LE)

05-Aug-2014 - v1.1.4 (All builds)

  • Fixed bug which had prevented SMARTSViewer node from working

26-Mar-2014 - v1.1.3 (Nightly Build)

  • Added optional new columns to List Folders node
  • Re-worked Fingerprint Properties node to use ColumnRearranger (should improve performance for large input tables and reduce datatable filesize)
  • Removed redundant NodeView Classes

25-Mar-2014 - v1.1.2

  • Applied the 1.1.2 update to the stable builds (v2.8, v2.9)

17-Mar-2014 - v1.1.2 (Nightly build)

  • PDB Connector node updated to provide options to use new POST or old GET service.  Existing workflows will default to the new POST service
  • PDB Connector (XML Query) node added

17-Mar-2014 - v1.1.1

  • Stable versions 2.8 and 2.9 updated to v1.1.1

28-Feb-2014 - v1.1.1 (Nightly Build)

  • Added Fingerprint Properties node

26-Feb-2014 - v1.1.0 (Nightly Build)

  • 5 New flow control nodes for flow variables added, emulating IF/CASE nodes in core KNIME product
  • European PubMed Central Advanced Search node added
  • PDB Sequence Extractor node added

05-Feb-2014 - v1.0.4

  • The maximum URL length fix has now been transferred to the stable builds (v 2.8 & v 2.9)

30-Jan-2014 - v1.0.4 (Nightly Build)

  • Maximum URL length has been reduced to 2000 chars to fix issues with proxy handling.

20-Jan-2014 -v1.0.4

  • Changes to fix the PDBConnector node applied to the stable builds.

10-Jan-2014 - v1.0.4 (Nightly Build)

  • Retry after increasing delay periods added to PDB connector node to fix intermitent failure to retrieve results from webservice.

04-Dec-2013

  • Stable builds for v2.7, 2.8 and 2.9 updated to match the nightly build.

29-Nov-2013

  • SMARTSViewer node updated in nightly build to require SMARTS-typed datacell.  The original version also accepted SMILES and String types, which allowed nonsense to be sent to the remote server too easily.

14-Oct-2013

  • Stable builds updated to match the nightly build with local text file IO nodes

11-Oct-2013

  • Local text file load and save nodes added to the nightly build

25-Jun-2013

  • Vernalis Community Contribution released