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)

• Added benchmarking nodes (see https://tech.knime.org/book/vernalis-cheminformatics-nodes#testing)

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