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
