The table shows the latest version of the nodes available in each update site for the KNIME Analytics Platform
| KNIME AP Desktop Version | Vernalis Plugin Version |
|---|---|
| Nightly | v1.36.7 |
| 5.3* | v1.36.7 |
| 5.2* | v1.36.7 |
| 5.1* | v1.36.7 |
| 4.7* | v1.36.7 |
| 4.6 | v1.36.2 |
| 4.5 | v1.36.1 |
| 4.4 | v1.34.1 |
| 4.3 | v1.31.0 |
| 4.2 | v1.31.0 |
| 4.1 | v1.30.1 |
| 4.0 | v1.27.0 |
| 3.7 | v1.27.0 |
| 3.6 | v1.18.1 |
| 3.5 | v1.15.0 |
| 3.4 | v1.12.1 |
| 3.3 | v1.12.0 |
| 3.2 | v1.12.0 |
| 3.1 | v1.8.2 |
| 3.0 | v1.6.5 |
| 2.12 | v1.5.0 |
| 2.11 | v1.5.0 |
| 2.10 | v1.4.0 |
| 2.9 | v1.1.5 |
| 2.8 | v1.1.4 |
| 2.7 | v1.0.4 |
* Currently supported versions
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Bug Fixes
- Add missing classes to prevent start-up errors relating to original PDB Connector node
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Enhancements
- Added Missing value and uniqueness options to Collection Size node
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Bug Fixes
- Fixes errors in new UI NodeDescription implementations
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Bug Fixes
- Fixes error in complexity estimation when a single bond cut is not being made (See #20)
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Enhancements
- Add option to fail if no collection columns selected in Collection multi-selection-based Collection nodes with default behaviour to mimic legacy (#18)
- Abstracted common code from all multi-selection-based Collection nodes to abstract Node Dialog and Node Model classes
- Node Dialog layout improvements to Collection nodes
Bug Fixes
- Added feature dependency to RDKit Binaries feature to enforce installation (#17)
- Fixes addition of default value in Sparse List representation in List to Set node when that value is not actually present in the collection (#19)
Other Changes
- Updated to build as JDK17
- Updated to require RDKit v 4.6.1 or higher
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Bug Fixes
- Fixed 2020 upper bounds on PDB Connector Date query fields (See #16)
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New Nodes
- See also under Bug Fixes
- DB Port Comparator
- DB DISTINCT
- DB Extract Table Dimension
- DB List Catalogues
- DB Insert Column Header
- DB List Foreign Keys
- DB List Primary Keys
- DB List Schemas
- DB List Table Types
- DB List Tables
- DB Numeric Range
- DB Remove SQL from connection
- DB Select Table (Interactive)
- DB Table Exists IF Switch
- DB To Empty Table
- DB To Variable
- Reference DB Table Exists IF Switch
Enhancements
- Node Migration Rules added for all database 'Legacy' / 'DB' node pairs to allow workflow migration
- DB Table Exists IF Switch is configurable - either or both output ports can be swapped between flow variable and DB Session port types
- Reference DB Table Exists IF Switch is configurable - the table input/outputs can be swapped for any other port type
Other Changes
- All database nodes have been renamed with the suffix '(Legacy)' following the KNIME core database style
- New
com.vernalis.database.coreplugin - New
com.vernalis.knime.testing.coreplugin for maven-execution of test cases - New annotations in
com.vernalis.knime.coreplugin (@NoTest,@NodeTestFlow,@NodeTestFlows) - New
.testsfragment for JUnit tests and Workflow Tests for the corresponding plugin for the pluginscom.vernalis.knime.database.core,com.vernalis.knime.testingandcom.vernalis.knime.db - New
com.vernalis.knime.testingplugin with nodes for test flows - Moved
Empty Column Checkernode from flow control plugin to testing plugin (and NodeFactoryClassMapper supplied) - Updated builds to use Tycho v 2.7.5
Bug Fixes
- Fixed missing node icons for various 'database' nodes
- Added missing 'Database replace table header' node to plugin.xml
- Added missing 'Database Remove SQL' node to plugin.xml
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New Nodes
- Speedy Sequence to SMILES node
- Speedy Sequence Analysis node
- Speedy Sequence Alignment Visualisation node
Bug Fixes
- PDB Connector dynamic 'suggester' dropdowns fixed following remote API change
- Removed much unused code from original PDB Connector implementation
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Minor Updates
- Renamed AbstractDrawableSeriesPlotNodeDescription#getShortDescription() to #getShortDescriptionImpl() due to name clash with new method in updated parent
- Updated Jackson dependency versions to avoid security CVEs in PDB Connector plugin
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Bug Fixes
- Minor bug fix to Regex String Match flow variable condition reference value box
- Minor bug fix to Wildcard String Match flow variable condition reference value box
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New Nodes
- Added
Ertl Scaffold Keysnode
Enhancements
- Added new 'streams' package in core plugin
- Added
DataCellCollectorsclass to streams package - Added
ArrayOfListCellCollectorclass to streams package - Added
ToListCellCollectorclass to streams package - Added
BitSetCollectorsclass to streams package - Added
NonOverlappingBitSetCollectorclass to streams package - Added
OverlappingBitSetGroupingCollectorclass to streams package
- Added
- Added
getRDKitObjectFromCell(DataCell cell, boolean sanitizeMol, boolean removeHsstatic method to RdkitCompatibleColumnFormats enum in chem.core plugin - Added new
com.vernalis.knime.chem.rdkitplugin
New Nodes
- Added Column to Singleton Collection node
- Added Mask Lists Node
- Added GZip Compress Binary Object node
- Added GZip Decompress (Un-gzip) Binary Object node
- Added Zip Binary Object node
- Added UnZip Binary Object node
Enhancements
- Added RemoveColumnsDataRow class to core plugin
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New Nodes
- Configurable Empty Table Switch
- Configurable IF/Case Switch (Flow Variable Value)
- Configurable IF/Case Switch
- Configurable Crossover (Flow Variable Value)
- Configurable End IF/Case
New Features (See also API section)
- New flow variable conditions for String, String Array, Integer, Integer Array, Long, Long Array, Double, Double Array, Boolean, Boolean Array and Path variable types
- New Port Combiners for Buffered Data Table, Flow Variable and RCSB Advanced Query port types
Deprecated Nodes
- Deprecated all IF Switch / Case Switch, End IF and End Case nodes
API
- Added 2 new extension points:
com.vernalis.knime.flowcontrol.variablecondition(Variable Condition) - Used to provide conditions to the Flow Variable value based nodescom.vernalis.knime.flowcontrol.porttypecombiner(Port Type Combiner) - Used to allow merging of multiple active ports in Configurable End IF/Case nodes
Enhancements
- Fixed links in main CHANGELOG.md summary table
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New Nodes / Features
- Added UI Selection modifier tools
Enhancements
- Updated to switch to v2 of RCSB Query API automatically on 13-Apr-2022
- Made verbose JSON output optional in Query Executor node
- Modified SettingsModelRegistry implementation of QueryExecutorNodeModel to allow saved model versioning
- SettingsModelRegistry has new methods to allow saving of model versions, and adding backwards compatible new versions (Changes made backwards compatible)
- AbstractSimpleStreamableFunctionNodeModel updated to match new SettingsModelRegistry
- Added SettingsModelRegistryImpl class and SettingsModelWrapper class
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- Updates for changes in RDKit v4.5.0 (#14)
- Fixes bug when show loop body node timings option is checked for benchmark nodes not at root level of workflow (#15)
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- Bug fixes and feature enhancements to PDB Connector
- Updated for changes to remote query API
- Centralised handling of QueryPanel borders
- Added RemovableQueryField and associated RemoveMe button
- Only apply border highlights when mouse-over component is active
- Added code to allow for removal of QueryFields from API and display of invalid fields
- Added new chemical descriptor query types
- Only display valid scoring types in Query Executor node when a query is available at the incoming port
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- Made all
NodeFactoryClassMappers subclassMapNodeFactoryClassMapper - Fixed bug whereby
MolSanitizeExceptionthrown in fragment canonicalisation throws MMP Fragment nodes over - Added optional hit count to PDB Connector Query Executor node
- Moved some of the query execution control from the node model to the query executor
- Made all RCSB.org service calls point to
https://rather thanhttp://
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- Fixed various bugs in RDKit Templated conformer generation node
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New Nodes
- KNIME URI Resolver
- KNIME URI Resolver (Variable)
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New Nodes
- Multiport Loop End
Enhancements
- Multiport Loop End, 3-Port Loop End, Upto 4-port loop end and Upto 6 port Loop end nodes have table preview view
Deprecated Nodes
- Loop End (3 Ports)
- Loop End (Upto 4 Ports)
- Loop End (Upto 6 Ports)
Other
- Added
FixedLengthQueueto collections package in core plugin
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- Added retries to failed download in Query Execution (Fixes #9)
- Added optional limit to returned hits in Query Execution Node (Closes #10)
- Added Substructure chemical query types (Closes #11)
- PDB Saver node now correctly handles
knime://URL protocol in both full paths in columns and in parent folder settings (#12) - Save File Locally node now correctly handles
knime://URL protocol in both full paths in columns and in parent folder settings (Fixes #12)
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- Fixes #8 (Over-zealous sequence query validation)
- Removes unused dependency in SpeedySMILES
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Minor enhancements and bug fixes to MMP plugin:
- Added rdkit jar to extra jars in classpath
- Corrected bug in key HAC calculation
- Added Filter for minimum key HAC
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- Retired original PDB Connector family
- New PDB Connector query nodes
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- Add
RDKitRuntimeExceptionHandlerclass to allow RDKit version before 4.1 or after 4.1 to work seemlessly
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- Requires RDKit Types plugin v4.1.0 or higher
- RDKit exception handling updated to use
#what()method in place of removed#message()method
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- Complete fix of PDB Connector issue (v1.27.1 did not fully fix)
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- Added optional 'new' attribute to query option and ignored settings exceptions for query options so tagged (Fixes #2)
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New Nodes
- Append to Collection
- Insert into List
- Credential Variable Extractor (see https://forum.knime.com/t/credentials-input-node-extract-username/25079)
Bux Fixes / Enhancements
- PMI Properties node now works with two-character element symbols e.g. Cl, Br etc (see https://forum.knime.com/t/vernalis-pmi-node-failure/24979/28)
- List Folders node no longer throws
NullPointerException(see https://forum.knime.com/t/id-like-to-download-files-from-s3-to-knime-server/23289/5?u=s.roughley) - Memory monitoring performance loop nodes re-written to remove possible IOExceptions due to table ownership of memory usage table
- Performance loop end nodes now allow use of new or legacy date-time systems in timing and memory usage output tables
- PMI calculation errors no longer causes node execution failure
SettingsModelIntegerRange#createClone()now returns correct type- Added all missing version constraints in
MANIFEST.MF
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- Bug-fixes and minor enhancements to PDB Connector family of nodes
- Fixed broken date query fields (Deposition Date, Release Date, Revision Date)
- Added searches for Entity IDs, Chain IDs, Uniprot Gene Names
- Fixed mouse scroll speed
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New Nodes
- Templated Conformer Generation (RDKit)
- Force Field Conformer Energies
- RMSD Conformer List Filter
Enhancements
- Added
DialogComponentMultilineStringFlowvarto core plugin - Added
SettingsModelMultilineStringto core plugin
Bug Fixes
- Force requirement of RDKit v4.0.0
- Fixed bug in inject column properties node causing
IndexOutOfBoundsExceptionto be thrown if < 3 input columns present in the 2nd table - Fixed bug in which PDB Connector Custom Report node overwrites xmlQuery flow variable. This bug causes crashes in KNIME 4.1 due to changes in flow variable handling
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- Fixed bug in Random Numbers Generator node in range of doubles returned
- Added optional random seed in Random Numbers Generator node
- Added summary flow variables to Random Numbers Generator node output
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- Updates RDKit Dependencies to include RDKit version 4.x.x
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- Corrected bug in Plate Nodes resulting in Well ID columns returning Row IDs
- Fixed bug in file reader nodes resulting in loss of final newline combination if no characters follow it
- Fixed bug in file reader nodes resulting in conversion of all newlines to unix-style '\n'
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- Read / Write variables nodes now support
knime:URL protocol - Fixed bug in Read Variables node resulting in file chooser showing 'Save' chooser and errors rather than 'Open'
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New Nodes
- Empty Collection to Missing Cell
- Missing Cell to Empty Collection
- Collection Size
Bug Fixes
- Thread safety issue parsing dates in Bruker Amix Peaklist reader and SD-file reader nodes
- ePMC Advanced Query node updated to v6.2 of webservice API
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New Nodes
- 1D Kernel Density Plot
- 2D Kernel Density Plot
- Kernel Loop Start
- Notched Boxplot
- PMI Kernel Density Plot
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New Nodes
- New PMI-Derived Properties Calculation node (accepts more column input formats, e.g. CTab and PDB), and many more properties
- PMI Scatter Plot
- PMI Convex Hull Plot
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New Nodes
- Trim Table node
Enhancements
- MMP Node Icons restored
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- Minor enhancement allow File Encoding Guess to work with non-markable InputStreams (see https://forum.knime.com/t/get-fails-if-the-response-does-not-have-content-type-set/17295/10 for original issue)
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- Changed RDKit dependency to v3.8.0 to force non-RDKit node users with Vernalis nodes to update past the RDKit 3.7.0 version which is broken on some platforms.
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- Update version constraints to
[3.0.0,5.0.0)to accommodate update to KNIME v4.0.0 - Standardised licence text in feature.xml (defunct URL removed and linebreaks/indents standardised)
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- Fixes MMP bug https://forum.knime.com/t/mmp-molecule-fragment-rdkit-node-indexoutofboundsexception/15469/3
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- Minor bug fix to
Load text-based filesandPDB Loadernodes, which means that the removed input column names is not de-dupicated in the output table (e.g. 'File' as input column would be rendered 'File(#1)' in the out table, even when the 'Remove input column' option was checked)
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New Nodes
- URL Decode Node
- Set To List Node
- Collection To String Node
- Flow Variable Benchmarking start / end nodes (with/without memory monitoring)
New Features
- 'PDB Saver' / 'Save File Locally' nodes now allow option to specify parent folder / directory path to save all files to
- 'PDB Loader' / 'Load text-based files' nodes now allow removal of input column (In both cases, legacy behaviour is retained in existing nodes, and new nodes default to existing behaviour)
Bug fixes
- 'PDB Saver' / 'Save File Locally' nodes now handle directory creation correctly when using multiple threads, preventing some files from being saved
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New Nodes
- Added Run Garbage Collector node
- Added Run Heavy Garbage Collector node
Bug fixes / Enhancements
- Major overhaul of performance monitoring plugin:
- Refactored most nodes and rationalised class structure
- Improved error handling for missing / mismatched loop starts
- Optional monitoring of individual loop body node timings (preserves legacy behaviour by default)
- Node descriptions now all created dynamically, allowing simplification of addition of further nodes with alternative port types
- Missing icons restored to MMP Nodes
- Fixed URL change for SMARTSViewer node
- Update core plugin about.ini file with current date
- Enhanced error handling in
MemoryUtilsclass and corresponding nodes (Benchmarking loops and Memory use node) - Allowed unix-style dates in 'Load Bruker AMIX Peaklist Files' node
- Added createTab method to
NodeDescriptionUtils
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- Performance improvement in MMP Calculate Maximum Cuts (RDKit) node
- Removed unused imports in other MMP classes and fixed typos in javadoc
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- Fixes bug in international support for memory usage nodes
- Fixes bug in Mac OS support for memory usage nodes
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- Fixes compatibility issue in
NodeDescriptionUtilsclass introduced in v 3.7.0 of KNIME Core
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New Nodes
- New Load FASTA node (accepts .fasta and .fasta.gz file extensions)
- Added URL Encode / URL Decode nodes
- Flow Control Crossover node
- Database DISTINCT node
- Extract Database Table Dimensions node
- Database to Empty table node
- Database Range node
- List Catalogues node
- List Foreign Keys node
- List Primary Keys node
- List Schemas node
- List Tables node
- List Table Types node
- Database to variable node
- Speedy SMILES Organic subset Filter / Splitter nodes
- Speedy SMILES s-Block metals Filter / Splitter nodes
- Speedy SMILES p-Block metals Filter / Splitter nodes
- Speedy SMILES d-Block metals Filter / Splitter nodes
- Speedy SMILES f-block metals Filter / Splitter nodes
- Speedy SMILES Cyclise end atoms node
Enhancements
- Load SDFiles node now accepts sd.gz and sdf.gz extensions
- Load XXX Nodes now report progress (Maybe misleading for .gz)
- Improved node dialog refresh performance of interactive database table selector node
Bug Fixes
- Random Numbers Generator bug fixed (2 instances of node shared output table spec causing errors at execution if they were producing different types)
- Fixed node dialog bug leading to settings not being displayed correctly in node dialog on load
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- Fixes further bugs in FASTA sequence extractor when '>' occurs other than at start of header line
- Updates RDKit changes in v3.4.0
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- Fixes bug in FASTA sequence extractor when '>' occurs other than at start of header line
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- Adds optional Flow variable input ports to all Load XXX files
- Adds Mol Block to output from Load SD-File (SDF) node
- Adds Output properties selection for the Multiline Text-Based Object nodes (SDF and Amix Peak List)
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- Added SDF file reader with charset detection/choice
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New Nodes
- Speedy SMILES Explicit Double Bond Geometry Filter/Splitter
- Extract / Inject column properties nodes
- 1D, 2D, 3D, nD Vector distance nodes
- Plate Well ID Nodes (Source and Manipulator)
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New Nodes
- Added Geometric Distance nodes (1D, 2D, 3D and nD)
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- Fixes minor bug in Database Table Selector node resulting loss of table name during node dialog reload
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New Nodes
- Adds Database plugin with database table chooser and table exists switches
- Adds Bruker Amix Peaklist reader
- Adds 'Include filename in output table' option in all 'Load ... files' nodes
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New Nodes
- New Speedy SMILES nodes
Enhancements
- Improved behaviour of new column name prefix/suffix
- Column name retained unchanged when input column is removed
- New
AbstractStreamableParallelisedFilterSplitterNodeModelbase class added to core plugin
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- Fixes bug in 'Load Local...' files node dialogue resulting in
NullPointerExceptionduring initial configuration - Fixes bug in 'Load Local...' files node dialogue meaning file selector buttons remained disabled once a flow variable had been used as file source, even after removing flow variable setting
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- Updates to RDKit 3.3.1 compatibility
- Changed
RWMol#AddAtom()andRWMol#AddBond()method signatures in deprecated nodes
- Changed
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- Fixes MMP XML generation bug (https://forum.knime.com/t/mmp-molecule-fragment-node-output-svg-cells-and-system-locale/10315)
- Code clean-up removing many compiler warnings
- Corrected deprecation of FVVal IF Switch node missed previously to plugin.xml deprecation method
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- 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,InvalidSettingsExceptionsduring node settings load/validate are ignored
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- Fixed version constraint and resolved code issues for RDKit drawing API change
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- 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
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- Fixed error in rendering of 1-cut 'reverse' fragmentations which flipped the key/value colours
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- 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
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- 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
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- Fixed bug in string comparison of Flow Variable Value If Switch nodes
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- Added 29 new fingerprint manipulation nodes
- Added new Aggregation operators for fingerprint manipulations in GroupBy and related nodes
- Deprecated original Vernalis Fingerprint Properties node
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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
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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)
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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 vectors 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
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- 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
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- Existing PDB Downloader nodes deprecated
- New PDB Downloader nodes introduced
- More file type options (NMR shifts & constraints)
- New versions do not 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:)
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- Fixed undesired node execution failure when SpeedySMILES de-salt node encounters empty or missing input cell
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- Fixed bugs introduced into Matched Molecular Pairs plugin double bond stereochemistry handling by latest updates to RDKit
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- Fixed bug in Speedy SMILES row filter/splitters which cause missing cells to throw NullPointerException
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- Addresses 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
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- 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
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- '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)
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- 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
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- Fixed bug introduced to PDB Connector nodes due to changes in RCSB webservices
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- 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
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- 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 objects
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- 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
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- 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
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This is a significant update. No new functionality is provided, but the contribution is fully KNIME 3.0-ready General
- All nodes are now parallelised wherever possible
- All plugins manifests were updated to bind KNIME component versions into range
[3.0.0, 4.0.0) - All plugin.xml's had deprecated nodes re-added, and the deprecation flag set
- All plugin.xml's had disused expert-mode property of node extensions removed
Main Vernalis Plugin
- Parallelised execution
- Fingerprint type names no longer end 'Cell', so are
SparseBitVector,DenseBitVector,SparseByteVector,DenseByteVector - Test case updated to reflect this change
- Fixed bug - Although the node could process ByteVectors, the column selector does not let it select them
- Updated all counters for rows and subrows to
longs
- Updated hit, page and row counters to
longs (flow variables for hit counter may therefore behave strangely)
- Updated file and added row counters to
longs
- Parallelised
- Converted to use
PDBCellFactory
- Parallelised
- Converted to use
BooleanCellFactoryfor result cell
- Parallelised
- Converted to use PDBCellFactory
- Updated row and PDB ID counters to
longs (NB this is probably irrelevant as they are processed via arrays!)
- Parallelised
- Parallelised
- Add logging explanation for save failures where easily possible
- Return value now uses
BooleanCellFactory
- Original Version deprecated due to change in settings model type
- Maximum number of rows changed to a
Long(and Settings Model changed toSettingsModelLongBounded), and artificial 10,000 row cap removed - Row counters changed to
longs - Generator methods changed to not work via intermediate collections but add directly, and thus to allow cancelling during number generation as well as table writing, and old methods deprecated
- New Test Case created for new version
- Updated to handle long tables
- Parallelised
- Updated to allow long tables at both outputs
MMPs Plugin
- Modified canonicalisation during fragmentation to resolve duplicate leaves canonically (results in possible changes to canonicalisation)
- Converted to
SmilesCellFactory - MMP canonicalisation is modified to deal with duplicate components in the 'Key'
Flow Control Plugin
- All PortType constructors replaced with
PortTypeRegistry.getInstance().getPortType()constructors - Now all use
#size()in place of#getRowCount() - Iteration counters now all
long(flow variables for iteration counters may therefore behave strangely)
Performance Monitoring Plugin
- Iteration counters now
long(flow variables for iteration counters may therefore behave strangely) - Iteration column in timing table now
LongCell(previouslyIntCell)
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- Major re-release of the MMP nodes. The first generation nodes have been retired, and a new faster, more efficient implementation released
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- Fixed intermittent problem with nodes ending in uncategorised folder
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- Added benchmarking nodes
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- 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
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- 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 capabIlity during fragmentation process
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- Added
knime:protocol support to Load Text-based files and Load local PDB files nodes
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- Corrected bug in Load Text-Based files node for non-'Guess' options
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Removed erroneous reference to SMILES in MMP node dialogues
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Added Matched Molecular Pairs nodes
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- 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
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- 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)
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- Fixed bug which had prevented SMARTSViewer node from working
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- 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
NodeViewClasses
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- 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
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- Added Fingerprint Properties node
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- 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
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Updates between 25-Jun-2013 and v1.0.4 on 30-Jan-2014 are a little unclear, and where never assigned individual version IDs
- Maximum URL length has been reduced to 2000 chars to fix issues with proxy handling.
- Changes to fix the PDBConnector node applied to the stable builds.
- Retry after increasing delay periods added to PDB connector node to fix intermitent failure to retrieve results from webservice.
- 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.
- Local text file load and save nodes added to the nightly build
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- Vernalis Community Contribution released
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