New Nodes

• Recalculate Table

  • Recalculate structure tables of relational databases.

• Scalar Descriptor

  • Calculate the Scalar Descriptor.

Improvements

• Marvin Cell

  • KNIME's Java Snippet node can be used to work with Marvin Cell data types like ChemAxon Molecule object.

• MarvinRenderer

  • Wireframe with knobs display option has been eliminated.

• Markush Composer

  • 'Ignore input molecules not containing the scaffold' has been added.

  • 'Keep all of multiple results or only the most relevant one' has been added.

New Nodes

• CNMR Prediction

  • Calculate the CNMR Prediction.

• HNMR Prediction

  • Calculate the HNMR Prediction.

Improvements

• Advanced MolConverter

  • Support Image formats.

New Nodes

• JC4O Reader

  • Reads the contents of an Office file created with JChem For Office.

• JC4O Writer

  • Writes the incoming data table contents to a JChem For Office compatible docx and pptx file.

Improvements

• MolConverter, Advanced MolConverter

  • Add 'Remove small fragments' options.

  • Add 'Cleaning' options.

• JChem Search, MolSearch

  • The default Vague Bond Level has changed.

• Marvin Renderer

  • Add 'S-group Attachment' options.

Improvements

• The node icon has been changed.

Improvements

• The following nodes have supported concurrent processing.

  • Converter nodes

  • Marvin nodes (in part)

  • Calculator Plugins nodes (in part)

  • Standardizer

  • Screen nodes (in part)

• Marvin Renderer

  • Add 'Transparent' options.

Improvements

• All nodes and renderer.

  • Support adaptor type cell (e.g. CDK, RDKit) which contains structural data type.

New Nodes

• Markush Composer

  • Automatically generate Markush structures based on a set of compounds.

Improvements

• DocumentExtractor, TextExtractor

  • Extract option has been enhanced.

• Structure Checker

  • Output Fixes Applied, Problems Remaining information.

• Markush Enumeration

  • Node repository tree has been moved to JChem > Markush.

New Nodes

• Markush Overlap

  • Calculates the overlapping space between two Markush structures.

Improvements

• DocumentExtractor, TextExtractor

  • Extract option has been enhanced.

• Markush Viewer, R-group Decomposition, R-group Composition

  • Node repository tree has been moved to JChem > Markush.

New Nodes

• HLB

  • Calculate the hydrophilic-lipophilic balance number (HLB number).

Improvements

• JChem Search, JChem Update, JChem Cartridge

  • Support Boolean, DateAndTime and BinaryObject type cell

• Tautomers

  • Improving and modifying the tautomerization options.

• logP

  • Improving and modifying the logP calculation methods.

• logD

  • Improving and modifying the logD calculation methods

New Nodes

• Maccs Fingerprint

  • The fingerprints encode the Maccs Key. It is based on the following information. https://www.chemaxon.com/forum/ftopic8138.html

• Atom Selection

  • Handle atom selection information.

Improvements

• MolSearch

  • Add hit atom indexes option has been added.

• Marvin Renderer

  • Add 'Margin size' options.

Improvements

• All nodes and renderer.

  • Support adaptor type cell (e.g. CDK, RDKit) which contains structural data type.

New Nodes

• Aqueous Solubility

  • Calculate the solubility.

Improvements

• JC4XL Writer

  • Supports ImageCell(PNGImageCell).

• Marvin Renderer

  • Automatic Scaling option has been enhanced.

Improvements

• All nodes and renderer.

  • Support adaptor type cell (e.g. CDK, RDKit) which contains structural data type.

Improvements

• Tautomers, Conformers, Stereoisomers, Molecular Dynamics

  • Keep input columns option has been addded.

• MCS

  • Ring handling mode option has been added.

• Reactor

  • The Reactor nodes can use input data as reaction schemes.

  • Generate synthesis code option has been added.

• Fragmenter, Screen nodes

  • Example config files are bundled and added to a file list.

Improvements

• Sphere Exclusion

  • Clustering method option has been added.

Improvements

• MolConverter

  • Support Inchi data type.

• DocumentExtractor, TextExtractor

  • Extract option has been enhanced.

• Marvin Renderer

  • Support Inchi data type.

• All nodes

  • Skip weird cases and keep the execution of workflow.

New Nodes

• Sphere Exclusion

  • Calculate the Sphere Exclusion.

Improvements

• MolImporter, MolExporter

  • Performance of I/O was increased by using concurrent processing in molecule import/export.

• MolExporter

  • 'Including data types of properties' option has been added.

• JC4XL Writer

  • Support xlsm file for appending data.

• Advanced MolConverter

  • Support binary data type (SKC, CDX format).

• Topology Analysis

  • 'Fsp3' option has been introduced

• Standardizer

  • Standardizer GUI has been updated based on JChem / Marvin updated.

  • StandardizerResult output has been added.

• Structure Checker

  • Structure Checker GUI has been updated based on JChem / Marvin updated.

• Library MCS

  • Library MCS uses the newly developed MCS module.

  • Add 'Structure output is split in level' option (output is Collection Column).

• Metabolizer

  • Metabolizer GUI has been updated based on JChem / Marvin updated.

  • Metabolizer uses the newly developed Metabolizer module.

• Marvin Renderer

  • Add 'IUPAC Numbering' option.

• The following nodes have supported part of streaming processing.

  • MolImporter, MolExporter

  • JC4XL Reader, JC4XL Writer

  • Fuse Fragments, Join Reaction

  • MolSearch, Formula Search

  • Document Extractor

  • LibraryMCS

  • Reactor

  • Metabolizer

New Nodes

• MCS

  • The MCS finds the maximum common substructure (MCS) of two molecules.

• Similarity Calculator

  • Calculate the similarity based on a Fingerprint.

Improvements

• JC4XL Writer

  • 'Append / Overwrite' option has been added.

• JChem Search, MolSearch

  • Advanced option has been enhanced.

• Topology Analysis

  • 'Aromatization method' option has been added.

• Reactor

  • 'Mark reaction center' option has been added.

• MolSimilarity, RxnSimilarity

  • If query and target structures are from same data, only a half is outputted to reduce execution time.

• FingerPrint

  • A result can be outputted as a bit format.

New Nodes

• Screen3D

  • Calculate the three dimensional similarity comparison of molecular pairs.

• MolFragmenter

  • Molecule fragmenter.

Improvements

• The following nodes have supported streaming processing. (requirement:KNIME 2.7.4 and DataRush 6.1.0-18)

  • Converter nodes

  • Set MolName And Comment, Get MolName And Comment, Split Into Fragments, Split Reaction, RCSB PdbImporter

  • Calculator Plugins nodes

  • Standardizer

  • Structure Checker

  • Text Extractor

  • Fragmenter, MolFragmenter

  • Screen nodes (except for MolSimilarity, MolSimilarity, Screen3D)

• Multiple MolImporter, Multiple PdbImporter

  • In order to delete a file, multiple files can be selected.

• Isoelectric Point

  • 'Keep explicit hydrogens' option has been added.

• Molecular Dynamics

  • New MMFF94 forcefield implementation has been introduced.

• JChem Search, MolSearch

  • Advanced option has been enhanced.

• R-group Decomposition

  • 'Include scaffold in the output' option has been added.

• Fragmenter

  • Some Fragmenter options have been added.

New Nodes

• Dipole Moment Calculation

  • Calculate the Dipole moment.

Improvements

• MarvinSketch

  • Output molecule properties that are added in MarvinSketch GUI.

• pKa, Major Microspecies

  • 'Keep explicit hydrogens' option has been added.

• LibraryMCS

  • 'Keep properties of structure' option has been added.

New Nodes

• Shape Descriptor

  • Shape descriptor implements a 3D alignment based similarity calculation.

• Join Reaction

  • Join reaction from reactants and products.

Improvements

• Marvin Renderer

  • Add 'Peptide Display' options.

• MarvinSketch

  • Add 'Outputting multiple fragments' options.

• MolExporter

  • Add 'Export empty (missing) structure' options.

• Reactor

  • Outputs both of successful products / reactions and failed reactants.

• MolSearch

  • Add 'Add match count to the search result' options.

Improvements

• MolImporter

  • Support the common office document formats.

  • Add 'Add the input file name' option.

• MolExporter

  • Add 'Encoding' option.

  • Support URL as file path to export structural file.

• JC4XL Writer

  • Support URL as file path to write xlsx file.

• pKa

  • Add 'Number of acidic pKa / basic pKa' options.

• R-group Decomposition

  • Add 'Undefined R-atom matches' option.

• R-group Composition

  • Add 'Filter out duplicate structures on each rgroup set' option.

  • Add 'Add selected rgroup structures to all rgroup set' option.

• JChem Cartridge

  • GUI has been improved.

  • Add 'Database Schema Browser'.

  • Add 'SQL Statement' which supports DML (SELECT, INSERT, UPDATE, DELETE) SQL statement with input data and variable.

• Document Extractor / Text Extractor

  • Support the common office document formats.

  • Add 'Accept elements / generic names / ions' options.

• ECFP/FCFP

  • Node name has been renamed.

  • Add 'Substructure' output type.

• Reactor

  • Add 'Reaction rules' options.

• MarvinSketch

  • The information on the selected atoms and bonds can be stored in MRV format.

• Marvin Cell

  • Unique Smiles is used for comparison of data.

  • This affects the GroupBy, Sorter nodes.

New Nodes

• Markush Viewer

  • Markush Viewer is a application of ChemAxon to view the various R-group definitions of Markush structures in an organized way.

Improvements

• Marvin Renderer

  • Add 'Quality' options.

  • Add 'Coordinate Bond Line Style' options.

Improvements

• Document Extractor

  • Support URL as file path to extract file document.

New Nodes

• JC4XL Reader

  • Reads the contents of an Excel file created with JChem For Excel.

• JC4XL Writer

  • Writes the incoming data table contents to a JChem For Excel compatible xlsx file.

Improvements

• MolImporter, PdbImporter

  • Support URL as file path to import structural file.

• MolConverter, Advanced MolConverter

  • Support output (export) options.

• Structure Checker

  • Support output to separate port (Fixed and unfixed structures).

• Document Extractor, Text Extractor

  • Add 'Lookup of CAS numbers' options.

• MarvinView

  • Support hilite filter features (HiLite > Filter menu).

• MarvinTable

  • Sort data in table view by clicking the column header (based on KNIME feature).

New Nodes

• Split Reaction

  • Splitting products and reactants from reaction.

• Formula Search

  • Filters molecules based on sophisticated chemical formula search.

Improvements

• JChem Cartridge, JChem Manager

  • Support workflow credential for "User name and password" to connect to the database.

• MCES

  • Support matrix type output.

  • Output MCS Distance.

• MolExporter

  • Support multiple structural columns to export the file.

• JChem Manager

  • Support added JDBC driver file in Preference dialog of KNIME File > Preferences menu.

• Split Into Fragments

  • Add 'Split into columns as collection' options.

New Nodes

• Structure Checker

  • Filtering drawing mistakes or special structural elements.

• Predictor

  • Molecular property prediction as the sum of atomic contributions.

• Pharmacophore Fingerprint

  • Pharmacophore Fingerprint descriptors.

• ECFP

  • Extended-Connectivity Fingerprints descriptors.

• MCES

  • Find the largest common substructure of two molecules.

• TextExtractor

  • Extract chemical names from text (in KNIME table) and converts them to chemical structures.

Improvements

• Marvin Renderer

  • Support other structure format than MrvType.

  • Various options/preferences can be specified in Preference dialog of KNIME File > Preferences menu.

• MolImporter, MolExporter

  • Performance improvements in importing/exporting.

  • Export image files.

• Fuse Fragments

  • Add 'Fragments per molecule/No. of fuse molecules' options.

  • Add 'Arrange molecules in a 2D square lattice/Number of colums' options.

• Calculator Plugins

  • Modify GUI and features based on JChem/Marvin updating.

• JChemSearch, JChemUpdate, JChemDelete

  • The accessible tables are listed based on the database connection information.

• JChemSearch, MolSearch

  • Performance improvements in structural searching.

  • Add 'Markush reduction according to the hit' option.

  • Add 'Allow duplication of the search result' option.

  • Add 'Add query data to the search result' option.

• R-group Decomposition

  • Add 'Generate Markush output' option.

  • Add 'Process all hits' option.

  • Add 'Hit ordering' option.

  • Add 'Allow duplication of the search result' option.

  • Add 'Add query data to the search result' option.

• R-group Composition

  • Add 'Scaffold modification' option.

• Document Extractor

  • Support PDF, XML formats.

• MolSimilarity, RxnSimilarity

  • Add 'Descriptors' options.

  • Add 'Dissimilarity metric' options.

• Chemical Fingerprint, ECFP, Pharmacophore Fingerprint, BCUT, Reaction Fingerprint

  • Output fingerprint as Integer data type.

• Reactor

  • Add 'Generate Unsuccessful reactions' option.

• All nodes

  • Some nodes (For instance, MarvinSketck, MolImporter, JChemSearch) that have output port support other structure format than MrvType.

  • All of node that have input port support other structure format than MrvType.