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Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Fri Feb 03, 2017 1:26 pmPost subject: Reply with quote

The forum is in archive mode.

For the latest history of changes please see:

https://docs.chemaxon.com/display/docs/KNIME+Nodes+History+of+Changes

 

We have just released JChem Extensions version 3.1.0.v0506.
It is available for download at https://www.infocom.co.jp/bio/knime/update/3.1
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Feb 3rd, 2017: Version 3.1.0.v0506 for KNIME 3.1.0 and JChem 17.1.30.0 (System requirement:KNIME 3.1.0 or later)

New Features and improvements
   Marvin/JChem 17.1.30.0 are used.

 New Nodes
  -CNMR Prediction
   Calculate the CNMR Prediction.

  -HNMR Prediction
   Calculate the HNMR Prediction.

 Improvements
  -Advanced MolConverter
   Support Image formats.

Bugfixes
  -MarvinView
   MarvinView node caused KNIME to hang on the Mac.

  -MolSimilarity
   MolSimilarity node could not be used without Molecular Descriptors license.

  -PubChem Search
   PubChem Search node could not access to the PubChem Power User Gateway via HTTP protocol.

Takahiro

Joined: 07 Mar 2005
Posts: 71

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Link to postPosted: Tue Nov 29, 2016 4:10 amPost subject: Reply with quote

We have just released JChem Extensions version 3.1.0.v0505.
It is available for download at https://www.infocom.co.jp/bio/knime/update/3.1
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Nov 29th, 2016: Version 3.1.0.v0505 for KNIME 3.1.0 and JChem 16.11.21.0 (System requirement:KNIME 3.1.0 or later)

New Features and improvements
   Marvin/JChem 16.11.21.0 are used.

 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.

Bugfixes
  -DocumentExtractor
   OSR external tool option could not be off.

Takahiro

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Posts: 71

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Link to postPosted: Fri Sep 30, 2016 7:40 amPost subject: Reply with quote

We have just released JChem Extensions version 3.1.0.v0504.

It is available for download at https://www.infocom.co.jp/bio/knime/update/3.1

This is composite update site that includes both of JChem and Marvin Extensions.

 

JChem Extensions Changes

 

Sep 30th, 2016: Version 3.1.0.v0504 for KNIME 3.1.0 and JChem 16.9.26.0 (System requirement:KNIME 3.1.0 or later)

 

New Features and improvements

   Marvin/JChem 16.9.26.0 are used.

Takahiro

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Posts: 71

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Link to postPosted: Fri Apr 15, 2016 1:40 pmPost subject: Reply with quote

We have just released JChem Extensions version 3.1.0.v0503.

It is available for download at https://www.infocom.co.jp/bio/knime/update/3.1

This is composite update site that includes both of JChem and Marvin Extensions.

 

JChem Extensions Changes

Apr 15th, 2016: Version 3.1.0.v0503 for KNIME 3.1.0 and JChem 16.4.11.0 (System requirement:KNIME 3.1.0 or later)

 

New Features and improvements

   Marvin/JChem 16.4.11.0 are used.

 

Improvements

  -The node icon has been changed.

Takahiro

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Posts: 71

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Link to postPosted: Fri Feb 19, 2016 12:30 pmPost subject: Reply with quote

We have just released JChem Extensions version 3.1.0.v0502.
It is available for download at https://www.infocom.co.jp/bio/knime/update/3.1
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Feb 19th, 2016: Version 3.1.0.v0502 for KNIME 3.1.0 and JChem 16.2.15.0 (System requirement:KNIME 3.1.0 or later)

New Features and improvements
   Marvin/JChem 16.2.15.0 are used.

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.

Takahiro

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Posts: 71

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Link to postPosted: Wed Dec 09, 2015 6:01 amPost subject: Reply with quote

We have just released JChem Extensions version 3.1.0.v0501.
It is available for download at https://www.infocom.co.jp/bio/knime/update/3.1
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Dec 9th, 2015: Version 3.1.0.v0501 for KNIME 3.1.0 and JChem 15.12.7.0 (System requirement:KNIME 3.1.0 or later)

New Features and improvements
   Marvin/JChem 15.12.7.0 are used.

Improvements
  -All nodes and renderer.
   Support adaptor type cell (e.g. CDK, RDKit) which contains structural data type.

Takahiro

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Posts: 71

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Link to postPosted: Fri Sep 25, 2015 1:58 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0306.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Sep 25th, 2015: Version 2.8.2.v0306 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x, 2.12.x) and JChem 15.9.21.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 15.9.21.0 are used.

Takahiro

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Link to postPosted: Fri Sep 11, 2015 12:55 pmPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0305.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Sep 11th, 2015: Version 2.8.2.v0305 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x, 2.12.x) and JChem 15.9.7.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 15.9.7.0 are used.

 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.

 Bugfixes
  -Standardizer, Structure Checker
   Sometimes the full interface did not display.

  -Structure Checker
   In some case, the node did not work correctly.

Takahiro

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Posts: 71

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Link to postPosted: Fri Sep 04, 2015 3:09 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0304.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Sep 4th, 2015: Version 2.8.2.v0304 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x, 2.12.x) and JChem 15.8.31.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 15.8.31.0 are used.

 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.

Takahiro

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Link to postPosted: Thu Jul 30, 2015 7:48 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0303.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Jul 30th, 2015: Version 2.8.2.v0303 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x) and JChem 15.7.20.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 15.7.20.0 are used.

 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.

Takahiro

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Link to postPosted: Wed Apr 08, 2015 2:00 pmPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0302.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Apr 8th, 2015: Version 2.8.2.v0302 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x) and JChem 15.3.30.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 15.3.30.0 are used.

 New Nodes
  -Maccs Fingerprint
   The fingerprints encode the Maccs Key.
   It 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 addded.

  -Marvin Renderer
   Add 'Margin size' options.

Takahiro

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Link to postPosted: Tue Feb 17, 2015 4:26 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0301.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Feb 17th, 2015: Version 2.8.2.v0301 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x) and JChem 15.2.9.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 15.2.9.0 are used.

 Improvements
  -All nodes and renderer.
   Support adaptor type cell (e.g. CDK, RDKit) which contains structural data type.

 Bugfixes
  -Standardizer, Structure Checker
   The previous version could not work in headless environment (KNIME Batch Mode).

  -MarvinSpace
   Close the view the whole application will close.

Takahiro

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Link to postPosted: Mon Dec 08, 2014 3:56 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0300.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Dec 8th, 2014: Version 2.8.2.v0300 for KNIME 2.8.2 (also KNIME 2.9.x, 2.10.x, 2.11.x) and JChem 14.11.24.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 14.11.24.0 are used.

 New Nodes
  -Aqueous Solubility
   Calculate the solubility.

 Improvements
  -JC4XL Writer
   Supports ImageCell(PNGImageCell).

  -Marvin Renderer
   Automatic Scaling option has been enhanced.

Takahiro

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Link to postPosted: Mon Jul 07, 2014 2:35 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0205.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Jul 7th, 2014: Version 2.8.2.v0205 for KNIME 2.8.2 (also KNIME 2.9.x) and JChem 6.3.1.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 6.3.1.0 are used.

 Improvements
  -All nodes and renderer.
   Support adaptor type cell (e.g. CDK, RDKit) which contains structural data type.

 Bugfixes
  -MarvinSpace
   The previous version could not work due to OpenGL libraries version issue.

Takahiro

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Link to postPosted: Fri May 23, 2014 1:42 pmPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0204.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
May 23rd, 2014: Version 2.8.2.v0204 for KNIME 2.8.2 (also KNIME 2.9.x) and JChem 6.3.0.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 6.3.0.0 are used.

 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.

 Bugfixes
  -JChem Search, JChem Update
   The unnecessary data field was outputted.

Takahiro

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Link to postPosted: Wed Apr 02, 2014 2:40 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0203.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Apr 2nd, 2014: Version 2.8.2.v0203 for KNIME 2.8.2 (also KNIME 2.9.x) and JChem 6.2.1.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 6.2.1.0 are used.

 Improvements
  -Sphere Exclusion
   Clustering method option has been added.

 Bugfixes
  -JChem Cartridge
   SQLException was thrown, if SQL statement has multi line breaks.

  -All nodes
   The previous version could not work on Mac environment due to java version issue.

Takahiro

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Link to postPosted: Thu Feb 06, 2014 5:18 amPost subject: Reply with quote

We have just released JChem Extensions version 2.8.2.v0202.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.8
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Feb 6th, 2014: Version 2.8.2.v0202 for KNIME 2.8.2 (also KNIME 2.9.x) and JChem 6.2.0.0 (System requirement:KNIME 2.8.0 or later)

New Features and improvements
   Marvin/JChem 6.2.0.0 are used.

 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.

 Bugfixes
  -JChem Update
   Bits to be set for patterns could not be more than 3.

  -Sphere Exclusion
   Sphere Exclusion could not work with Chemical Fingerprints

  -All nodes
   The previous version could not work on Mac environment due to java version issue.

Takahiro

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Link to postPosted: Tue Nov 12, 2013 7:41 amPost subject: Reply with quote

We have just released JChem Extensions version 2.7.4.v0201.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.7
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Nov 12th, 2013: Version 2.7.4.v0201 for KNIME 2.7.4 (also KNIME 2.8.x) and JChem 6.1.3.0 (System requirement:KNIME 2.7.0 or later)

New Features and improvements
   Marvin/JChem 6.1.3.0 are used.

 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

 Bugfixes
  -JChem Search, JChem Update
   The unnecessary data field was outputted.

Takahiro

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Link to postPosted: Wed Jul 03, 2013 10:50 amPost subject: Reply with quote

We have just released JChem Extensions version 2.6.3.v0200.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.6
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Jul 3rd, 2013: Version 2.6.3.v0200 for KNIME2.6.3 (also KNIME 2.7.x) and JChem6.0.2.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 6.0.2.0 are used.

 New Nodes
  -MCS
   The MCS finds the maximum common substructure (MCS) of two molecules.

  -Similarity Calculator
   Calculate the similarity based on a Fingerprint.

 Improvements
  -JJC4XL 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.

 Bugfixes
  -MolSimilarity, RxnSimilarity
   Preprocessing time has been reduced.

  -FingerPrint
   The length of the result as binary format was not fixed.

Takahiro

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Link to postPosted: Mon May 20, 2013 12:22 pmPost subject: Reply with quote

We have just released JChem Extensions version 2.6.3.v0138.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.6
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
May 20th, 2013: Version 2.6.3.v0138 for KNIME2.6.3 (also KNIME 2.7.x) and JChem5.12.4.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.12.4.0 are used.

 Bugfixes
  -JChem Search
      If search time takes longer than 6 seconds, the search stops as time out error.

Takahiro

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Link to postPosted: Thu Apr 25, 2013 11:52 amPost subject: Reply with quote

We have just released JChem Extensions version 2.6.3.v0137.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.6
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Apr 25th, 2013: Version 2.6.3.v0137 for KNIME2.6.3 (also KNIME 2.7.x) and JChem5.12.3.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.12.3.0 are used.

 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.

 Bugfixes
  -Database nodes
   Database nodes did not recognize non-standard character sets such as MacRoman.

  -MolSimilarity
   If there were two or more query structures, the result was not correct.

Takahiro

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Link to postPosted: Thu Nov 01, 2012 11:36 amPost subject: Reply with quote

We have just released JChem Extensions version 2.6.3.v0135.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.6
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Nov 1st, 2012: Version 2.6.3.v0135 for KNIME2.6.3 and JChem5.11.3.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.11.3.0 are used.

 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.

Takahiro

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Link to postPosted: Thu Sep 06, 2012 11:30 amPost subject: Reply with quote

We have just released JChem Extensions version 2.6.0.v0134.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.6
This is composite update site that includes both of JChem and Marvin Extensions.

JChem Extensions Changes
Sep 6th, 2012: Version 2.6.0.v0134 for KNIME2.6.0 and JChem5.10.3.0 (System requirement:KNIME 2.5.0 or later)

 Bugfixes
  -JC4XL Reader
   Since the unnecessary log was outputted, processing speed was slow.

  -JC4XL Reader, JC4XL Writer
   In the KNIME 2.6.1, could not work correctly.

  -Join Reaction, MolExporter, Reactor, R-group Composition
   In Windows7 and Linux, dialog layout was broken.

Takahiro

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Link to postPosted: Fri Aug 24, 2012 11:02 amPost subject: Reply with quote

We have just released JChem Extensions version 2.6.0.v0133.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.6

Note:
You will have to install the Marvin Extensions before the JChem Extensions.
Marvin Extensions 2.6.0.v0133 can be downloaded from http://www.knime.org/downloads/update

JChem Extensions Changes
Aug 24th, 2012: Version 2.6.0.v0133 for KNIME2.6.0 and JChem5.10.3.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.10.3.0 are used.

 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.

 Bugfixes
  -MolImporter
   MolImporter nodes did not recognize non-standard character sets such as MacRoman.

  -JC4XL Reader
   If there are some blank or error cells on an Excel sheet, then they were not ignored.

  -JC4XL Writer
   Empty (missing) data was not written correctly.

  -logP, logD
   Selected Method was not recognized correctly.

Takahiro

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Posts: 71

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Link to postPosted: Thu May 10, 2012 2:52 pmPost subject: Reply with quote

We have just released JChem Extensions version 2.5.4.v0132.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.5

JChem Extensions Changes
May 10th, 2012: Version 2.5.4.v0132 for KNIME2.5.4 and JChem5.9.3.0 (System requirement:KNIME 2.5.0 or later)

 Bugfixes
  -MolImporter, (also other nodes that have file path parameter)
   File path parameter would be blank in case of importing older workflows.
   This version can load an older workflow which is built at 2.5.0.v0127 or later.

  -JChem Cartridge
   IOException was thrown by saving / loading an executed workflow, if SQL statement which is an INSERT, UPDATE, or DELETE statement.

  -3D Alignment
   NullPointerException was thrown, if the alignment type was "atom pairs",

Backward compatibility
We have also created JChem Extensions version 2.4.2.v0132.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.4.2
All of features are same except for the sortable table feature of MarvinTable node.
May 10th, 2012: Version 2.4.2.v0132 for KNIME2.4.2 and JChem5.9.3.0 (System requirement:KNIME 2.3.4 or later)

Takahiro

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Link to postPosted: Thu Apr 26, 2012 2:46 amPost subject: Reply with quote

We have just released JChem Extensions version 2.5.4.v0131.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.5

Note:
You will have to install the Marvin Extensions before the JChem Extensions.
Marvin Extensions 2.5.4.v0131 can be downloaded from http://www.knime.org/downloads/update

JChem Extensions Changes
Apr 26th, 2012: Version 2.5.4.v0131 for KNIME2.5.4 and JChem5.9.3.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.9.3.0 are used.

 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.

 Bugfixes
  -Importer / Exporter
   If the extension of structural file is upper case, could not work.

  -JC4XL Writer
   The result sheet was grouped with the structure data sheet (hidden sheet).
   The result file did not recalculate the formula (for rendering structure).

  -Chemical Fingerprint / Reaction Fingerprint
   If input data has missing cell, could not work continual.

  -All nodes
   GUI has been improved.
    Support resizing the window.
   Node color has been improved.

Backward compatibility
We have also created JChem Extensions version 2.4.2.v0131.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.4.2
All of features are same except for the sortable table feature of MarvinTable node.
Apr 26th, 2012: Version 2.4.2.v0131 for KNIME2.4.2 and JChem5.9.3.0 (System requirement:KNIME 2.3.4 or later)

Takahiro

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Posts: 71

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Link to postPosted: Tue Jan 24, 2012 3:12 amPost subject: Reply with quote

We have just released JChem Extensions version 2.5.1.v0129.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.5

Note:
You will have to install the Marvin Extensions before the JChem Extensions.
Marvin Extensions 2.5.1.v0129 can be downloaded from http://www.knime.org/downloads/update

JChem Extensions Changes
Jan 24th, 2012: Version 2.5.1.v0129 for KNIME2.5.1 and JChem5.8.0.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.8.0.0 are used.

 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.

 Bugfixes
  -MolImporter, (also other nodes that have file path parameter)
   File open/save dialog could not work correctly.

  -JChemSearch
   Always returned no hit results.

Backward compatibility
We have also created JChem Extensions version 2.4.2.v0129.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.4.2
All of features are same except for the sortable table feature of MarvinTable node.
Jan 24th, 2012: Version 2.4.2.v0129 for KNIME2.4.2 and JChem5.8.0.0 (System requirement:KNIME 2.3.4 or later)

Takahiro

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Posts: 71

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Link to postPosted: Thu Dec 08, 2011 1:34 pmPost subject: Reply with quote

We have just released JChem Extensions version 2.5.0.v0128.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.5

JChem Extensions Changes
Dec 8th, 2011: Version 2.5.0.v0128 for KNIME2.5.0 and JChem5.7.0.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements

 Improvements
  -Document Extractor
   Support URL as file path to extract file document.

 Bugfixes
  -MolImporter, (also other nodes that have file path parameter)
   When using with KNIME Server, could not work correctly.

Backward compatibility
We have also created JChem Extensions version 2.4.2.v0128.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.4.2
All of features are same except for the sortable table feature of MarvinTable node.
Dec 8th, 2011: Version 2.4.2.v0128 for KNIME2.4.2 and JChem5.7.0.0 (System requirement:KNIME 2.3.4 or later)

Takahiro

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Posts: 71

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Link to postPosted: Mon Dec 05, 2011 10:01 amPost subject: Reply with quote

We have just released JChem Extensions version 2.5.0.v0127.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.5

Note:
You will have to install the Marvin Extensions before the JChem Extensions.
Marvin Extensions 2.5.0.v0127 can be downloaded from http://www.knime.org/downloads/update

JChem Extensions Changes
Dec 5th, 2011: Version 2.5.0.v0127 for KNIME2.5.0 and JChem5.7.0.0 (System requirement:KNIME 2.5.0 or later)

New Features and improvements
   Marvin/JChem 5.7.0.0 are used.

 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).

 Bugfixes
  -MolExporter
   When using with KNIME Server, could not work correctly.

  -JChem Manager, JChem Cartridge
   When using with KNIME Server (Web Portal), workflow credential could not work correctly.

  -LibraryMCS
   The 'Maximum level count' option on the 'Clustering' tab can not be set smaller than 5.

Takahiro

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Link to postPosted: Tue Aug 09, 2011 8:00 amPost subject: Reply with quote

We have just released JChem Extensions version 2.4.1.v0125.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.4

Note:
You will have to install the Marvin Extensions before the JChem Extensions.
Marvin Extensions 2.4.1.v0125 can be downloaded from http://www.knime.org/downloads/update

JChem Extensions Changes
Aug 9th, 2011: Version 2.4.1.v0125 for KNIME2.4.1 and JChem5.5.1.0 (System requirement:KNIME 2.3.4 or later)

New Features and improvements
   Marvin/JChem 5.5.1.0 are used.

 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.

 Bugfixes
  -MarvinSpace
   Support MacOS 64 bit.

  -Marvin Renderer
   Empty data issue has been fixed.

  -All nodes
   Calculating requirement and dependency could not work correctly and it has been fixed.
   Executing workflow in KNIME batch mode could not work and it has been fixed.

 Removed nodes
  MrvConverter
  MrvFromCmlConverter
  MrvFromMol2Converter
  MrvFromMolConverter
  MrvFromPdbConverter
  MrvFromRxnConverter
  MrvFromSdfConverter
  MrvFromSmilesConverter
  MrvToCmlConverter
  MrvToMol2Converter
  MrvToMolConverter
  MrvToPdbConverter
  MrvToRxnConverter
  MrvToSdfConverter
  MrvToSmilesConverter
  MrvToStringConverter

  Use the 'MolConverter' node instead.

Takahiro

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Posts: 71

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Link to postPosted: Fri May 27, 2011 11:44 amPost subject: Latest version, history of changes Reply with quote

We have just released JChem Extensions version 2.3.4.v0124.
It is available for download at https://www.infocom.co.jp/bio/knime/update/2.3

Note:
Since this version, we have separated the Marvin Extensions from the JChem Extensinos.
Therefore, you will have to install the Marvin Extensions before the JChem Extensions.
Marvin Extensions 2.3.4.v0124 can be downloaded from http://www.knime.org/downloads/update

JChem Extensions Changes
May 25th, 2011: Version 2.3.4.v0124 for KNIME2.3.4 and JChem5.4.1.1

New Features and improvements
   Marvin/JChem 5.4.1.1 are used.
   Node repository tree has been changed based on JChem/Marvin products.

 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.

 Bugfixes
  -Reactor
   If check the 'Keep properites' option, the columns order in output table are changed automatically.

  -Markush Enumeration
   Markush library size returns a wrong value, therefore, the return type is changed from IntCell to LongCell.

  -All nodes
   Workflow process speed might be dramatic slowdown on KNIME2.3 or later.

 Deprecated nodes
  MrvConverter
  MrvFromCmlConverter
  MrvFromMol2Converter
  MrvFromMolConverter
  MrvFromPdbConverter
  MrvFromRxnConverter
  MrvFromSdfConverter
  MrvFromSmilesConverter
  MrvToCmlConverter
  MrvToMol2Converter
  MrvToMolConverter
  MrvToPdbConverter
  MrvToRxnConverter
  MrvToSdfConverter
  MrvToSmilesConverter
  MrvToStringConverter

  Will be removed. Use the 'MolConverter' node instead.

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