Pipeline Pilot Components History of Changes

    History of Changes for the LTS branch "Europium" (19.21.x).

    NOTE: For the sake of brevity only versions with significant changes are listed here.

    The appropriate versions are available for all released JChem versions.

    Version 19.18, August 4, 2019

    • Bugfix: "Marvin JS" compatibility with Internet Explorer 11 restored

    Version 19.17, July 16, 2019

    • Bugfix: "ChemAxon Reactor" threw exception for reactions containing R-groups

    Version 19.7, March 12, 2019

    • Bugfix: configuration property names were not read properly in some cases

    Version 19.1, January 14, 2019

    • Compound Registration:
      • Advanced registration options added
      • Compatible with Compound Registration version Carbon.2 (18.22.2)

    Version 18.28, November 28, 2018

    • "ChemAxon Document Extractor", "ChemAxon Name to Structure" and "ChemAxon Structure to Name" : Parameter names and legal values relating to CAS Registry Numbers® have been modified due to legal request. NOTE: Incompatible changes. Please update all usages of "ChemAxon Document Extractor" and "ChemAxon Name to Structure" by right-click and "Replace with Latest Version", and if needed set the relevant option to True again. Notice about CAS Registry Numbers® : https://docs.chemaxon.com/display/docs/notice-about-cas-registry-numbers-r.md

    Version 18.20, August 21, 2018

    • "JChem for Office Writer" bugfix: did not run with default Document Style

    Version 18.13, June 12, 2018

    • Required Compound Registration version: 18.5.14

    • "Insert to JChem Table" bugfix: inserting of non-string type additional data fixed

    Version 18.8, March 14, 2018

    • Marvin Applets are no longer supported

    • "ChemAxon HTML Molecular Table Viewer"

      • Opens default browser, with option to override
      • On click always pop-up image
      • ChemAxon rendering is default
      • Pipeline Pilot image options updated
    • "MarvinSketch Applet" component removed

    Version 17.29.0, December 8, 2017

    • Pipeline Pilot 17.2.0 or later is required. For earlier versions the 17.24.x LTS releases are available (bugfixes only).

    • Fixed Marvin JS installation instructions (reverse proxy setting could be lost)

    • Bugfix: fixed example "JChem Base Insert and Search"

    Version 17.27.0, October 26, 2017

    • Bugfix: some components did not remove some properties in certain cases

    Version 17.26.0, October 20, 2017

    • Pipeline Pilot 9.5 or later is required.

    Version 17.23.0, September 16, 2017

    • Minimum required JChem Web Services version:

    • "JChem Web Services Search" : advanced search options string added

    Version 17.16.0, July 22, 2017

    • "ChemAxon Calculator" : new options added for logP and logD calculations
      • Calculation method
      • Consider tautomers

    Version 17.15.0, July 15, 2017

    • "JChem PSQL Cartridge Search" : Similarity Search support added

    • Required JChem PostgreSQL Cartridge version: 2.9 or later

    Version 17.14.0, July 7, 2017

    • "Compliance Checker" no longer blocks in filter mode until all records finished

    • Bugfix: "JChem for Office Writer" image quality fixed

    Version, February 15, 2017

    • Minimum required Pipeline Pilot version : 9.2

    • Minimum required Internet Explorer version : 11

    • Bugfix: JVM crash in certain cases during error reporting ("No server process") fixed.

    Version, February 4, 2017

    • "JChem for Office Writer", "JChem for Office Reader": regular page breaks are exported and recognized for Word documents from now on.

    Version, January 14, 2017

    • New components:
      • "JChem for Office Reader"
      • "JChem for Office Writer"

    Version, January 3, 2017

    • "Marvin JS" component: compatibility fix for newer FireFox versions

    Version, December 8, 2016

    • "ChemAxon Molecular Table Viewer" component removed (obsolete)

    Version, November 16, 2016

    • External documentation links fixed/updated for several components

    Version, October 26, 2016

    • New component: "JChem Web Services Search"

    Version, October 5, 2016

    • New components for Compliance Checker integration:
      • "Compliance Checker"
      • "Compliance Checker Categories"

    Version, September 7, 2016

    • "Chemical Terms Calculator" : molecule type results are allowed

    Version, August 16, 2016

    • Marvin JS is now included as integral version of the package for simplified installation

    • Upgraded and simplified installation instructions

    • "ChemAxon HTML Molecular Table Viewer" bugfix: did not find applet if it was selected for pop-up

    Version, June 21, 2016

    • "JChem for Excel Writer" bugfix: exception when conditional formatting was missing fixed

    Version, June 7, 2016

    • New options for "JChemSearch" and "JChem Oracle Cartridge Search":

      • Homology Narrow Translation
      • Homology Broad Translation
    • "MolConverter" bugfix: exception if "Keep Properties" parameter is used

    Version, May 31, 2016

    • New component: "MarvinSketch Applet": Completely re-written component, earlier prototypes removed.

    Version, May 25, 2016

    • New component: "JChem PSQL Cartridge Search"

    Version, April 20, 2016

    • "ChemAxon Name to Structure" : added option to allow CAS lookup by web service, new default is disabled

    Version, April 4, 2016

    • New components for compound registration:
      • "Registration Connection"
      • "Registration Auto Register"
      • "Registration Get Structure by ID"
      • "Registration Structure Search"

    Version, March 23, 2016

    • The default Vague Bond Level has changed for "JChemSearch", "JChem Cartridge Search" and "ChemAxon Structure Search Filter" components according to JChem changes:

      • Vague bond level "Default" (Level 1) option renamed to "Ligands and bridging bonds of aromatic rings"
      • The new default vague bond level is "Ambiguous aromaticity 5 membered rings" (Level Half)
    • "ChemAxon Tautomerization"

      • "Generic Tautomer" option removed
      • New options added: normal tautomers, protect ester groups, ring-chain tautomers

    Version, February 26, 2016

    • "ChemAxon Structure to Name" : added option to generate CAS numbers

    Version, February 20, 2016

    • "Drop JChem Base Table" : Added "Ignore Missing Table" option

    • "Molecule from IUPAC Name (ChemAxon)" renamed to "ChemAxon Name to Structure"

    • "Molecule to IUPAC Name (ChemAxon)"

      • Renamed to "ChemAxon Structure to Name"
      • Added option to generate traditional names
      • "Z" atoms treated as attachment points (not as carbon)

    Version, February 5, 2016

    • "Marvin JS" component:
      • Web services URL have to be set centrally in chemaxon.conf, GUI options removed.
      • Option for embedded or popup mode
      • Multiple instances per form supported

    Version, November 26, 2015

    • New component: "Marvin JS"

    Version, September 30, 2015

    • Error reporting and logging has been improved

    Version, September 24, 2015

    • "JChem Cartridge Search"
      • Retrieval of hits is faster in most cases
      • Coloring and alignment is now off by default
      • Bugfix: in version incorrect vague bond level was applied for previous cartridge versions (Level 1 instead of Half)

    Version, September 10, 2015

    • "ChemAxon Document Extractor":
      • CAS lookup default changed to off (bugfix), but extra interactive warning of web service usage was removed
      • Options added to enable/disable systematic and common names; elements, ions and groups
      • Options added to retrieve the context of hits
      • Document section information (for USPTO XML patents)

    Version, August 26, 2015

    JChem Cartridge Search bugfix:

    • "ORA-01000: maximum open cursors exceeded" for larger result sets fixed

    Version, May 20, 2015

    • "JChem for Excel Writer" component:
      • Conditional Formatting Expression option added
      • NOTE: became subprotocol, GUID changed

    Version, March 13, 2015

    • Configuration file "chemaxon.conf" file instead of environment variables for global settings:
      • license location
      • log directory
      • OSR tools
    • Default log directory changed to "logs" directory inside package

    Version, January 29, 2015

    • New component: "JChem for Excel Reader"

    • Component "ChemAxon Fragmenter" removed (discontinued product)

    Version, January 13, 2015

    • JChem Cartridge components: backwards compatibility tested and set to minimum version 6.1.0
    • "ChemAxon Standardize" bugfixes:
      • Did not work with configuration string and configuration file (only with simple actions)
      • Relative path for custom Standardizer configuration file was not resolved properly
      • Order changed for simple actions: Clean 2D and 3D moved to the end of list, Dearomatize moved up

    Version, January 8, 2015

    • "JChemSearch", "JChem Cartridge Search": "Remove Unused R-group Definitions" option added, unused groups no longer removed by default
    • "Insert to JChem Table" : rejected empty structures no longer considered as an "error" (i.e. no error message, does not affect "Halt on Error" option)
    • "JChemSearch" bugfix: dissimilarity values were not returned
    • "JChem Cartridge Search" bugfixes:
      • Filter Query caused exception in certain cases
      • removed unused (ineffective) option "Ordering"
    • "Create JChem Base Table" bugfix : relative path for custom Standardizer configuration file was not resolved properly

    Version, December 18, 2014

    • "ChemAxon HTML Molecular Table Viewer": "Display R-Logic" option added
    • "ChemAxon Image from Molecule": "Display R-Logic" option added
    • "ChemAxon Structure Search Filter"
      • Bugfix: ineffective "Markush Hit Representation" option removed. Markush search is not supported by this component, please use the JChemSearch component.
      • Bugfix: illegal default value for Tautomer Search removed

    Version, December 10, 2014

    • "ChemAxon MolConverter" bugfix: file input property selection was not effective in case of file output
    • "ChemAxon Structure Checker":
      • "Ignore OCR Errors" option removed in line with JChem changes as separate option. Use the OCR checker("ocr") in the configuration instead.
      • Bugfix: Structures with no remaining issues were not fixed properly
      • Bugfix: Fixes are always executed for checkers with fix mode "Ask" (e.g. action strings)

    Version, November 20, 2014

    • External documentation links updated due to ChemAxon website changes.

    • "Create JChem Base Table" bugfix: default fingerprint parameters were incorrect for Reaction and Markush table types.

    Version, November 5, 2014

    • New components:

      • "JChem Cartridge Search"
      • "JChem Cartridge Information"
    • "JChemSearch" and "ChemAxon Structure Search Filter" components:

      • New "Default" Vague Bond Level option corresponding to new default Level 1 in JChem.
      • New "Stereo Search" option "Enantiomer Search", other stereo options renamed
      • Bugfix for "Stereo Search", "Charge Matching", "Isotope Matching", "Radical Matching": The "Default" option was not incorrect default for "Duplicate" search type, as non-specific query could match specific targets. New "Default" option changes behavior to Exact matching in case of "Duplicate" search.

      NOTE: Please update usages of "JChemSearch" and "ChemAxon Structure Search Filter" components by right-click and "Replace with Latest Version"

    Version, October 2, 2014

    • Pipeline Pilot 9.0 or later is required.

    Version, September 24, 2014

    • "ChemAxon Markush Filter" Prototype component removed, no advantage over "Chemaxon Chemical Terms Filter" since Pipeline Pilot 8.5

    Version, August 9, 2014

    • Some "Advanced" parameters were converted to normal in several components, so they will not behave "Hidden" in Pipeline Pilot 9.0

    Version, July 23, 2014

    • "ChemAxon Reactor" component : "Generate Unsuccessful Reactions" option added

    Version 2.9, July 10, 2014

    • New component: "JChem Table Information"

    • "Create JChem Base Table":

      • New options added: fingerprint parameters, custom standardization, absolute stereo, duplicate filtering, tautomer duplicate filtering
    • "Insert to JChem Table" component:

      • Duplicate filtering is table option, with override option for compatibility
    • "Delete from JChem Base Table" component:

      • Bugfix: backward compatibility fix

    Version 2.8.1, May 16, 2014

    • Supported JChem versions:

      • 6.3.x : 6.3.0 and above
      • 6.2.x : 6.2.0 and above
    • "ChemAxon Calculator" component:

      • Bugfix: backward compatibility fix for pKa "Mode" option

    Version 2.8, April 27, 2014

    • "ChemAxon Reactor" component : temporary disk space usage significantly reduced

    • "Create JChem Base Table": extra fields can be specified for table creation

    • "Delete from JChem Base Table": can accept cd_id values as input data

    • "JChemSearch" component:

      • Bugfix: cd_id values were not returned if neither molecular structure nor data fields were requested

    Version 2.7.1, February 13, 2014

    • Supported JChem versions:

      • 6.2.x : 6.2.0 and above
      • 6.1.x : 6.1.0 and above
    • "ChemAxon Document Extractor": support added for multiple File/URL input

    • "ChemAxon HTML Molecular Table Viewer": aromatization option did not work for ChemAxon image option

    • "ChemAxon HTML Molecular Table Viewer" and "ChemAxon Image from Molecule": Option "ChemAxon Image Options (De)aromatization" renamed to "ChemAxon Image Options Aromatization"

    Version 2.7, January 10, 2014

    • "ChemAxon Document Extractor" upgraded (in 6.1.x version only):
      • Support for a total 3 OSR tools (CLiDE, OSRA, Imago)
      • NOTE: parameter OSRA on/off parameter removed (!), replaced by "OSR Tool" with multiple options
      • Several new options added: start page, end page, OSR filtering, OSR timeout, acronyms, OLE object conversion and more
    • "ChemAxon Document Extractor" fix:
      • Better compatibility for extraction from certain web sites

    Version 2.6.4, September 29, 2013

    • Supported JChem versions:

      • 6.1.x : 6.1.0 and above
      • 6.0.x : 6.0.0 and above
    • "LibMCS Clustering" component updated (in 6.1.x version only):

      • Uses new clustering algorithm, faster execution time
      • New atom matching options: Radicals, Isotopes
      • Clustering method options changed: please "Replace with Latest Version"

    Version 2.6.3, July 29, 2013

    • Pipeline Pilot 8.5 or newer is required

    • "ChemAxon HTML Molecular Table Viewer" component:

      • Bugfix: did not work with structure source property

    Version 2.6.2, June 6, 2013

    • "JChem for Excel Writer" component:
      • Vertical Alignment option added

    Version 2.6.1, May 30, 2013

    • "JChem for Excel Writer" component:

      • Bugfix: style setting for mixed case properties did not work
    • "ChemAxon Calculator" component:

      • Option for micro pKa calculation (6.0 version only)

    Version 2.6, May 23, 2013

    • Supported JChem versions:

      • 6.0.x : 6.0.0 and above
      • 5.12.x : 5.12.0 and above
    • "JChem for Excel Writer" component:

      • Option for overwrite / append behaviour
      • Options for formatting:
        • column width
        • horizontal alignment
        • text wrapping
    • "ChemAxon Calculator" component:

      • Option for pKa correction library file (6.0 version only)
    • "ChemAxon HTML Molecular Table Viewer" component:

      • Bugfix: exception in case the input contained no molecule

    Version 2.5.2, April 16, 2013

    • "JChem for Excel Writer" component:
      • Option for controlling the relative position of the structure column
      • Bugfix: data columns did not keep order

    Version 2.5.1, March 7, 2013

    • Supported JChem versions:

      • 5.12.x : 5.12.0 and above
      • 5.11.x : 5.11.0 and above
    • "JChemSearch" component:

      • String parameter added for advanced search options

      -"ChemAxon Standardize" component:

      • Also accepts molecule source as input

    Version 2.5, December 25, 2012

    • New component:
      • "ChemAxon Structure Checker"

    Version 2.4.1, November 20, 2012

    • JChem Base "Insert" component:
      • support for binary input formats added

    Version 2.4, October 22, 2012

    • Supported JChem versions:

      • 5.11.x : 5.11.0 and above
      • 5.10.x : 5.10.0 and above
    • Pipeline Pilot 8.0 or newer is required

    • New component:

      • "JChem for Excel Writer"
    • "ChemAxon Structure Search Filter" bugfix: explicit H removal was not disabled during query structure standardization

    • Support for binary structure formats in: "ChemAxon MolConverter", "ChemAxon Image From Molecule", "ChemAxon HTML Molecular Table Viewer"

    • Example protocols updated / fixed

    Version 2.3.3, June 29, 2012

    • Supported JChem versions:
      • 5.10.x : 5.10.0 and above
      • 5.9.x : 5.9.0 and above

    Version 2.3.2, April 20, 2012

    • Improved error handling in "ChemAxon Calculator" and "Chemical Terms Calculator"

    Version 2.3.1, March 15, 2012

    • Improved error handling in "ChemAxon Ionize Molecule at pH"

    Version 2.3, March 6, 2012

    • Supported JChem versions:

      • 5.9.x : 5.9.0 and above
      • 5.8.x : 5.8.0 and above
    • "ChemAxon Document Extractor" upgraded (in 5.9 version only):

      • Optical Structure Recognition support via OSRA
      • More options and result properties
    • "Create JChem Base Table" creates the JChem property table if does not exist

    • "Connection" accepts empty login and password

    Version 2.2, February 18, 2012

    • Supported JChem versions:

      • 5.8.x : 5.8.0 and above
      • 5.7.x : 5.7.0 and above
    • New component:

      • "Delete from JChem Base Table"

    Version 2.1, November 29, 2011

    • Supported JChem versions:

      • 5.6.x : and above
      • 5.7.x : 5.7.0 and above
    • New component:

      • "ChemAxon Document Extractor"

    Version 2.0, October 17, 2011

    • New component:

      • "ChemAxon Formula Search Filter"
    • "ChemAxon Reactor" component : speedup by multi-threading and more efficient reactant selection

    • "ChemAxon Structure Search Filter" : improved error handling

    • "ChemAxon Calculator" : more options for pKa data export and visualization

    • "JChemSearch" : BigDecimal return type support added for hit data retrieval

    Version 1.9, May 12, 2011

    • Supported JChem versions:

      • 5.4.x : and above
      • 5.5.x : 5.5.0 and above
    • New component:

      • "ChemAxon Structure Search Filter"
    • Added error handling options for Naming components

    • "LibMCS Clustering" component: reduced memory need

    • Minor improvements in error handling, installation, system information dialog

    Version 1.8.1, January 17, 2011

    • Restored Pipeline Pilot 7.5 compatibility

    • "ChemAxon Reactor"

      • Fused reaction output option added
      • Reactant ratio option added
      • "ChemAxon_Last_Record_Tag" temporary property wasn't removed (bugfix)
    • Obsolete component "CTAB from Molecule" removed

    Version 1.8, December 21, 2010

    • Requires JChem 5.3.0 or newer, JChem 5.4.x support added

    • Pipeline Pilot 8.0 or newer is required

    • New component:

      • "ChemAxon Fragmenter"
    • Markush Enumeration options added:

      • coloring (scaffold, R-group)
      • homology group enumeration
      • MRV source output
    • JChemSearch:

      • Markush hit reduction option (with homology expansion)
      • threw exception if NULL value was found in exported data columns (bugfix)
    • "Create JChem Base Table": support for various table types

    • Reactor: Synthesis Code also enabled for reaction output

    • JChem Base "Insert" component:

      • structure source input did not work (bugfix)
      • did not accept Pipeline Pilot reactions (bugfix)

    Version 1.7, July 1, 2010

    • New components:

      • "ChemAxon Image From Molecule"

      • "ChemAxon HTML Molecular Table Viewer"

    • "JChemSearch" (JChem Base):

      • Query-filtering (flow-trough) mode

      • Hit coloring and alignment

      • Various output options: PP molecule, MRV source, Original source

      • Search modes renamed according to new JChem terminology

      • "Duplicate" search type added

      • Fetching data fields of hit records from JChem Base table

      • Stereo search option updated

      • "Insert" (JChem Base):

        • Option to continue on error, problem structures directed to Fail port

        • Option to enable empty structures

      • "Chemical Terms Calculator" : byte[] result type supported

    Version 1.6.2, February 18, 2010

    • "ChemAxon MolConverter":

      • able to use ByteArray input as ASCII source (e.g. obtained from cd_structure field)

      • threw exception on properties not convertible to String ot StringArray (bugfix)

    Version 1.6.1, January 8, 2010

    • "ChemAxon Reactor" : keeps properties of reactants in products (option added)

    • "ChemAxon MolConverter" : keeps properties also in file output

    Version 1.6, August 31, 2009

    • "ChemAxon 3D Conformers" component added

    Version 1.5.1, June 9, 2009

    • JChemSearch component returns result structures faster after search

    Version 1.5, May 29, 2009

    • Requires JChem / Marvin 5.1.3 or newer

    • New components:

      • "ChemAxon MolConverter"

      • "ChemAxon Tautomerization"

      • "ChemAxon Markush Enumeration"

    • "Chemaxon Reactor" component can now skip errors

    • Error reporting was further improved. Error log always present at a default location.

    • "Show ChemAxon Environment" component improved (displays info in Notepad).

    Version 1.4, November 24, 2008

    • "LibMCS Clustering" component added

    • "Molecule to IUPAC Name" component added

    • "Molecule from IUPAC Name" component added

    • "ChemAxon Reactor" component:

      • New options added:
        • Synthesis Code generation
        • Unambiguous only (single) mode
        • Output reaction mapping
        • Options to ignore 3 types of reaction rules
      • Bugs fixed:
        • reaction output always contained all products
        • premature termination with "No Server Process" message for large input sets
    • Utility protocol added for displaying ChemAxon software properties

    Version 1.3.1, October 22, 2008

    • Bugfix: ChemAxon Reactor only returned the first set of products for a given pair of reactants resulting in fewer products in certain cases.
    • Bugfix: ChemAxon Calculator threw exception for inconsistent input structures in some cases (instead of just adding an error tag, and letting processing go on).

    Version 1.3, July 11, 2008

    • Chemical Terms Calculator component added

    • New error reporting system: more informative error text, ability to write detailed error log to file if CHEMAXON_PP_LOG_DIR environment variable set.

    • Collection recompiled for Marvin / JChem 5.1 compatibility (while still maintaining JChem 3.2 / Marvin 4.1.2 backwards compatibility)

    Version 1.2, March 5, 2008

    • ChemAxon Reactor component added

    • ChemAxon Standardize component upgraded:

      • more simple actions (checkboxes)
      • also accepts configuration string and configuration file for advanced tasks
    • JChem Base Insert:

      • Duplicate filtering option (using Pass and Fail ports)
      • Returns cd_id (primary key) values
      • Two input modes:
        • read structure source from a specified property
        • if property not specified uses PP input molecule
      • Insert into additional data fields (only for string column types yet)
    • JChemSearch

      • Several search options were added
      • Easier protocol integration and better performance due to concentrated functionality
    • Create JChem Base Table component added

    • Drop JChem Base Table component added

    • General documentation upgrade of most components