Pipeline Pilot Components History of Changes

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

    The appropriate versions are available for all released JChem versions.

    Versions 22.14 and 22.15 were not released due to technical reasons

    Version 22.12, June 16, 2022

    • JChem library included for simpler installation

    Version 22.1, January 17, 2022

    • Compatible with Compliance Checker 21.4.0 or later

    Version 21.19, December 14, 2021

    • Pipeline Pilot 21.2.0 or later is required.

    Version 21.14, August 26, 2021

    • Bugfix: Problem with coordination bonds during Chemaxon Molecule > Pipeline Pilot Molecule conversion

    Version 21.13, August 3, 2021

    • Bugfix: "Insert to JChem Table" sent all records to Fail Port if CD_ID was not requested in result ("ID Property Name" was not set)

    Version 21.12, July 18, 2021

    • Bugfix: Enhanced stereo in the Pipeline Pilot molecule output of various components no longer simplified according to "Molecule from CTAB" and "SD Reader" defaults.

    Version 21.10, June 9, 2021

    • Standardizer adds result properties (e.g. stripped salt info) to data record.

    Version 21.7, April 28, 2021

    • Compatibility with latest Compound Registration versions fixed

    • Usage of Marvin JS Web Services as MJS back-end supported as default

    Version 21.4, March 25, 2021

    • Pipeline Pilot 19.1.0 or later is required.

    Version 20.20, October 30, 2020

    • Compatible with Compound Registration 20.8.0 or later

    • "Registration Auto Register": new option "Send to Staging" for pre-registration

    • Compatible with Compliance Checker 20.8.0 or later

    Version 20.8, March 19, 2020

    • New component: "ChemAxon logD"

    Version 20.4, February 9, 2020

    • Pipeline Pilot 18.1.0 or later is required.

    Version 20.1, January 14, 2020

    • New component: "ChemAxon Major Microspecies"

    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: 17.2.6.0

    • "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 17.2.13.0, 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 17.1.30.0, 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 17.1.9.0, January 14, 2017

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

    Version 17.1.2.0, January 3, 2017

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

    Version 16.12.5.0, December 8, 2016

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

    Version 16.11.7.0, November 16, 2016

    • External documentation links fixed/updated for several components

    Version 16.10.24.0, October 26, 2016

    • New component: "JChem Web Services Search"

    Version 16.10.3.0, October 5, 2016

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

    Version 16.9.5.0, September 7, 2016

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

    Version 16.8.15.0, 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 16.6.20.0, June 21, 2016

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

    Version 16.6.6.0, 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 16.5.30.0, May 31, 2016

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

    Version 16.5.23.0, May 25, 2016

    • New component: "JChem PSQL Cartridge Search"

    Version 16.4.18.0, April 20, 2016

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

    Version 16.3.28.0, April 4, 2016

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

    Version 16.3.21.0, 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 16.2.22.0, February 26, 2016

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

    Version 16.2.15.0, 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 16.1.25.0, 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 15.11.16.0, November 26, 2015

    • New component: "Marvin JS"

    Version 15.9.28.0, September 30, 2015

    • Error reporting and logging has been improved

    Version 15.9.21.0, 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 15.9.14.0 incorrect vague bond level was applied for previous cartridge versions (Level 1 instead of Half)

    Version 15.9.7.0, 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 15.8.24.0, August 26, 2015

    JChem Cartridge Search bugfix:

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

    Version 15.5.18.0, May 20, 2015

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

    Version 15.3.9.0, 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 15.1.26.0, January 29, 2015

    • New component: "JChem for Excel Reader"

    • Component "ChemAxon Fragmenter" removed (discontinued product)

    Version 15.1.12.0, 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 15.1.5.0, 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 14.12.15.0, 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 14.12.8.0, 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 14.11.17.0, 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 14.11.03.0, 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 14.9.29.0, October 2, 2014

    • Pipeline Pilot 9.0 or later is required.

    Version 14.9.22.0, September 24, 2014

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

    Version 14.8.4.0, 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 14.7.7.0, 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 : 5.6.0.1 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 : 5.4.0.1 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