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.
Version 23.6.4, January 26, 2024
-
Compliance Checker components use newer service "cc-api"
-
"Compliance Checker":
- New option to include similar hits, the new default is "Highly similar"
-
"Compliance Checker Categories":
- New option to select regulation categories
- Old option for "hidden categories" removed
- Bugfix: Some categories were not listed
-
"Chemical Terms Calculator" : double[][] result type supported
-
Minimum recommended versions changed for related Chemaxon software:
- Compliance Checker: 23.6.1 (Mercury.1)
- Compound Registration: 23.6.1 (Mercury.1)
- JChem Oracle Cartridge: 23.6.1 (Mercury.1)
- JChem PSQL Cartridge: 23.6.1 (Mercury.1)
- Marvin JS Web Services: 23.6.1 (Mercury.1)
Version 23.6.1, May 27, 2023
- Compliance Checker
- Always clones all input data to the result, the "Query Tag Property Name" parameter removed
- Significant speedup via batch processing
Version 22.22, January 10, 2023
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
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/general_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
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
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
Version 17.14.0, July 7, 2017
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
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
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
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
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
Version 2.6.3, July 29, 2013
Version 2.6.2, June 6, 2013
- "JChem for Excel Writer" component:
- Vertical Alignment option added
Version 2.6.1, May 30, 2013
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
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:
-
"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
Version 2.1, November 29, 2011
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
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:
-
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
Version 1.6.2, February 18, 2010
Version 1.6.1, January 8, 2010
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 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