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History of Changes for the Frequent Release branch. For LTS branches please click here.



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


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