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 most released JChem versions.
NOTE: From version 23.10 the Chemaxon Java API requires Java 17.
BIOVIA is expected to support Java 17 in Pipeline Pilot 2024 2025.
Until this version is available the mainstream release of the components is suspended.
For older Pipeline Pilot versions the Mercury LTS versions are available.
- Compliance Checker
- Always clones all input data to the result, the "Query Tag Property Name" parameter removed
- Significant speedup via batch processing
- JChem library included for simpler installation
- Compatible with Compliance Checker 21.4.0 or later
- Pipeline Pilot 21.2.0 or later is required.
- Bugfix: Problem with coordination bonds during Chemaxon Molecule > Pipeline Pilot Molecule conversion
- 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)
- Bugfix: Enhanced stereo in the Pipeline Pilot molecule output of various components no longer
simplified according to "Molecule from CTAB" and "SD Reader" defaults.
- Standardizer adds result properties (e.g. stripped salt info) to data record.
- Pipeline Pilot 19.1.0 or later is required.
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
- New component: "ChemAxon logD"
- Pipeline Pilot 18.1.0 or later is required.
- New component: "ChemAxon Major Microspecies"
- Bugfix: "Marvin JS" compatibility with Internet Explorer 11 restored
- Bugfix: "ChemAxon Reactor" threw exception for reactions containing R-groups
- Bugfix: configuration property names were not read properly in some cases
- Compound Registration:
- Advanced registration options added
- Compatible with Compound Registration version Carbon.2 (18.22.2)
- "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
- "JChem for Office Writer" bugfix: did not run with default Document Style
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
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"
- Bugfix: some components did not remove some properties in certain cases
- Pipeline Pilot 9.5 or later is required.
- "ChemAxon Calculator" : new options added for logP and logD calculations
- Calculation method
- Consider tautomers
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.
- "JChem for Office Writer", "JChem for Office Reader":
regular page breaks are exported and recognized for Word documents from now on.
- New components:
- "JChem for Office Reader"
- "JChem for Office Writer"
- "Marvin JS" component: compatibility fix for newer FireFox versions
- "ChemAxon Molecular Table Viewer" component removed (obsolete)
- External documentation links fixed/updated for several components
- New component: "JChem Web Services Search"
- New components for Compliance Checker integration:
- "Compliance Checker"
- "Compliance Checker Categories"
- "Chemical Terms Calculator" : molecule type results are allowed
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
- "JChem for Excel Writer" bugfix: exception when conditional formatting was missing fixed
- New component: "MarvinSketch Applet":
Completely re-written component, earlier prototypes removed.
- New component: "JChem PSQL Cartridge Search"
- "ChemAxon Name to Structure" : added option to allow CAS lookup by web service,
new default is disabled
- New components for compound registration:
- "Registration Connection"
- "Registration Auto Register"
- "Registration Get Structure by ID"
- "Registration Structure Search"
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
- "ChemAxon Structure to Name" : added option to generate CAS numbers
"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)
- "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
- New component: "Marvin JS"
- Error reporting and logging has been improved
- "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)
- "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)
JChem Cartridge Search bugfix:
- "ORA-01000: maximum open cursors exceeded" for larger result sets fixed
- "JChem for Excel Writer" component:
- Conditional Formatting Expression option added
- NOTE: became subprotocol, GUID changed
- 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
- 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
- "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
- "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
- "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)
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"
- Pipeline Pilot 9.0 or later is required.
- "ChemAxon Markush Filter" Prototype component removed, no advantage
over "Chemaxon Chemical Terms Filter" since Pipeline Pilot 8.5
- Some "Advanced" parameters were converted to normal in several
components, so they will not behave "Hidden" in Pipeline Pilot 9.0
- "ChemAxon Reactor" component : "Generate Unsuccessful Reactions" option added
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
"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
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"
- "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
- "JChem for Excel Writer" component:
- Vertical Alignment option added
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
- "JChem for Excel Writer" component:
- Option for controlling the relative position of the structure column
- Bugfix: data columns did not keep order
- New component:
- "ChemAxon Structure Checker"
- JChem Base "Insert" component:
- support for binary input formats added
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
- Supported JChem versions:
- 5.10.x : 5.10.0 and above
- 5.9.x : 5.9.0 and above
- Improved error handling in "ChemAxon Calculator" and "Chemical Terms Calculator"
- Improved error handling in "ChemAxon Ionize Molecule at pH"
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
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
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
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)
- "ChemAxon 3D Conformers" component added
- JChemSearch component returns result structures faster after search
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).
"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
- 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).
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)
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