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JChem Changes

November 13th, 2008, 5.1.3_2

Marvin 5.1.3_2 is included.

Bugfixes

• JChem Cartridge
  • jchem_table_pkg.jc_insert threw NullPointerException when null was specified for the jchemproperty table name.
• Standardizer
  • Attribute values of Clean2D, ConvertDoubleBonds and RemoveFragment actions at Standardizer Configuration Editor GUI are now case insensitive.

November 11th, 2008, 5.1.3_1

Marvin 5.1.3_1 is included.

November 7th, 2008, 5.1.3

Marvin 5.1.3 is included

New features and Improvements

• JChem Base:
  • Tautomer search now considers explicit Hydrogens in the query.
  • Developers Guide was extended with molecular descriptor similarity search example.
• JKlustor:
  • Enhanced histograms in LibraryMCS SAR table view.

Bugfixes

• JChem Base:
  • Empty query search in database was corrected for exact and superstructure searches.
  • EXACT and PERFECT search did not work for reaction tables Forum topic
  • HashCode generation expands S-groups before calculation (this bugfix effects API behavior change) Forum topic
  • Exact stereo search did not work for substructure and exact fragment search types if the query was not stereo-specific but the target was.
• JChem Cartridge:
  • ALTER INDEX REBUILD didn't work with non-default jchemproperties tables Forum topic
  • Speeded up import into JChem structure tables with jc_idxtype index by about 25%

Regeneration

current table version is: 50103
Hash code of reaction tables has changed, so reaction tables have to be regenerated.

October 1st, 2008, 5.1.2

Marvin 5.1.2 is included

New features and Improvements

• JChem Base:
  • Similarity search speedup (for the default chemical hashed fingerprints with Tanimoto formula).
• Standardizer:
  • New option added to "sgroups" Standardizer action, which allows to exclude specified sgroup names from sgroup conversions (expand/ungroup/contract).

Bugfixes

• JChem Base
• Reaction search + filter query threw ArrayIndexOutOfBoundsException
• JChem Cartridge
• Importing certain structures into Oracle databases using multi-byte character sets (such as AL32UTF8) failed with "ORA-24816: Expanded non LONG bind data supplied after actual LONG or LOB column.
• Non-index-owner was unable to search with JCC privileges granted through a role.
• JKlustor
• Bug in histogram calculation in the treetable view fixed and improved.

API changes

• JChem Base
• New method implemented in MatchCountOptions: toString()
• New methods implemented - Updater: performCurrentUpdate(ProgressWriter pw), TableInfo: getJChemVersion(ConnectionHandler ch, String tableName), ProgressWriter: reset(), getText(), setText(String text)

Regeneration

current table version is: 50101
The database version does not change, but if you have tautomer duplicate filtering tables and they contains structures with isotope H (deuterium, tritium) we recommend the regeneration.

September 1st, 2008, 5.1.1

Marvin 5.1.1 is included

New features and Improvements

• JChem Base:
  • RGroupDecomposition (rgdecomp) colors atoms by atom sets if output format is MRV. The former property-based coloring is used for SDF output.

Bugfixes

• Standardizer:
  • Standardizer threw NullPointerException in some cases when "clearstereo" was performed. Forum topic
  • Bugfix in tautomerize Standardizer action Forum topic
  • The "clearstereo:doublebond" action in Standardizer did not clear all double bond stereo data. Forum topic

August 7th, 2008: 5.1

Marvin 5.1 is included

New features and Improvements

• JChem Base:
  • Position variation bonds can be used in queries.
  • Position variation can be used in Markush structures (target side).
  • New architecture for tautomer duplicate filter table/JChem index option: generic tautomers are used. This allows more correct and faster operation. Stereo features are ignored in the tautomer regions.
  • Tautomer search ignores stereo features in the tautomer regions (all relevant search types). Stereochemistry outside tautomer regions are checked by default.
  • Aromatization of query structures: rings containing atom lists, not lists and query atoms are aromatized if query expresses aromatic rings also. See documentation
  • Stereo search type options (stereo and exact stereo) are unified in one option which also provides a new stereo search type: diastereomer search. See documentation and api for more details.
  • New search option: check sp hybridization.
  • New search option: undefined R-atom matches other undefined R-atoms only (by default, it matches anything).
  • SMARTS "x" property supported in searching, meaning the number of ring bonds for the given query atom. forum topic
  • Superstructure search is now default for query tables in jcsearch.
  • Empty structure for SUPERSTRUCTURE search now matches everything.
  • Search uses explicit H-s on target in case of Markush structures.
  • A new Chemical Terms filter was added for db_search JSP example: Rule of 3.
  • JChem Developers Guide has a new chapter: JChem chemical database concepts.
• JChem Cartridge:
  • Search option for including non-committed recently inserted/upgraded records for perfect search forum topic
  • Duplicate filtering for non-JChem tables including tautomer duplicate filtering
  • Alter index option for regular structure tables to recalculate the index data without having to drop the index.
  • jc_evaluate allows CT expressions evaluating to Boolean. forum topic
  • Removing the mappingStyle option from jc_react. (This option has been deprecated since JChem 3.2.)
• Chemical terms
  • The Chemical Terms Evaluator engine has been moved to Marvin (however, match and dissimilarity functions are still only available from JChem). Chemical Terms changes are therefore logged in Marvin changes.
• Standardizer
  • Action string and XML tag changes in Standardizer configuration
  • Standardizer and Reactor Wizard GUI facelifting
  • Standardizer configuration editor facelifting and refactor. Stand-alone runmode. New engine, new icon sets, new action editor panels. Old version exists, but deprecated
  • Standardizer action for converting alias and label to abbreviated group
• Fragmenter
  • CCQ Fragmenter. A new product for fragmenting molecules without complex rules, just cleaving carbon-carbon single bonds next to a hetero atom (CCQ) in all permutations. Molfragment is the releated command line tool, MoleculeFragmenter is the related API class.

Bugfixes

• Standardizer
  • "clearstereo:doublebond" action did not clear all double bond stereo data. forum topic

July 28th, 2008, 5.0.7

Marvin 5.0.7 is included

New features and Improvements

• JChem Cartridge
  • jchem_core_pkg.get_hit_count function is available.

Bugfixes

• JChem Cartridge
  • Search errors may have gone undetected. Error reporting fixed.
  • Search parameters (jcSearchThreadsPerCall, reservedMemory) settable in jcart.properties had no effect.
  • NULL query structure threw NullPointerException.
  • JChem Server threw NullPointerException for license files in the licenses sub-directory. (Forum topic)
  • Upgrade failed to update the RMI parameters.
• Chemical Terms
  • Chemical Terms Evaluator threw exception if a Chemical Terms expression contained more than 1000 sub-expressions. (Forum topic)

July 8th, 2008, 5.0.6.1

Marvin 5.0.6_1 is included

Bugfixes

• JChem Base
  • Occasional deadlock during regeneration. (forum topic)

June 20th, 2008: 5.0.5

Marvin 5.0.5 is included

New features and Improvements

• JChem Base:
  • Hash Code is used for exact search whenever possible to speed up screening (forum topic)
  • A new public table type option has been created: mysqlTableType in StructureTableOptions for MySql. Created JChem table type is depending on it's value
    Values:
    - MYSQL_DEFAULT_TABLE_TYPE - uses the default table type
    - MYSQL_FORCE_INNO_DB - create InnoDb table
    - MYSQL_FORCE_MYISAM - create MyIsam table.
    For the property table a new API method was created: createPropertyTable for mysql in DatabaseProperties, it has an additional parameter. The table type setting is possible with this parameter.
  • JChemSearchOptions, MatchCountOptions implements Serializable
• JChem Cartridge:
  • jc_compare accepts VARCHAR2 queries for BLOB structure columns

Bugfixes

• JChem Base:
  • Search in database sometimes returned a few more hits than the limit set for maximum result count (forum topic)
  • Hit coloring fix: superatom S-groups are now colored if the S-group contains hit atoms
  • If an upper case character was in the table name, molecular descriptors didn't work in some cases
  • Occasional bug when regeneration Chemical Terms columns for Markush structures in fixed (appeared in Instant JChem)
• JChem Cartridge:
• Extending cost estimation to JChem structure tables and BLOB structure columns ()
• jcf_evaluate(b)/jcf.evaluate always return 0

May 24th, 2008: 5.0.4

Marvin 5.0.4 is included

New features and Improvements

• JChem Base:
  • API documentation of sss.search.JChemSearchOptions has been improved.

Bugfixes

• JChem Base:
  • JChemSearchOptions.setMatchCountOptions() had no effect. (forum topic)
  • When adding new Chemical Terms columns to an existing query table, the results were calculated with normal standardization (opposed to query standardization)
  • The following settings were lost if set via JChemSearch.setSearchOptions(JChemSearchOptions): dissimilarityMetric; descriptorConfig; descriptorName; optimizeQueries
  • Some Markush structures with Superatom Sgroup were not found due to incorrect attachment point calculation.
  • Deprecated applet parameters were used in Legend.jsp in db_search JSP example.
• JChem Cartridge:
  • Specifying null as jchemproperties table for jc_insert resulted in ORA-00903. (forum topic)
  • Fixed wrong jc_compare results due to incorrect evaluation order of search properties. (forum topic)
  • DELETE row and direct locator INSERT did not work with regular structure tables having CLOB structure column".
• Standardizer:
  • Standardization of query structures with transform rule threw License exception.
• Reactor:
  • Reactor returned incorrect results in some cases if a bond in the reaction scheme connected to a nitrogen was transformed from non-aromatic to aromatic. (forum topic)

April 21st, 2008: 5.0.3

Marvin 5.0.3 is included

New features and Improvements

• JChem Cartridge:
  • jc_insert(b) with duplicate filtering (and with halt on duplicates turned off) now returns the the cd_id of matching structures in the database as negative numbers
• Chemical Terms:
  • Some Chemical Terms functions are renamed: enumerationCount() -> markushEnumerationCount(), enumeration() -> markushEnumerations(), randomEnumeration() -> randomMarkushEnumerations() (old names are still available)
• Standardizer:
  • New command line option "--export-fields-to-smiles" added to Standardizer

Bugfixes

• JChem Base:
  • SearchOptions.get/setOption() could not handle similarity search type.
  • Improved reaction searching speed in case of reacting center query property. (forum topic)
• JChem Cartridge:
  • "jc_matchcount always returned 1" (forum topic)
  • When finding duplicates, jc_insert always reported 1 as the cd_id of the matching structure found in the database.
  • jc_compare's tautomerSearch options always turned on tautomer searching, even if value 'n' was specified.
  • jc_compare's tautomerSearch option is now deprecated. Instead, "tautomer" should be used (in order to be consistent with jcsearch).
  • jc_insertb didn't accept table name value as string constant in PL/SQL
• Chemical Terms:
  • Changed the default values of "min basic pka" and "max acidic pka" parameters from -1000 and 1000 to -10 and 20 in functions using pKaPlugin (pKa(), acidicpKa(), basicpKa(), acidicpKaLargeModel(), basicpKaLargeModel())
• Reactor:
  • Reactor threw exception if there were unmapped reaction components in the reaction scheme without changing atoms.

March 20., 2008: 5.0.2.1

• Marvin 5.0.2.1 is included
• JChem Base:
  • Fix for incorrectly applied ringatom property in search.

March 18., 2008: 5.0.2

• Marvin 5.0.2 is included
• Chemical Terms:
  • Initialization of Chemical Terms Evaluator is faster
  • hasValenceError() function has been added
• Bugfixes:
  • JChem Base: Fix for "Hits may appear multiple times in hit list in case of enumerated PERFECT search"
  • JChem Base: Fix for "No valid license has been found. Product name: Markush Enumeration Plugin" (in case of searches containing query features)
  • JChem Cartridge: Fix for "JChem Server stops on user log-off when installed as a Windows Service"
  • JChem Cartridge: Fix for "Deadlock in DELETE FROM update log table"
  • JChem Cartridge: Fix for "Indexing without index parameters aborts with error message"

February 18, 2008: 5.0.1

• Marvin 5.0.1 is included
• JChem Cartridge: support for automatic Chemical Terms calculation
• Chemical Terms:
  • enumeration() returns all or a given number of enumerated structures
  • evaluate command line parameter -f has been changed: now -f, --format <format> specifies the output format if the result is molecule
• Standardizer:
  • neutralize action does not neutralize mesomeric atoms in the form of A+A- (like nitro)
  • neutralize action also removes mapped and isotopic hydrogens if required
  • unmap action removes atom maps from molecules, too (not only from reactions)
• LibraryMCS: the API is more concise and clear
• JChemSearch: setStructureCaching() was removed from API, only cached mode is available from now.
• Bugfixes:
  • Problems with new column "cd_sortable_formula" with certain databases (MySQL 4.1 and older, MS Access, Derby) fixed.
  • Missing Markush license problem (in case of some searches containing query features) fixed.
  • Regeneration speedup for "jcman u" and at JChemManager GUI startup
  • Exporter.setSelectStatement(): problem fixed when specifying additional data fields
  • JChem Cartridge: fixes in server.sh and server.bat
  • JChem Cartridge: fixing "haltOnBadFormat index parameter has no effect"
  • MCS: methods getResultQueryBonds() and getResultTargetBonds() always returned null
  • Chemical Terms: majorMs() function threw exception in JChem 5.0.0
  • Chemical Terms: Fixing "Boolean operator "!" (NOT) is not always recognized in Chemical Terms expressions"
    
  • LibrayMCS: ClusterEnumerator.next() failed when cluster count was zero

January 9, 2008: 5.0

• Marvin 5.0 included.
• Tautomer searching of JChem Base and Cartridge does not require explicit tautomer plugin license key.
• Standardizer groups "query" and "target" for JChem Base and Cartridge are deprecated, but still work. Instead, RemoveExplicitH actions are not performed on queries. See the documentation for more details.
• Support of coordination compound representation in JChem Base and Cartridge. See the documentation for more details.
• New table types:
  • Query structures
  • Markush libraries
• Improved API support for hit coloring
  • JChemSearch.getHitsAsMolecules() to support coloring of database search hits
  • HitDisplayTool to support hit coloring of arbitrary Molecule objects
• Structure searching in database and memory:
  • Progressive return of results in JChem Base and JChem Cartridge
  • New generic query atom types for structural search types: AH, QH, M, MH, X, XH, G1-G18. See the documentation for more details.
  • API: Unified search options of database and in-memory search See: API documentation.
  • API: Custom atom & bond comparators to modify search behaviour (for advanced usage) See: example instructions and and sources.
  • Search with Chemical Terms filter can use stored sub-expressions from C.T. columns.
  • Substructure and exact structure searching in combinatorial Markush structures, Markush structure reduction to hit. See details.
  • Performance enhancements of structure searching in database with queries containing atom lists, query bonds and higher vague bond options.
  • Only narrow ends of wedge bonds are considered in 2D representation of the molecules, following IUPAC recommendations. To convert your existing 2D molecules created with the both-end interpretation to the new convention, use the ConvertWedgeInterpretation Standardizer action.
  • Aromatization will not aromatize rings that contain query bonds, to allow specification of explicit non-aromatic bonds. Example: [#6]=,:1-[#6]=,:[#6]-[#6]=,:[#6]-[#6]=,:1 SMARTS query is now not changed by aromatization.
• JSP example improvements
  • Checkbox for duplicate checking at insert and update dialog
  • Sophisticated search options(ignore stereo, charge, isotope, vague bond options, etc.)
  • Display options for search results
  • Enumeration controls for Markush tables
• Table option to considers tautomers during duplicate filtering
• JChemManager (jcman) GUI : table options dialog
• New field in JChem Base tables "cd_sortable_formula" to allow sorting by formula
• Simplified installation/configuration for JChem Cartridge
• JChem Cartridge provides cost estimation for Oracle Optimizer
• Hit coloring and alignment support in JChem Cartridge
• Reactor:
  1. Improved abbreviated group support
  2. Output reactions can be mapped in "changing" (ChemAxon) style
  3. Improved reaction mapping checker and automapper algorithm
  4. Added command line parameter -A (--skip-reaction-mapping-check ): skip reaction mapping check (API: Reactor.setSkipReactionMappingCheck(boolean)).
  5. Minor changes in Reactor API
  6. Various bug fixes
• Standardizer:
  1. New tasks: ClearIsotopes, Neutralize, WedgeClean, and ConvertWedgeInterpretation
• Chemical Terms:
  1. Integration of user-developed calculations as plugin calculations made easier
  2. New functions and plugin calculations:
     • Molecular surface area calculations: waterAccessibleSurfaceArea / ASA, ASAPlus, ASANegative, ASAHydrophobic, ASAPolar
     • Match functions: disjointMatchCount
     • Other: resonantCharge, molBinFormat / molImage

December 3, 2007: 3.2.12

• Marvin 4.1.14 included.
• LibraryMCS 0.6:
  • Speed and cluster quality improvements
  • Export bottom layer
  • Various bug fixes
• Bugfixes:
  • JChem Base CLOB handling fix for Oracle
  • jsp database example: hit coloring fixed for exact fragment search
  • JChem Cartridge mark structures having fingerprints without ring info
  • Evaluation of Chemical Terms expressions containing '&&' and '||' logical operators failed in some cases

September 19, 2007: 3.2.11

• Marvin 4.1.13 included.
• Synthesis table creation fixed for PostgreSQL
• Standardizer:
  • "Tautomerize" and "Mesomerize" actions can handle molecules with SRU S-groups
  • "ConvertDoubleBonds" action cleans 0D input molecules in 2D

August 17, 2007: 3.2.10

• Marvin 4.1.12 included.
• R-group search: support for s* (substitution as drawn) query property
• Structure flipping fixed for hit alignment
• JChemManager: Chemical Terms evaluation error alone doesn't result in the structure being discarded during import when "Halt on error" is turned off.
• JChem Cartridge: Fixing "DELETE row and direct locator INSERT not working with regular structure tables having CLOB structure column"
• JChem Cartridge: Fixing concurrency bug which occurs with jc_react when used with combinatorial reactant matching.

July 23, 2007: 3.2.9

• Marvin 4.1.11 included.
• JChem Cartridge: fixing bugs in user defined operator.
• JChemSearch/JSP example: JChemSearch does not round the molweights any more. Client application gets molweights with proper precision from elemental analyzer
• Chemical Terms:
  • New functions: dominantTautomer(), dominantTautomers(), dominantTautomerCount()

July 6, 2007: 3.2.8

• Marvin 4.1.10 included.
• Bugfix in Marvin API

June 26, 2007: 3.2.7

• Marvin 4.1.9 included.
• JChem Cartridge: fixing problem "jc(f)_standardize doesn't work when options are specified in addition to 'config'".
• JChemSearch.setOrder() fixed
• Export of Chemical Terms columns fixed
• R-group search fix (in case of matching implicit hydrogens)
• Exception with bond topology query fixed
• Deprecated classes (API): SerialMoleculeGenerator, MoleculeGenerator, MoleculeGeneratorConfig (these classes will be removed in JChem 3.3 release)
• JSP db_search example: cut end of custom field values in default layout, if field value is longer than 30 chars.

May 17, 2007: 3.2.6

• Marvin 4.1.8 included.
• UpdateHandler.setIgnoreChemicalTermsExceptions() to allow insert / update in spite of errors during the calculation of one or more Chemical Terms columns
• Standardizer:
  1. "Set" action of AbsoluteStereo task clears the absolute stereo flag if the molecule doesn't contain chiral atom(s)
  2. New task: ConvertDoubleBonds (converts the representation of double bonds with unspecified CIS/TRANS stereo information to wiggly or crossed type)
• Chemical Terms:
  • New function: totalCharge
• Bugfixes:
  • UpdateHandler CLOB support fixed
  • JSP database example: coloring fixed for implicit hydrogens and R-group queries
  • JChem Cartridge: fixing bug "jchem_core_pkg.use_password may cause pending operations to abort with 'Connection closed' error message"
  • JChem Cartridge: fixing bug "jc_evaluate and jcf.t_evaluate cannot be used with CLOB queries"

April 16, 2007: 3.2.5

• Marvin 4.1.7 included.
• Improved alignment for reactions in MolHandler.align(). Rotation is performed on a per-fragment basis.
• JChem Cartridge: vagueBond search option added
• JChem Cartridge: CLOB support (limited to "US-ASCII" encoding) added
• JChem Cartridge: VARCHAR2 operators overloaded with CLOB/BLOB
• JChem Cartridge: jcf package for overloaded functional equivalents created
• Chemical Terms:
  • New functions: name, traditionalName, molBinFormat
• Bugfixes:
  • JChemSearch: setDoubleBondStereoMatchingMode() did not work in multi-processing environments.
  • UpdateHandler: CLOB support fixed
  • CombinationEnumerator/Reactor/JChemCartridge: concurrency problem fixed in jc_react.
  • Standardizer: fixes in template based clean

March 14, 2007: 3.2.4

• Marvin 4.1.6 included.
• LibraryMCS:
  • Keep rings option
  • Speed improvement
  • Enhanced clustering algorithm
  • Various bug fixes
• JChem Cartridge: jchem_core_pkg.set_password function added
• JSP examples
  • jsp1_x example has been moved to a new directory: db_search.
  • The simple JSP example accessible from local jchemsite.
• Bugfixes:
  • Fix for rare problem during the import of multi-line SDF data fields
  • JSP database example: Hit alignment fix in case of different query and target dimensions
  • jcman command line import: cd_id field import fix
  • JChem Cartridge: Fix for password field behaviour in the administration GUI
  • JChem Cartridge: Fix for mapping style deprecation problem in jc_react
  • Reactor: pyridinium ions in the reagents became doubly protonated in the products bug fixed
  • Standardizer: bug in Tautomerize action fixed

January 9, 2007: 3.2.3

• Marvin 4.1.5 included.
• Bugfixes:
  • Fingerprint generation: possible search problem for certain queries fixed, slight search performance improvement
  • R-group search: restH option fixed
  • ...MatchCountInRelation() performance enhancements (classes chemaxon.sss.Search, chemaxon.jchem.db.JChemSearch and jc_matchCount cartridge operation comparisons are affected)
  • Coloring fix in the JSP database example for superstructure mode
  • Fixed: pKa calculation through Chemical Terms was slow in JChem 3.2.2 version.

December 8, 2006: 3.2.2

• Marvin 4.1.4 included.
• New search option: stereo model
• jcsearch returns property(SDF tag) CD_ID when searched in database
• LibMCS: Enhanced user interface
• Bugfixes:
  • BCUT: missing multiple eigenvalues
  • Standardizer: bug in "remove all R-group definitions" action fixed
  • Fixes in JSP examples

November 21, 2006: 3.2.1

• Marvin 4.1.3 included.
• JChem Cartridge: Reaction similarity search works with operators placed before the WHERE clause as well
• JChem Cartridge: Tautomer search support added
• Reactor:
  1. Removed command line parameter -V (--filter-valence-error) and Reactor.setFilterValenceError(boolean) method from API.
  2. Command line parameter -a (--mapping-style) works again, because automatic handling of mapping styles is slow in some cases. It will be removed in the near future. (API: deprecated Reactor.setMappingStyle(int)).
• Bugfixes:
  • JChemSearch: default metric fixed for reaction similarity search
  • HitAlignmentAndColoring.java example fixed (alignment was missing)
  • JChem Cartridge: handle structure tables without explicit table type

October 17, 2006: 3.2

• Marvin 4.1.2 included.
• .NET Support via JNBridge
• JChem Base
  • Derby support added.
  • Installer for easier deployment
  • chemaxon.jchem.db.Importer does not write duplicate structure information to standard error by default, use setInfoStream() if needed.
  • Multi-processor support during import and regeneration.
  • Structural search:
    • Searching of mixture, formulation and component brackets
    • Reacting center bond query feature
    • Tautomer search option
    • Default aromatization type changed to general
    • No-structures return only no-structures in exact and superstructure search
    • Flexible search options: ignore charge, valence, isotope and radical, mixture brackets, vague bond matching
    • New class: chemaxon.sss.search.StandardizedMolSearch for doing standardization and search in the same step.
    • R-group search support for reactions
  • Utility class Updater to help the upgrade process in JChem-based applications.
  • MolHandler.align()expands S-groups for correct alignment.
  • Table types were introduced in JChem.
  • Reaction similarity search:
    • ReactionFingerprint descriptor (implemented as MolecularDescriptor)
    • API classes: ReactionFingerprint, RFParameters, RFGenerator
    • Reaction fingerprint metrics: ReactantTanimoto, ProductTanimoto, CoarseReactionTanimoto, MediumReactionTanimoto, StrictReactionTanimoto
  • UpdateHandler.setValuesForFixColumns[...] methods were deprecated. Use setStructure(String) or setStructure(byte[]) and setID()
• JChem Cartridge:
  • Bug fixes:
    • Superstructure search fails on NULL structures
    • Operator jc_formula_eqb returns bogus results
  • New features:
    • jchem_core_pkg.get_idx_stats added to allow obtaining index statistics
    • DDL functions for handling JChem-tables added
    • config_jcart_users.sql added for access rights management of JChem Cartridge users.
    • jc_react4accepts SELECT statements for reactants (direct insert into product table)
    • more options for jc_react
• R-group decomposition API extension: added findLigand(int ligandId, int[] hit, int[] ligandIds), getLigandIds(int rindex, int[] hit, int[] ligandIds), getLigandId(int rindex, int[] hit, int[] ligandIds).
• Reactor:
  1. Graphical user interface for Reactor
  2. Reactor configuration XML files are no longer supported.
  3. Command line parameter -g (--single) is changed to -l (--single).
  4. Added command line parameter -M (--map-result): maps output reaction in specified style (API: Reactor.setOutputReactionMappingStyle(int)).
  5. Added command line parameter -V (--filter-valence-error): using this option products with valence error(s) can be filtered out (API: Reactor.setFilterValenceError(boolean)).
  6. Added command line parameter -T (--standardize-products): standardize products according to configuration (API: Reactor.setProductStandardizer(Standardizer)).
  7. Separate standardization of each reactant and product using standardizer task groups.
  8. Removed command line parameter -y (--standardization-type), because reactants and products can be standardized separately (API: removed Reactor.setStandardizationType(int)).
  9. Removed command line parameter -a (--mapping-style), because reaction mapping style is handled automatically (API: deprecated Reactor.setMappingStyle(int)).
• Standardizer:
  1. Graphical user interface for Standardizer
  2. Graphical configuration builder utility for Standardizer configurations
  3. R-group definition removal method added to Removal
  4. New tasks: Tautomerize, Mesomerize, MapReaction, and UnmapReaction
  5. Added task groups: an option to select the tasks to be processed. Added command line parameter -u (--active-groups). API: setActiveGroups(String[] groups) and setActiveGroup(String group).
• Chemical Terms:
  1. Molecules and functional groups can also be referred by names, not only by explicit SMARTS strings.
  2. Chemical Terms editor with syntax highlighting (in Reactor GUI).
  3. Several new plugin calculations: distance, angle, dihedral, stericHindrance, leconformer, conformers, hasValidConformer, canonicalTautomer, stereoisomers, tetrahedralStereoisomers, doubleBondStereoisomers, chiralCenter, sigmaOrbitalElectronegativity, piOrbitalElectronegativity, solventAccessibleSurfaceArea, vanDerWaalsSurfaceArea
  4. New function: molString
• Fragmenter:
  1. Changed parameter -n (--no-data): atom label and/or fragment ID is not written depending on the setting ("L" and/or "I")
  2. FragmentStatistics: added parameter -m (--min-atom-count) to exclude small fragments from the statistics.
• Added parameter -g (--ignore-error) to most of the command line tools. If this is specified, molecule import errors are ignored and processing is continued with the next molecule. Otherwise the program exits with error (as before).
• Markush enumeration API (R-group, atom list, bond list, link node)

July 20, 2006: 3.1.7.1

• Bugfixes:
  • The bug "omitting last structure during RDFile import" fixed
  • PosgreSQL: OutOfMemoryException during cache loading fixed

May 26, 2006: 3.1.7

• Marvin 4.0.6 included.
• JChem Cartridge: new table functions: jctf_evaluate and jctf_react4
• JChem Cartridge: upgrade process refined (abort upgrade on error)
• Importer option to collect the cd_id values for imported structures
• Empty lines in SMILES files are now accepted as empty structures during JChem import
• Bugfixes:
  • JChem Cartridge: fix bug "jc_evaluate fails with ORA-06502"
  • JChemSearch: EXACT search mode vs. setFilterQuery() bugfix
  • UpdateHandler will not detect the modified structure as duplicate during UPDATE operation
  • JSP database example: fix for Safari browser

March 24, 2006: 3.1.6

• Marvin 4.0.5 included.
• JChemSearch.setStrucureCaching() has been deprecated. Only cached mode will be available in the future.
• JChem Cartridge: jc_insert function supports SDF and RDF tags
• JChem Cartridge: jc_react supports synthesis codes
• Bugfixes:
  • Superstructure search reinitialization bug in database.
  • Reaction search: atom maps without pair are ignored in query.
  • JChem Cartridge: "option 't:e[^f]' is ignored and search type SSS is used"
  • JChem Cartridge: "calling use_password with corrected pw has no effect"

January 23, 2006: 3.1.5

• Marvin 4.0.4 included.
• Standardizer task name changes:
  • AddExplicitH replaces the former Hydrogenize task.
  • RemoveExplicitH replaces the former Dehydrogenize and ImplH tasks.
  The old names are deprecated but kept for compatibility.
• JChem Cartridge: Non-intrusive upgrade process to minimize impact on users' dependent objects.
• Bugfixes:
  • Search: bug concerning generic bonds connected to R-groups fixed.
  • Structure cache: occasional NullPointerException and possibility of a deadlock fixed.
  • HSQLDB: improved cache loading (reduced memory footprint), uses BITAND in non-cached mode, HXSQL treated as HSQLDB
  • JChemSearch: bugfix for empty query
  • UpdateHandler: custom DB field names treated case-insensitive (fixes "SQL type not supported" problem for MS SQLServer)
  • JChem Cartridge:
    • Fixing bug "jcf_tanimoto returns incorrect results"
    • Bug fixes for the ASP example (including documentation)

December 14, 2005: 3.1.4

• JChemSearch: EXACT search mode uses hash code for screening if possible (speedup).
• The upgrade of the JChem table structure (might be necessary when migrating from an older version) is also available from command-line by invoking
  jcman u
• Bugfixes:
  • JChemSearch: structures specified inside the Chemical Terms expressions were not standardized.
  • JChemSearch: in some cases false hits with -1 cd_id were returned.
  • JChemSearch: exception for SIMILARITY search + empty query + Max. result count fixed.
  • UpdateHandler: fix for Oracle JDBC bug workaround of inserting big LOB values (caused import problem in some cases).

November 11, 2005: 3.1.3

• Marvin 4.0.3 included.

November 4, 2005: 3.1.2

• Marvin 4.0.2 included.
• New search mode: EXACT_FRAGMENT
• Support for queries with link nodes
• JChemSearch.setFilterIDNotList() for excluding a subset of the table from the search.
• JChem Cartridge:
  • jc_evaluation_x and jc_evaluationb_x added to enable generation of tautomers, resonants....
  • haltOnBadStructures option added to jc_insert (allow to discard badly formatted structures in order to insert all correct structures)
  • Added a few PL/SQL utility functions in the jchem_utils package.
• Bugfixes:
  • JChem Cartridge:
    • Confusing error message "ORA-00942: table or view does not exist" during installation removed.
    • Workaround for the bug "dbms_lob.freetemporary does not free temporary BLOBs".
  • Search: fixed ArrayIndexOutOfBoundsException on hydrogens with query properties.
  • Search: Fixed isotope matching inconsistencies related to complex smarts expressions.
  • Exception for nameless SDF data fields fixed

September 9, 2005: 3.1.1

• Change in caching system: the cache logs are stored in separate tables for each structure table.
  The log tables are created automatically on the first start of the jcman GUI.
  The number of update logs to keep after cache update can also be changed from the jcman GUI in the Advanced tab of the Options dialog.
• JChem Cartridge
  • Multiple query structures can be specified to a single search operator with implicit UNION operations between the result sets.
  • jc_compare_vb for VARCHAR2 targets and BLOB queries
• Bugfixes:
  • UpdateHandler update operation fixes
  • Importer : file and DB field names are treated in case-insensitive way
  • Search: R-group search bug fixed for EXACT search mode
  • JChem Cartridge
    • Fixed bug: 'file format not recognized' error for functions and functional invocations
    • Fixed bug: standardizer config ignored for search functions and functional invocations

August 31, 2005: 3.0.15

• Bugfixes:
  • Search: Fixed exception with component level grouping query.
  • JChem Cartridge
    • Fixed bug: SELECT ... INTERSECT SELECT ... returns corrupt results
    • Fixed bug: options for jc_compare are evaluated all lower-cased.
    • Fixed bug: unfetched results "come back" to queries with no results.
  • Fixed bug concerning JChemSearch.setFilterIDList() with empty result set.
  • Minor cache improvements

August 23, 2005: 3.1

• Marvin 4.0.1 included.
• JChem Base
  • HSQLDB support added.
  • Structural Keys for speeding up substructure search of a user-defined set of query structures.
  • JChemSearch
    • New Search features
      • Filtering by a set of specified cd_id values via setFilterIDList(int[]).
      • The default setting for setStructureCaching changed to true.
    • The SQL specified for setFilterQuery(String) can also be used for ordering the result with an "ORDER BY" clause.
  • Custom select statement can be sepecified for Exporter allowing the export of related data from other tables and the ordering of structures.
  • The compression of the cd_structure field can be disabled in the options menu of JChemManager.
  • All RDBMS-dependent options are hard coded for the supported databases, the correspondig menus have been removed from the GUI.
• JSP example web application
  • Ability to search on previous hit lists.
  • Improved administration in setup.jsp.
  • Session ID prevents sessions interfering if accessed from the same computer.
• Search: new query properties: substitution count (s<n>, s*), ring bond count (rb<n>, rb*), unsaturated atom (u); searching lone pairs
• Standardizer:
  • stoichiometry expansion
  • template based clean
  • new Removal methods: "keepSmallest" and "removeLargest"
  • API: added methods
    • getAppliedTaskIDs()
    • getAppliedTaskIndexes()
• Reactor: standardization can be specified directly in the -S, --standardize parameter.
• New and improved reactions in the ChemAxon Reaction Library.
• FragmentStatistics: added parameter -e, --default-activity to set activity for fragments with no activity value.
• R-group decomposition added.
• Bugfixes:
  • Search: searching for chiral atoms with symmetrical ligands
  • Search: Database storage of H2 molecules
  • Search: R-atoms match to themselves in EXACT search mode
  • Search: stereo double bond matches target double bond with implicit H ligand and various other double bond stereo fixes
  • PMapper: output reflects the original atom order (instead of the atom order in the standardized molecule)
  • PMapper: improved pharmacophore type perception based on calculator plugins
  • Reactor: requires double bond stereo matching for all reactant double bonds, marks unspecified double bond stereo on product side by wiggly bond ligand
  • JChem Cartridge: Fix for bug "All users use connections with the same identity in Tomcat even if Tomcat is not configured for 'superuser-mode'".

July 29, 2005: 3.0.14

• Marvin 3.5.9 included.
• JChem accepts SDFiles with missing molfile section
• Bugfixes:
  • JChem Cartridge: Fixed problem with jc_evaluate when applied to empty/null smiles.
  • JChem Cartridge: Fixed bug "Similarity search fails with 'instance creation' error when executed in non-index-scan mode"
  • JChem Cartridge: Fixed bug "jc_insert treats isotope as duplicate of element".

June 28, 2005: 3.0.13

• Marvin 3.5.8 included.
• Bugfixes:
  • LibMCS -m flag ignored the minimum MCS size set, it works now
  • PERFECT search fix for certain cases
  • Search fix for explicit H-s near query bond
  • Search fix for inconsistent results of some bond topology queries
  • Cartridge: custom standardization table setting fixed for non-JChem cartridge tables
  • Cartridge: Fix bug "absoluteStereo index parameter has no effect on search"
  • Cartridge: Fix bug "chemical terms returning values of types other than java.lang.Double are not allowed"
  • Cartridge: Fix bug "setting fingerprint properties as index parameters has no effect"
  • Cartridge: Documentation bug (superstructure search)
• New Features:
  • Cartridge: allow the absoluteStereo index parameter to be changed using ALTER INDEX

May 30, 2005: 3.0.12

• Marvin 3.5.7 included.
• New Features
  • JChem Cartridge
  • empty and null string support
  • BLOB support
  • superstructure search (isin())
  • maxHitCount
  • Operator jc_standardize added
  • multi-threaded index creation
  • use_password() to avoid the need for a highly privileged user in Tomcat
  • support in the administration GUI for Tomcat security domains
• Bugfixes:
  • Transaction related bug fixed for generateResultTable
  • Molecular weight always has the desired number of decimals in the table
  • UpdateHandler: exception handling fix in deleteRows()
  • Search bugfix: double bond stereo matching with isotopic H ligand fixed.
  • Search bugfix: matching of implicit H to isotopic H in case of EXACT searching fixed.
  • Unlabeled chiral center in enhanced stereo molecule is considered ABS.

April 18, 2005: 3.0.11

• Bugfixes:
  • Oracle 8 compatibility restored for JChem Base.
  • MolSearch.findAll() initialization bug when using the same MolSearch object repeatedly.

March 30, 2005: 3.0.10

• Marvin 3.5.5 included.
• Bugfixes:
  • JChemSearch treats input strings as SMILES in the default query mode (QM_DEFAULT) if the search mode is SUPERSTRUCTURE.
  • Fixes for empty structures.
  • Fix for MS Access
  • Compare closes output streams properly.
  • Convenience scirpt/batch program optimize in examples/bin is fixed.
  • Ring count query property [R] in SSS mode of MCS fixed.
  • Fix of perfect search for certain molecules with multiple chiral centres.
  • JChem Cartridge: fixes bug resulting in "ORA-00942: table or view does not exist" errors for certain search operations accessing JChem tables with non-domain-index scan method.
  • JChem Cartridge: fix bug resulting in "ORA-01000: maximum open cursors exceeded" errors for certain operations on Oracle 10g.
  • JChem Cartridge: fixes for various documentation bugs.

March 3, 2005: 3.0.9

• Bugfixes:
  • Marvin Document (MRV) import bugfix.
  • Structures with undefined R-groups (R1, R2, etc. atoms) will import without error.
  • Cartridge : bugfix for structures that cannot be described in cxsmiles format.
  • MCS: strongly interconnected structures like cubane will not crash MCS.
  • Search: bugfixes related to bond topology query property at double bonds and excluded atoms.

February 8, 2005: 3.0.8

• Marvin 3.5.4 included.
• New features:
  • in LibraryMCS
    • fast search option: up to 5 times faster than standard mode
    • low memory mode: bit slower than normal mode, though uses significantly less memory
    • new termination condition: minimal similarity measurement
    • more suitable default values
• Bugfixes:
  • LibraryMCS: wrong license key name
  • Search: chiral centre next to superatom group in query
  • JChem Cartridge for Oracle: fixed out of memory error with Oracle 10g

January 26, 2005: 3.0.7

• Bugfixes:
  • JChem Cartridge: Could not be installed.

January 25, 2005: 3.0.6

• Marvin 3.5.3 included.
• Bugfixes:
  • Speedup: Molecular Descriptor screening queries with Chemical Terms filter expressions are faster.
  • Minor GUI fix in SynthesisBrowser.
  • UpdateHandler fix: >4k molecules are properly inserted into Oracle LOB (BLOB, CLOB) cd_structure field in INSERT_WITH_ID mode.
  • Cartridge: the administrator password is stored with MD5 encoding for the configuration interface. Since this is an incompatible change, the file [user_home]\chemaxon\.cartridge (under Windows) or [user_home]/.chemaxon/.cartridge (under Linux) should be deleted to provide access again to the administration page.
  • ChemicalFingerprint generation does not require Standardizer license when used with the default configuration.
• Improvements
  • JChem Cartridge: Improve search speed on Oracle 10g.
• Changes in behavior
  • JChem Cartridge: Accept ANY ATOM in SMILES targets.
  • JChem Cartridge: jc_insert(<structure>, <target-table>, <jchemproperties>, 'true', 'false') discards duplicates. In previous versions, duplicates were inserted and a warning output in the session trace files.
• Reaction library update.

January 10, 2005: 3.0.5

• Bugfixes:
  • JChem Cartridge: Fix result set -- REF CURSOR problem with Oracle 10g.
  • JChem Cartridge: Fix problem with jc_insert when the 'checkDuplicates' parameter is set to 'true'.
  • JSP example: displaying of data fields fixed.
  • Exception when changing the layout in Synthesis Browser fixed.

December 23, 2004: 3.0.4

• Bugfixes:
  • JChem Cartridge: Fix memory leak during domain index scanned searches
  • JChem Cartridge: Fix hang during domain index scanned searches
  • JChemSearch bugfix: slight chance of deadlock in multi-thread mode eliminated
  • JChemSearch: getResult() no longer throws exception if result table is used.
  • BLOB and CLOB type cd_structure can store bigger than 4K structure strings (Oracle bug workaround).

December 15, 2004: 3.0.3

• Search
  • LP (lone pair) support
• Bugfixes:
  • JChemSearch bugfix for cases when matchCount includes 0 (only fixed in cached mode yet).
  • NullPointerException at the end of import fixed.
  • JChem Cartridge: jc(f)_molweight and jc(f)_formula no more fail when when used in "SELECT ... FROM dual" statements
  • JChem Cartridge: Fix "non statement parsed" error for DDL operations.
  • JChem Cartridge: "specifying the TABLESPACE index parameter without the STORAGE parameter has no effect" fixed.
  • JChem Cartridge: installation made more fool-proof.

December 7, 2004: 3.0.2

• Bugfixes:
  • Import problem with converted old Jchem tables fixed.
  • JSP example fix.
  • Reactor and Standardizer set the radical atom property according to the reaction equation.
  • Bug "Oracle EXP utility hangs in processing extended indexes" fixed.

December 6, 2004: 3.0.1

• Bugfixes:
  • Occasional exception in Importer fixed
  • jcman failed to run in command-line mode without a graphical environment
  • License management problem fixed.
• New Features:
  • Default properties added in JChem Cartridge.
  • Functions equivalent to index operators added in JChem Cartridge.

December 1, 2004: 3.0

• Marvin 3.5.1 included.
• JChem Base
  • The structure of JChem tables changed, 3 more columns were added:
    • cd_hash : hash code for speeding up duplicate filtering during import (registration). With this column there's no need for a composite index on the fingerprint columns, therefore the length of the fingerprint is no longer limited by the maximum length of composite fingerprints in the database.
    • cd_flags : for storing molecule-specific tags. Currently only indicates if the missing chiral flag should be overridden in imported structures. This means there's no need to change the chiral flag field in the original molecule string when the import option "Set chiral flag for MDL formats" is enabled.
    • cd_timestamp: the timestamp of the insertion of the structure.
    The old tables are transformed automatically into the new format on the first start of the jcman GUI.
  • JChemSearch
    • Multiple search threads for increased performance on multi-processor systems. Currently only for searches that use structure cache.
    • Timeout option to abort searches which the client stopped checking.
    • New search options:
      • Stereo search can be turned off
      • Double bond stereo matching mode
      • Exact charge matching
      • Exact isotope matching
      • Exact query atom matching
      • Exact radical matching
      • Exact stereo matching
      • Hydrogen count matching
      • Match count with boundaries
      • Match count in relation
  • Structure Cache improvements:
    • Incremental cache update: the cache won't be reloaded after every change to the table, only the changed rows are updated if possible.
    • Improved memory control:
      • maximum cache size may be specified with setMaxCacheSize
      • auto detection of available memory
      • minimum non-cached memory size may be specified with setMinNonCachedMemory. This amount will be reserved for other allocations.
      • least recently used tables are dropped from the cache if necessary.
    Note: StructureCache is no longer a public API, and direct use of the class is not recommended any more, since some incompatible changes had to be made for the new features.
  • Rxnfile import / export
  • Structure search speedup
  • Import speedup
  • JSP example web application
    • Chemical Terms expression can be specified for the query
    • Structure caching can be turned on / off using the configuration file.
      Please make sure you have set the appropriate cache setting after upgrading your JChem version..
      For more information see the JSP setup guide.
    • The status of the Structure Cache can be monitored from the "About" dialog
  • Evaluator
    • Added Language Reference.
    • Added Working Examples.
    • Added topology analyser plugin references (see the Short Reference).
  • Bugfixes
    • MySQL 4.x compatibility issue fixed
    • Compatibility issue fixed when upgrading early versions of JChem
    • JSP example : problem with deleted structures fixed
    • Other minor bugfixes
• Search
  • New search mode: SUPERSTRUCTURE search.
  • Double bond stereo: adjoining wiggly bond means "cis or trans"
  • new jcsearch options: --stereoSearch, --exactStereoSearch, -t:c (count hits), --maxResults:
• Standardizer
  • New actions: clear stereo and set/clear absolute stereo (chiral) flag
• Synthesizer
  • New algorithm: ExhaustiveAlgorithm.
• JChem Cartridge
  • New options to jc_compare.
  • jc_evaluate for calculation based on chemical terms.
  • Dramatically improved performance and stability.
• Maximum Common Structures of a compound set
  • Small/medium sized compound sets, libraries (100-10000 structures) can be analyzed
  • finds all scaffolds (molecular backbones), hierarchically clusters structures around these scaffolds
  • fast: 100 structures/s
  • experimental viewer

September 23, 2004: 2.3.4

• Bugfixes:
  • JchemSearch FilterQuery option fixed for empty query structure and for MySQL without caching.
  • JSP: problem with exporting of hits solved.

September 1, 2004: 2.3.3

• Bugfixes:
  • Structure Cache synchronization bug fixed.
  • Search speedup when caching is off.

August 23, 2004: 2.3.2

• Bugfixes:
  • Connection timeout and API fixed in StructureCache.
  • Update non-JChem tables fixed in JChem Cartridge.
  • Insert, update, index columns in non-JChem tables containing reaction SMILES fixed in JChem Cartridge.
• The speed of updating and deleting records from non-JChem tables with JChem Cartridge drastically improved.

August 16, 2004: 2.3.1

• Marvin 3.4.3. included.
• Search
  • New class MCS for Maximum Common Subgraph and Maximum Common Edge Subgraph (MCES) search. The class provides an alternative algorithm to substructure search too (less comprehensive though faster than MolSearch).
• Bugfixes:
  • JchemSearch FilterQuery option speedup.
  • NullPointerException fixed in DatabaseSearch.cacheStructures().
  • "List non-hits" (-n) option did not work in jcsearch in database mode.

August 6, 2004: 2.3

• Marvin 3.4.2. included.
• JChem Base
  • JChemSearch
    • FilterQuery option
    • SMILES/SMARTS input mode option
    • Reduced memory footprint for structure caching.
    • Restructured for efficiency.
  • Chiral flag can be set for MDL formats on import, if missing.
  • Filtering of empty structures is optional for import.
  • BLOB and CLOB columns can also be used for the cd_structure field of structure tables.
    Use DatabaseTools.readBytes to retrieve a BLOB, CLOB or LONGVARBINARY fields in a unified way.
  • Improved popup window check in the JSP example.
  • Bugfixes
    • SynthesisBrowser saves connection data
    • JSP example fixed for descriptors without coloring
    • Database compatibility fixes for PostgreSQL
    • Molecular Descriptor bug on MySQL fixed.
    • Other minor bugfixes
• JChem Cartridge
  • Overall stability on all platforms has been substantially improved.
  • Performance and stability of the jc_insert operator has been improved.
  • Performance of index creation on non-JChem tables have been substantially improved.
  • Automatic check of version conformance have been implemented between Java libraries installed in Oracle and those used for the JChem Streams WEB application.
  • Automatic check of JChem table versions have been implemented, means to upgrade to new table versions has been provided.
  • The following index parameters have been added (Extensible Index, jc_idxtype):
    • std_config, to specify standardizer configuration
    • RegenerateTable, to create index on a structure table generated by an earlier, incompatible version of JChem
  • The following operators have been added:
    • jc_compare
    • jc_tpsa
    • jc_react
    • jc_transform
    • jc_molconvert
    • jc_molconvertb
  • The following bugs have been fixed:
    • Cannot use a JChem Cartridge installation from a different schema.
    • If the destination table of jc_insert does not exist, the error message erroneously states that the table is not a JChem table.
    • Custom fingerprint attributes are not always used with jc_tanimoto.

Chemical Terms Evaluator

• Changes in chemical rule syntax.
• Added short syntax reference.

Reactor

• Changes in command line options.
• Changes in chemical rule syntax.
• Supporting different reaction mapping styles.
• Reaction sequence.
• JSP example.

Standardizer

• Supporting different reaction mapping styles.

Fragmenter

• Renamed short form of command line parameters --fragment-count, --set-count, added new option --statistics.
• Added FragmentStatistics.

Search

• Substantial performance improvement in MolSearch, especially when all hits are retrieved.
• Enhanced SMARTS support:
• Recursive smarts $()
• Logical expressions in atom and bond: high and low priority "and"(& and ;), "or" (,) and "not" (!).
• Now supported all atom properties: aADHhRrvX-+, atomic number, isotope, tetrahedral chirality
• Chiral or unspecified atoms @?, @@?
• Ring bond (@)
• Conditional directional bonds: /?,\?
• MDL bond topology support (chain, ring)
• Reaction search: reaction queries don't hit single molecules.
• Reaction search: mapped explicit H-s match implicit H-s.
• Timeout step control: setExhaustiveModeLimit() and setTimeoutLimit()
• Bugfixes.
• Maximum Common Subgraph (MCS) and Maximum Common Edge Subgraph (MCES) search.
• Expression search: filtering search hits with conditions formulated in our Chemical Terms language.

Screen

• New molecular descriptors:
  • Burden-matrix eigenvalues
  • BCUT values (charge, polarizability, hydrogen bonding properties)
  • Custom descriptor (real, integer and bit valued)
• Enhanced plug-in system for user-defined molecular descriptors.
• Existing descriptors can automatically be updated when new structures are imported into the structure table.
• All external XML configurations are optional.
• API changes:
  • Wired in default configurations.
  • New classes: CustomDescriptor, BCUT, Metrics (and related Parameters and Generator classes).
  • Automatic update of descriptors: setUpdateOnInsert()
• Bug fixes:
  • Saving database settings in generatemd, and screenmd.

February 17, 2004: 2.2.1

• Marvin 3.3.2. included.
• JChem Cartridge
  • jc_matchcount operator added
  • bugfixes
• Fragmenter
  • API improvement: a complete XML configuration can be set in the constructor.
• JSP example application:
  • Popup window check fixed
  • Multi-line data fields displayed correctly
  • Other minor bug fixes
• JChemSearch:
  • Fixed problem with filter table + empty query.
  • Fixed result table append mode.
• Other bug fixes

January 30, 2004: 2.2

• JChem Base
  • Custom standardization can be specified for structure tables.
  • "Assume absolute stereo flag" option for structure tables.
  • Import-export support for Marvin Document file format.
  • Minor GUI improvements in JChemManager (jcman).
  • Speedup for import with duplicate filtering.
  • Improved hit coloring.
  • Duplicate IDs can be retrieved from Importer by using setStoreDuplicates(boolean) and getDuplicateIDs().
  • Negated (not contains) searches supported by JChemSearch and available in the JSP example application.
  • Absolute stereo matching mode can be specified for JChem search with setAbsoluteStereo(int)
  • SMARTS import mode can be explicitly specified for MolHandler.
  • Bugfixes
    • Retrieving the ID of last inserted structure got much faster for MySQL
    • Proper error message from JChemSearch when specified table doesn't exist.
    • Structure table field cd_smiles can contain more than 254 character long SMILES for Microsoft Access.
    • Occasional error at table regeneration fixed.
    • Properly determining maximum allowed fingerprint length for all supported databases.
• Oracle Cartridge
  • Improved speed and stability of JChem Cartridge
  • DML functionality (insert, update)
• Search
  • MDL Enhanced stereo representation for relative stereoconfiguration (handling of ABS, OR and AND labels at chiral centers.)
  • New options (get & set methods):
    • ExactRadicalMatching, ExactIsotopeMatching, ExactChargeMatching, ExactQueryAtomMatching replace ExactAtomMatching
    • DoubleBondStereoMatching replaces StereoCareChecking.
    • Query/TargetAbsoluteStereo (ignore chiral flag)
  • addMatch methods: Enhanced performance if certain query and target atoms are assigned to each other before the search.
  • getMatchCount() and isMatchCountInRelation() methods for counting the number of occurrences of a query in a target molecule and for efficiently deciding conditions related to this.
  • In script jcsearch:
    • multiple queries from file
    • && (AND), || (OR) for multiple queries
    • negated (not contains) searches
    • database search mode
• Screen
  • New molecular descriptors:
    • Topological Polar Surface Area
    • hydrogen bond donor/acceptor atom count
    • logP/logD values
    • molecular mass
    • heavy atom count
  • Plug-in system for user-defined molecular descriptors.
  • Molecular descriptor sets: user defined combination of arbitrary molecular descriptors; combined and component-wise dissimilarity calculations.
  • New pharmacophore definition using standard SMARTS notation.
  • API changes:
    • MDParameters and its derived classes for each molecular descriptor types (e.g. CFParameters, PFParameters, HBParameters) are publicly available.
    • New classes have been added: ScalarDescriptor, HAcc, HDon, LogD, LogP, TPSA, Heavy, Mass.
  • Bug fixes:
    • Scaled Tanimoto similarity formula corrected.
    • Generation of ChemicalFingeprint works with multithreading.
• Chemical Term Evaluator
  • New expression syntax
  • Input contexts
  • New command line interface
• Reactor
  • New options:
    • file storage of input molecules (--file-storage)
    • standardization type: pre, post, or pre-post (--standardization-type)
    • ignore reaction conditions (--no-condition)
    • return only some of the products (--extract)
    • remove duplicated product references (--remove-duplicate-refs)
  • New expression syntax in reaction definitions
• Synthesizer
• Fragmenter
  • New options:
    • maximum number of fragment sets (--set-count) (replaces old parameter --algorithm: the old "greedy" algorithm corresponds to set-count 1)
    • include extendable fragment sets (--extensive)
    • skip unfragmented molecules (--skip-unfragmented)

August 14, 2003: 2.1

• JChem Base
  • Marvin 3.2 included.
  • Import of non-structural SMILES data fields is supported. (Strings after the SMILES, separated by TAB.)
  • Search:
    • Enhanced performance of substructure search, especially in case of reactions.
    • Combinatorial explosion is avoided in many cases.
    • Several bugs are also fixed.
    • Query bond types "Single or Double", "Single or Aromatic" and "Double or Aromatic" are supported during substructure search.
  • JSP example
    • Substructure hit coloring
    • Hit alignment
    • Bugfixes
  • API changes:
    • The order of query and target atom type has changed in MolSearch.areMatchingBondTypes()
    • 2D and 3D molecule alignment with MolHandler.align()
  • Bugfixes:
    • Exception fixed when JChemSearch was run with search type "Perfect", and logging enabled.
    • Fixed bug when empty field list was specified for Exporter.
• Oracle cartridge
• Screen
  • user defined fuzzy smoothing using pharmacophore type specific smoothing vectors
  • better formula for asymmetric Tanimoto metric, performs significantly better
  • median hypothesis is now available
  • improved pharmacophore perception (mapping)
  • hitstatistics outputs hits in molecular structure file
  • generatemd is capable of producing statistics on descriptors generated
  • generatemd replaces generfp

May 23, 2003: 2.0.1

• JChem Base
  • Marvin 3.1.3 included.
• Screen
  • enhanced fuzzy smoothing
  • explicit weights for pharmacophore point types and point distances, optimization of these weights

May 7, 2003: 2.0

• JChem Base
  • Marvin 3.1.1 included.
  • Structural fingerprints are changed for certain molecules, regeneration of structure tables suggested for optimal search results
  • R-group search
    • connections between R-groups allowed
    • speedup
  • RDfile import/export
  • Binary "AND" operator is used for Oracle (speedup)
  • JChemManager: Minor GUI improvements
  • JSP example
    • Multiple users (login page)
    • Multiple tables (table selection screen)
    • Supports Molecular Descriptor (e.g.: pharmacophore) similarity searches
    • Pharmacophore properties are displayed in hits via atom coloring
    • Remembers parameters set for last search
  • API changes:
    • ID of last inserted molecule is returned by all supported databases by UpdateHandler
      • Interbase users should export and recreate their tables due to changes in ID generation
    • Dissimilarity should be specified instead of similarity in JChemSearch
  • Bugfixes:
    • Duplicate filter did not work for some structures on import
    • R-group search: occasional Cis/Trans stereo problem fixed
    • Structure search bug concerning chirality fixed
    • Table creation with PostgreSQL fixed
    • DB2 export bug fixed
    • regeneration of tables from command line fixed
    • JSP example: problems with non-default property table fixed
    • R-logic bug fixed
  • Reaction search (search for reactions by reaction queries)
  • Search for transformation
  • Search for reaction component
  • Stereoselective reaction search (inversion/retention)
• Chemical expressions
  • Chemical Terms (chemical expression language)
  • Evaluator (evaluating chemical terms)
• Molecule Transformations
  • Standardization (mezomers, tautomers, counter ions, etc.)
  • Ionization (pH dependent ionized microspecies calculation)
• Screen (virtual screening)
  • Configurable molecular descriptor generator
  • Topological fingerprint
  • Pharmacophore fingerprint
  • automatic pharmacophore point identification
  • fuzzy smoothing
  • Hypothesis generation
  • Virtual screening
  • Dissimilarity metrics
  • Euclidean, Tanimoto
  • numerous varieties (normalization, scaling, weighting, directing) that can be combined
  • Metric optimizer
  • tweaks metric parameters (scale factor, asymmetry factor, weights) to enrich hits
  • hit statistics to analyze and evaluate metric performance
• SynthesisDesign.html (virtual synthesis suite)
  • Reaction modeling
  • Metabolism simulation
• Trillian (drug design suite)
  • RECAP fragmentation
• Configuration file editor

November 21, 2002: 1.7.4

• Fixed bug of missing implicit hydrogens in molecular formula.

September 16, 2002: 1.7.3

• Marvin 2.10.5 included.
• Fixed bug of parity handling affecting duplicate filtering on import
• Fixed bug of double bond stereo handling
• Fixed bug of exact matching in case of queries containing generic atoms
• Accelerated R-group search
• R-groups can have primary and secondary attachment point on the same atom (bugfix)
• New methods in MolSearch allow the exclusion of query and target atoms. setQuery(Molecule mol, int[] exclude) and setTarget(Molecule mol, int[] exclude)

August 14, 2002: 1.7.2

• Marvin 2.10.4 included.

August 6, 2002: 1.7.1

• Marvin 2.10.3 included.
• MolSearch bug concerning chirality fixed.

August 1, 2002: 1.7

• Marvin 2.10.2 included.
• R-group search
• New query atom conditions:
• aliphatic/aromatic
• valence
• connection count
• hydrogen connection count
• ring count
• smallest ring size
• New search options in MolSearch:
  • subgraphSearch
  • orderSensitiveSearch
  • exactAtomMatching
  • exactStereoMatching
• Isotope sensitivity (earlier versions did not distinguish different isotopes).
• Improved search performance in case of explicit hydrogens.
• User's guide for search
• JKlustor:
  • Two new parameters added to Compr.
  • Bug fixes including Compr overflow bug for very large datasets.
• The ID of the last imported molecule is returned by using UpdateHandler.execute(boolean returnLastId).
  Note: This feature works only for Oracle yet.
• Statistics after import/export in JchemManager.

May 16, 2002: 1.6.2

• Marvin 2.9.12 included.
• PostgreSQL support added.
• File-table field pairs can be specified also from command line on import.
• Bugfixes for trigger creation/removal, HTMLTools.convertForJavaScript(), connection dialog, stereo checking in exact search, and more.
• JKlustor improvements:
  • Public API for developers.
  • Table vs. file comparison in Compr.
  • The use of -w parameter changed: Only the weights of non-fingerprint columns should be specified relative to the weight of fingerprints.
  • Bugfixes in Ward and GenerFP.

March 14, 2002: 1.6.1

• Bug fixes, including import and export functions in the JSP example.

March 12, 2002: 1.6

• Marvin 2.9.11 included.
• DB2 support added.
• Enhanced multiuser support.
• A new import/export text file format, the JTF added.
• New classes added to JChem API providing import/export capabilities:
  • Importer
  • Exporter
  • ProgressWriter
• From now Oracle uses triggers for incrementing the CD_ID column.
  JChem will detect older tables and creates the triggers. Do not run another copy of JChemManager when asked to proceed. Closing other JChem applications is also recommended.
• Workaround for MM MySQL jdbc driver bug, reduced memory need in case of structure caching and exporting
• Bug fix: Sometimes not the correct parity information was calculated when explicit H atoms were connected to chiral atoms. In that case of databases containing such atoms, the regeneration of the structure tables is advised.
• Minor GUI improvements.
• Using older JChem versions after installing this version in not recommended.

December 22, 2001: 1.5.15

• Marvin 2.9.8 included.
• Bug fix for missing structures in SDF export.
• Workaround for dialog sizing problem in KDE.

November 28, 2001: 1.5.14

• Marvin 2.9.6 included.

November 26, 2001: 1.5.13

• Fixing bug: missing structures at SDF export.

November 19, 2001: 1.5.12

• Marvin 2.9.5 included.
• Method for checking if connection is alive: isConnectionAlive.
• Workaround for occasional communication link failure with MySQL
• Filtering rows and columns in SDfile export.

October 15, 2001: 1.5.11

• Marvin 2.9.2 included.
• Fix: Windows style line separators in the export operation of JChemManager under Windows.
• JKlustor:
  • Ward clustering includes Kelley type automatic cluster level selection.

August 22, 2001: 1.5.10

• Marvin 2.9 included.
• Faster structure searching due to caching SMILES strings and fingerprints at the same time. See JChemSearch.structureCaching(boolean).

June 25, 2001: 1.5.9

• Marvin 2.8.4 included.
• JKlustor:
  • Ward clustering using the RNN approach

June 12, 2001: 1.5.8

• Marvin 2.8 included.
• JKlustor:
  • Visualizing results. A new module, CreateView, composes an SDfile that contains both structures and calculation results. The generated SDfiles can be displayed by the MarvinView application.
  • Jarp: Optionally, nearest neighbor search can be run separately from clustering. (It helps to refine the setting of the clustering parameters, because the time consuming part of the process can be run before clustering.)

May 27, 2001: 1.5.7

• Marvin 2.7.12 included.
• JKlustor:
  • Compr: A new module for comparing libraries based on diversity/dissimilarity.
  • Fix in Jarp: Odd number of fingerprint columns are also accepted.
  • Jarp: Optional clustering and diversity statistics.

May 5, 2001: 1.5.6

• Marvin 2.7.9 included.
• Jarp:
  • Optionally, singletons may get negative cluster ids.
• Methods are added to the UpdateHandler class for creating and dropping structure tables and for retrieving the names of structure tables.

April 20, 2001: 1.5.5

• Marvin 2.7.7 included.
• Jarp:
  • common neighbors (-c option) are taken as a proportion of the number of elements in the shorter list. (Previously all elements in the two lists were used.) This results faster calculation and less singletons.
  • Optional centroid calculation.
  • Better command line syntax checking.
  • To save memory space, the descriptors are stored in float (4 bytes) instead of double (8 bytes) values.
• Fixing a bug (since 1.5.2) that spoiled the default setting for the existence of the bitwise AND operator in the case of MSSQL Server, MS Access, and MySQL.

April 8, 2001: 1.5.4

• Improvements in Jarp: bugfixes, non-fingerprint descriptors.

April 2, 2001: 1.5.3

• Marvin 2.7.6 included.
• Improvements in Jarp: bugfixes, faster comparison of neighbors.

March 22, 2001: 1.5.2

• Marvin 2.7.4 included.
• New add-on module for clustering: JKlustor.
• Improved compatibility with the Interbase Server product of Inprise (previously Borland).
• Support of auto-incrementing the cd_id column by trigger.
• Support of bitwise (binary) AND by built-in or user-defined functions in the database.
• Information on integrating JChem with Apache and Tomcat.
• Fix for exact searching of molecules containing pyrrole type N.

January 20, 2001: 1.5.1

Because of changes that affect fix columns in the database, regeneration of the structure tables is advised.

• Marvin 2.6.6 (includes bugfixes in stereo information retrieval from 3D, handling NOT lists, cleaning, ...)
• JChemSearch