What's new in Toxtree 2.6.6
Jun 16, 2014
- updated to Open Parser for Systematic IUPAC Nomenclature (OPSIN) 1.5.0;
- updated to ambit-2.5.6;
- fixed bug causing errors when starting in Linux;
- included jre-7u60-windows-i586.exe in Windows installer;
- updated manuals and README.
New in Toxtree 2.6.0 (Aug 5, 2013)
- updated to cdk 1.4.11;
- updated to Open Parser for Systematic IUPAC Nomenclature (OPSIN) 1.4.0;
- updated to ambit-2.4.12;
- added new plug-ins: In vitro mutagenicity (Ames test) alerts by ISS and Structural alerts associated with covalent DNA binding;
- The skin sensitisation alerts plugin renamed to Skin sensitisation reactivity domains;
- fixed bug causing instability under Java 7;
- fixed bug in the Decision rules editor ;
- fixed bug affecting substituents recognition in Carcinogenicity plugin;
- included jre-7u25-windows-i586.exe in Windows installer;
- updated manuals and README.
- Source code
- Maven repository
New in Toxtree 2.5.4 (May 21, 2013)
- added new plugin Protein binding
- updated CDK to v1.4.8;
- updated JChemPaint to v3.3.0;
- updated to jre-6u31-windows-i586;
- fixed bug 3493804 (Different results between 2.5.0 and earlier versions);
- fixed bug 3493431 (Cramer Rule 20 behaviour);
- fixed bug 3492853 (Some compounds not found in bodymol.sdf);
- fixed bug 3491753 (Non serializable exception in CYP450 module);
- fixed bug 3488950 (Cramer2 Q42 rule);
- fixed bug 3472325 (Micronucleus plugin SA34 rule);
- fixed bug 3431053 (Incorrect structure of protoheme in bodymol.sdf);
- fixed bug 3396489 (Name of the "skin sensitization alerts" plugin changed);
- fixed bug 3089700 (Cramer2 rule 4);
- fixed bug 3089699 (Cramer2 rule 40);
- updated installation and user manual;
- updated README.
- Source code
- Maven repository
New in Toxtree 2.5.1 (Feb 1, 2013)
- corrected Schiff base SMARTS;
- fixed ionic bonds matching;
- fixed explanation for RuleAliphaticWithSomeFuncGroups in Cramer rules and
- Extended Cramer rules;
- fixed recognition of carbonyl in amide group, affecting Q18 and Q20 of
- Cramer rules;
- included jre-6u30-windows-i586.exe in Windows installer;
- updated manuals and README;
- Toxtree-v2.5.0 (build date 05 Aug 2011):
- updated to cdk 1.3.8;
- updated to ambit-2.4.2;
- OpenBabel is no longer included in the distribution; in order to use
- OpenBabel (optionally) from within Toxtree, install OpenBabel separately
- and set the OBABEL_HOME environment variable to point to the folder where
- OpenBabel is installed;
- added metadata for all plugins (explanation, references, vendor, links to
- datasets);
- improved display of decision tree details;
- improved help menus (About / Files info / Help);
- enabled CAS & EINECS lookup in remote OpenTox service; this new
- functionality is disabled by default -- check "Method/Decision tree
- option/Remote Query" menu to enable it;
- added two new plug-ins: Modified Verhaar scheme, and Structural Alerts
- for Functional Group Identification (ISSFUNC);
- fixed Cramer rules Q2 (NC#N recognised as functional group associated
- with enhanced toxicity);
- fixed Cramer rules Q2 (secondary amine highlight);
- fixed Benigni / Bossa rulebase SA31b (biphenyls recognition);
- fixed Benigni / Bossa rulebase SA30 (coumarins recognition);
- fixed Benigni / Bossa rulebase rule (QSAR6,8 applicability domain);
- improved implementation of Verhaar scheme plugin; validated against a
- published dataset;
- SMARTCyp plug-in - added metabolite generation, based on Site of
- Metabolism, calculated by SMARTCyp and ambit-SMIRKS package.
- included jre-6u26-windows-i586.exe in Windows installer;
- updated manuals and README;
New in Toxtree 2.1.0 (May 26, 2011)
- new Skin sensitisation alerts plugin;
- new Kroes TTC decision tree plugin;
- new SMARTCyp plugin;
- upgraded to CDK 1.3.3 and JChemPaint;
- supports structural alerts highlighting;
New in Toxtree 1.60 (Oct 6, 2009)
- added Cramer rules with extensions plugin and updated bodymol.sdf
- added Structure Alerts for the in vivo micronucleus assay in rodents plugin
- added START biodegradation and persistence plugin
- added Structural Alerts for identification of Michael Acceptors plugin
- Skin irritation plugin: fixed bugs in rules Q52 and Q53
- Cramer rules plugin: fixed bugs in Q8 and Q21
- Begnini/Bossa rulebase plugin: fixed issue when results for structural alerts (e.g. SA10) are not displayed if the outcome is YES
- Begnini/Bossa rulebase plugin: QSAR8 question rephrased, to avoid confusion
- fixed issue when editing an example in the decision tree editor was not working
- introduced TOXTREE environment variable, which should be set to point to the Toxtree-version.jar and helps locating SDF files and plugins when Toxtree is used by third party software
- fixed issue when after creating a new tree it could not be saved.