What's new in Toxtree Portable 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 Portable 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 Portable 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.
New in Toxtree Portable 2.5.1 (May 21, 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
New in Toxtree Portable 2.5.0 (May 21, 2013)
- updated to cdk 1.3.8;
- updated to Open Parser for Systematic IUPAC Nomenclature (OPSIN) 1.0.0;
- updated to ambit-2.4.2;
- SMARTCyp plug-in - added metabolite generation, based on Site of Metabolism, calculated by SMARTCyp and ambit-SMIRKS package;
- improved implementation of Verhaar scheme plugin; validated against a published dataset;
- 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 Benigni / Bossa rulebase SA31b (biphenyls recognition);
- fixed Benigni / Bossa rulebase SA30 (coumarins recognition);
- fixed Benigni / Bossa rulebase rule (QSAR6,8 applicability domain);
- included jre-6u26-windows-i586.exe in Windows installer;
- 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;
- updated manuals and README.
New in Toxtree Portable 2.2.0 (May 21, 2013)
- updated to cdk 1.3.6 and jni-inchi 0.7;
- updated to jchempaint-3.1.3;
- fixed not working Edit/Preferences;
- removed valency labels that were appearing in JChemPaint by default;
- fixed rendering of disconnected structures (e.g. salts);
- fixed Cramer rule Q3 - Sulphur in aromatic ring is now recognized as divalent;
- included jre-6u22-windows-i586.exe in Windows installer;
- upgraded to Java 1.6;
- upgraded to OpenBabel v2.2.3;
- fixed SMILES parsing (OpenBabel v2.2.3);
- enabled InChI-to-structure conversion based on jni-inchi-0.7-std;
- enabled name-to-structure conversion based on OPSIN v0.8.0;
- fixed outcome from QSAR8;
- values "true" and "false" in input file will be parsed into 1 or 0;
- fixed batch processing "Non serializable exception" for micronucleus and skin sensitiation plugins;
- added check for phosphates in Q4 of Cramer Extended rules;
- updated manuals and README.
New in Toxtree Portable 2.1.0 (May 21, 2013)
- supports structural alerts highlighting (funded by Procter & Gamble)
- new Skin sensitisation alerts plugin (developed by Procter & Gamble)
- new Kroes TTC decision tree plugin
- new SMARTCyp plugin
- upgraded to CDK 1.3.3 and JChemPaint;