Toxtree – Download Toxtree 2.x.x

Toxtree is distributed with Java 6 installer. Please use Java 6 even if you have Java 7 already installed. There is a known problem, causing instability, when using Java 7. This will be fixed starting with Toxtree 2.5.8.

Toxtree-v2.5.4 is a bug fix release.

Windows installer (source and executable, Windows)
ZIP archive (source and executable, platform independent)

Change log

build date 02 Apr 2012
added new plugin Protein bindingProtein 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

Toxtree-2.5.1

oxtree is distributed with Java 6 installer. Please use Java 6 even if you have Java 7 already installed. There is a known problem, causing instability, when using Java 7. This will be fixed starting with Toxtree 2.5.8

Toxtree-v2.5.1 is a bug fix release

-Windows installer (source and executable, Windows)

-ZIP archive (source and executable, platform independent)

Change log

build date 3 Feb 2012
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;
Source code
Maven repository

Toxtree-2.5.0

Toxtree-v2.5.0 is a stable release including 2 new plugins, 2 improved plugins, new features and bug fixes

Windows installer (source and executable, Windows)
ZIP archive (source and executable, platform independent)
Installation manual
User manual

Toxtree 2.5.0 SMARTCyp module screenshot

Change log

build date 5 Aug 2011
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 REST service (OpenTox API). This new functionality is disabled by default – check “Method/Decision tree option/Remote Query” menu to enable it;
updated (manuals)(http://sourceforge.net/projects/toxtree/files/toxtree/Toxtree-v.2.5.0/Toxtree_user_manual.pdf/download) and README.
Source code
Maven repository

Toxtree-2.2.0

Toxtree 2.2.0 is a library upgrade and bug fix release.

Windows installer (source and executable, Windows)
ZIP archive (source and executable, platform independent)

Change log

build date 25 Oct 2010
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.
Source code

Toxtree 2.1.0

Toxtree 2.1.0 is released July 2010, and includes 3 new plugins and several bug fixes

Windows installer (source and executable, Windows)
ZIP archive (source and executable, platform independent)
Installation manual
User manual

Change log

build date 30 Jun 2010
supports structural alerts highlighting (funded by (http://www.pg.com)Procter & Gamble)))
new Skin sensitisation alerts plugin (developed by (http://www.pg.com)Procter & Gamble)))
new (./kroes.html)Kroes TTC decision tree plugin))
new (./smartcyp.html)SMARTCyp plugin))
upgraded to CDK 1.3.3 and JChemPaint;
(https://sourceforge.net/p/toxtree/svn/1623/tree/tags/2.1.0)Source code))

Download Toxtree 2.x.x

Toxtree-2.6.13

Toxtree-2.6.6

Toxtree-2.6.0

Toxtree-2.5.4

Toxtree-2.5.1

Toxtree-2.5.0

Toxtree-2.2.0

Toxtree 2.1.0

Toxtree-v1.*

Toxtree versions 1.x.x