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Readme.md

Ambit-SMIRKS

Ambit-SMIRKS is an extension of the AMBIT-SMARTS Java library, both part of the AMBIT project

The SMIRKS module is used to enable metabolite predictions in Toxtree, once that site of metabolisms are predicted by SMARTCyp

Main functionality

Transformation mapping modes

The transformations can be applied on various sites of the target molecule in several modes:

  • single
  • non-overlapping
  • non-identical
  • non-homomorphic or
  • externally specified list of sites
Test online

Maven artifacts

    <dependency>
      <groupId>ambit</groupId>
      <artifactId>ambit2-smarts</artifactId>
      <version>2.7.3</version>
    </dependency>
    <repository>
        <id>ambit-plovdiv-releases</id>
        <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases</url>
    </repository> 
    <dependency>
      <groupId>ambit</groupId>
      <artifactId>ambit2-smarts</artifactId>
      <version>3.0.0-SNAPSHOT</version>
    </dependency>
    <repository>
        <id>ambit-plovdiv-snapshots</id>
        <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/snapshots</url>
    </repository>

Code examples

    IAtomContainer target = (initialize)
    SMIRKSManager smrkMan = new SMIRKSManager();
    SMIRKSReaction reaction = smrkMan.parse(smirks);
    if (!smrkMan.getErrors().equals(""))  {
           throw(new Exception("Smirks Parser errors:\n" + smrkMan.getErrors()));
    }
    if (smrkMan.applyTransformation(target, reaction)) 
           return target; //all products inside the same atomcontainer, could be disconnected
    else return null;
  • Generate separate products for every possible reaction (used in Toxtree)
    SMIRKSManager smrkMan = new SMIRKSManager();
    SMIRKSReaction smr = smrkMan.parse(reaction.getSMIRKS());
    IAtomContainer product = reactant; //(IAtomContainer) reactant.clone();
    IAtomContainerSet rproducts = smrkMan.applyTransformationWithSingleCopyForEachPos(product, null, smr);
    //products returned in a separate atom sontainer set

Application in metabolite generation

Toxtree is an open-source application that predicts various kinds of toxic effects, mostly by applying structural alerts, arranged in a decision tree fashion. You could download the application or test Toxtree online

SMARTCyp (Cytochrome P450-Mediated Drug Metabolism) model is developed by Patrik Rydberg et al and is included as Toxtree module since Toxtree 2.1.0.

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