Package org.openscience.cdk.isomorphism.matchers

Examples of org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

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          }
        }
        if(smiles != null && smiles.contains("*")) {
          try {
            //System.out.println(name + "\t" + smiles);
            QueryAtomContainer qac = makeQAC(smiles);
            qacs.put(name, qac);
            qsmiles.put(name, smiles);
            qid.put(name, id);
          } catch (Exception e) {
            //e.printStackTrace();
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  }
 
  private QueryAtomContainer makeQAC(String smiles) throws Exception {
    IMolecule mol = sp.parseSmiles(smiles);
    ha.addExplicitHydrogensToSatisfyValency(mol);
    QueryAtomContainer qac = QueryAtomContainerCreator.createBasicQueryContainer(mol);
    for(int i=0;i<qac.getAtomCount();i++) {
      IAtom a = qac.getAtom(i);
      if(a.getSymbol().equals("R")) {
        a.setSymbol("C");
        a.setAtomicNumber(6);
      }
    }
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Related Classes of org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

  • uk.ac.cam.ch.wwmm.ptc.experimental.ChEBIGenerics
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