Examples of RGroupQuery

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

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                    }
        }

        // RGroupQuery reading
        if (cor.accepts(RGroupQuery.class) && chemModel==null) {
          IRGroupQuery rgroupQuery = (RGroupQuery) cor.read(new RGroupQuery(DefaultChemObjectBuilder.getInstance()));
          if(rgroupQuery!=null )
            try{
              chemModel = new ChemModel();
              RGroupHandler rgHandler =  new RGroupHandler(rgroupQuery, panel);
              panel.get2DHub().setRGroupHandler(rgHandler);
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Examples of org.openscience.cdk.isomorphism.matchers.RGroupQuery

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                            toPaste.add(ac);

                        }
                  } else if (reader.accepts(RGroupQuery.class)) {
                rgrpQuery=true;
                    IRGroupQuery rgroupQuery = (RGroupQuery) reader.read(new RGroupQuery(DefaultChemObjectBuilder.getInstance()));
                chemModel = new ChemModel();
                RGroupHandler rgHandler =  new RGroupHandler(rgroupQuery, this.jcpPanel);
                this.jcpPanel.get2DHub().setRGroupHandler(rgHandler);
                chemModel.setMoleculeSet(rgHandler.getMoleculeSet(chemModel));
                rgHandler.layoutRgroup();
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Examples of org.openscience.cdk.isomorphism.matchers.RGroupQuery

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   * Initializes an empty RGroupQuery.
   *
   * @return a new empty RGroupQuery
   */
  private IRGroupQuery newRGroupQuery(IChemObjectBuilder builder) {
    IRGroupQuery rgrpQuery = new RGroupQuery(DefaultChemObjectBuilder.getInstance());
    rgrpQuery.setRootStructure(builder.newInstance(IAtomContainer.class));
    rgrpQuery
        .setRootAttachmentPoints(new HashMap<IAtom, Map<Integer, IBond>>());
    rgrpQuery.setRGroupDefinitions(new HashMap<Integer, RGroupList>());
    return rgrpQuery;
  }
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