Examples of PseudoAtom

Examples of org.openscience.cdk.PseudoAtom

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            if(!atom.getSymbol().equals(symbolField.getText()))
              hub.setSymbol(atom, symbolField.getText());
            if(atom.getMassNumber()==null || atom.getMassNumber()!=majorIsotopeNumber+((Integer)isotopeField.getValue()).intValue())
              hub.setMassNumber(atom,majorIsotopeNumber+((Integer)isotopeField.getValue()).intValue());
          }else{
              PseudoAtom pseudo = new PseudoAtom(atom);
              pseudo.setLabel(symbolField.getText());
              pseudo.setImplicitHydrogenCount(((Integer)hCountField.getValue()).intValue());
              pseudo.setFormalCharge(((Integer)formalChargeField.getValue()).intValue());
              pseudo.setMassNumber(majorIsotopeNumber+((Integer)isotopeField.getValue()).intValue());
          }

        }catch(IOException ex){
          if(atom.getImplicitHydrogenCount()!=((Integer)hCountField.getValue()).intValue())
            hub.setImplicitHydrogenCount(atom,((Integer)hCountField.getValue()).intValue());
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Examples of org.openscience.cdk.PseudoAtom

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    range:
    while(atomsInRange.hasNext()){
            IAtom atom = atomsInRange.next();
          if(type.equals("normal")){
                PseudoAtom pseudo = (PseudoAtom)atom;
                IAtom normal = pseudo.getBuilder().newInstance(IPseudoAtom.class,pseudo);
                normal.setSymbol("C");
                jcpPanel.get2DHub().replaceAtom(normal,pseudo);
          }else {
            jcpPanel.get2DHub().convertToPseudoAtom(atom,label);
                AddAtomModule newActiveModule = new AddAtomModule(jcpPanel.get2DHub(), IBond.Stereo.NONE);
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