Examples of addAtomContainer()

Examples of org.openscience.cdk.AtomContainerSet.addAtomContainer()

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            // try to read a Molecule
                IAtomContainer mol = (AtomContainer) cor.read(new AtomContainer());
                if(mol!=null )
                    try{
                        IAtomContainerSet newSet = new AtomContainerSet();
                        newSet.addAtomContainer(mol);
                        chemModel = new ChemModel();
                        chemModel.setMoleculeSet(newSet);
                        if (chemModel == null) {
                            error = "The object chemModel was empty unexpectedly!";
                        }
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Examples of org.openscience.cdk.AtomContainerSet.addAtomContainer()

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            BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
            String line;
            while ((line = in.readLine()) != null) {
                if (line.toLowerCase().startsWith("inchi=")) {
                    moleculeSet.addAtomContainer(parseInChI(line));
                }
            }
            in.close();
        } catch (Exception e) {
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Examples of org.openscience.cdk.AtomContainerSet.addAtomContainer()

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            String line;
            while ((line = in.readLine()) != null)
            {
                if (line.toLowerCase().startsWith("inchi=")) {
                    IAtomContainer atc = parser.parseInchi(line);
                    moleculeSet.addAtomContainer(atc);
                }
            }
            in.close();
           
           
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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            // try to read a Molecule
                IAtomContainer mol = (AtomContainer) cor.read(new AtomContainer());
                if(mol!=null )
                    try{
                        IAtomContainerSet newSet = new AtomContainerSet();
                        newSet.addAtomContainer(mol);
                        chemModel = new ChemModel();
                        chemModel.setMoleculeSet(newSet);
                        if (chemModel == null) {
                            error = "The object chemModel was empty unexpectedly!";
                        }
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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        }

        if(moleculeSet.getAtomContainer(0).getAtomCount()==0)
            moleculeSet.getAtomContainer(0).add(molecule);
        else
            moleculeSet.addAtomContainer(molecule);

        IUndoRedoFactory undoRedoFactory= chemPaintPanel.get2DHub().getUndoRedoFactory();
        UndoRedoHandler undoRedoHandler= chemPaintPanel.get2DHub().getUndoRedoHandler();
       
        if (undoRedoFactory!=null) {
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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    IAtomContainerSet molSet = chemModel.getMoleculeSet();
    if (molSet == null) {
      molSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
      IAtomContainer ac = chemModel.getBuilder().newInstance(IAtomContainer.class);
      ac.addAtom(newAtom);
      molSet.addAtomContainer(ac);
      chemModel.setMoleculeSet(molSet);
    }
    IAtomContainer newAtomContainer = chemModel.getBuilder().newInstance(IAtomContainer.class);
    if (chemModel.getMoleculeSet().getAtomContainer(0).getAtomCount() == 0)
      newAtomContainer = (IAtomContainer) chemModel.getMoleculeSet()
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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    IAtomContainer newAtomContainer = chemModel.getBuilder().newInstance(IAtomContainer.class);
    if (chemModel.getMoleculeSet().getAtomContainer(0).getAtomCount() == 0)
      newAtomContainer = (IAtomContainer) chemModel.getMoleculeSet()
          .getAtomContainer(0);
    else
      molSet.addAtomContainer(newAtomContainer);
    newAtomContainer.addAtom(newAtom);
    updateAtom(newAtom);
    JChemPaintRendererModel model = this.getRenderer().getRenderer2DModel();
    double nudgeDistance = model.getHighlightDistance() / model.getScale();
    if (getClosestAtom(newAtom) != null)
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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      IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
      if (moleculeSet == null) {
        moleculeSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
        chemModel.setMoleculeSet(moleculeSet);
      }
      moleculeSet.addAtomContainer(atomCon);
    }

    // The AtomPlacer generates coordinates for the new atom
    AtomPlacer atomPlacer = new AtomPlacer();
    atomPlacer.setMolecule(chemModel.getBuilder().newInstance(IAtomContainer.class,atomCon));
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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      getUndoRedoHandler().postEdit(undoredo);
    }
    if (chemModel.getMoleculeSet() != null) {
      IAtomContainerSet molSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
      IAtomContainer ac = chemModel.getBuilder().newInstance(IAtomContainer.class);
      molSet.addAtomContainer(ac);
      chemModel.setMoleculeSet(molSet);

    }
    if (chemModel.getReactionSet() != null)
      chemModel.setReactionSet(chemModel.getBuilder().newInstance(IReactionSet.class));
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Examples of org.openscience.cdk.interfaces.IAtomContainerSet.addAtomContainer()

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      IAtomContainer mol = chemModel.getBuilder().newInstance(IAtomContainer.class);
      for (IAtom atom: moleculeToAddTo.atoms())
        mol.addAtom(atom);
      for (IBond bond: moleculeToAddTo.bonds())
        mol.addBond(bond);
      oldMoleculeSet.addAtomContainer(mol);
      moleculeToAddTo.add(toPaste);
    }
    if (toRemove != null) {
      oldMoleculeSet.addAtomContainer(toRemove);
      moleculeToAddTo.add(toRemove);
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