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static List<IAtomContainer> org::openscience::cdk::tools::manipulator::ChemModelManipulator::getAllAtomContainers ( IChemModel  chemModel ) [inline, static]

Returns all the AtomContainer's of a ChemModel.

Definition at line 287 of file ChemModelManipulator.java.

References org::openscience::cdk::interfaces::IMoleculeSet::add(), org::openscience::cdk::tools::manipulator::MoleculeSetManipulator::getAllAtomContainers(), org::openscience::cdk::tools::manipulator::ReactionSetManipulator::getAllMolecules(), org::openscience::cdk::interfaces::IChemObject::getBuilder(), and org::openscience::cdk::interfaces::IChemObjectBuilder::newMoleculeSet().

Referenced by org::openscience::cdk::tools::manipulator::ChemSequenceManipulator::getAllAtomContainers(), org::openscience::cdk::io::Gaussian98Reader::readNMRData(), and org::openscience::cdk::io::PDBWriter::write().

                                                                                  {
        IMoleculeSet moleculeSet = chemModel.getBuilder().newMoleculeSet();
        if (chemModel.getMoleculeSet() != null) {
            moleculeSet.add(chemModel.getMoleculeSet());
        }
        if (chemModel.getReactionSet() != null) {
            moleculeSet.add(
                ReactionSetManipulator.getAllMolecules(
                    chemModel.getReactionSet()
                )
            );
        }
        return MoleculeSetManipulator.getAllAtomContainers(moleculeSet);
    }

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