/** * create new instance in context of parent, overridable by subclasses. * * @param parent * parent of element to be constructed (ignored by default) * @return CMLList */ public CMLElement makeElementInContext(Element parent) { return new CMLList(); }
/** * copy node . * * @return Node */ public Node copy() { return new CMLList(this); }
private CMLList cdkChemSequenceToCMLList(IChemSequence sequence, boolean setIDs) { CMLList cmlList = new CMLList(); cmlList.setConvention("cdk:sequence"); if (useCMLIDs && setIDs) { IDCreator.createIDs(sequence); } if (sequence.getID() != null && !sequence.getID().equals("")) cmlList.setId(sequence.getID()); if (sequence.getChemModelCount() > 0) { for (int i = 0; i < sequence.getChemModelCount(); i++) { cmlList.appendChild(cdkChemModelToCMLList(sequence.getChemModel(i))); } } return cmlList; }
private CMLList cdkChemSequenceToCMLList(IChemSequence sequence, boolean setIDs) { CMLList cmlList = new CMLList(); cmlList.setConvention("cdk:sequence"); if (useCMLIDs && setIDs) { IDCreator.createIDs(sequence); } if (sequence.getID() != null && !sequence.getID().equals("")) cmlList.setId(sequence.getID()); if (sequence.getChemModelCount() > 0) { for (int i = 0; i < sequence.getChemModelCount(); i++) { cmlList.appendChild(cdkChemModelToCMLList(sequence.getChemModel(i))); } } return cmlList; }
private CMLList cdkChemModelToCMLList(IChemModel model, boolean setIDs) { CMLList cmlList = new CMLList(); cmlList.setConvention("cdk:model"); if (useCMLIDs && setIDs) { IDCreator.createIDs(model); } if (model.getID() != null && !model.getID().equals("")) cmlList.setId(model.getID()); if (model.getCrystal() != null) { cmlList.appendChild(cdkCrystalToCMLMolecule(model.getCrystal(), false)); } if (model.getReactionSet() != null) { cmlList.appendChild(cdkReactionSetToCMLReactionList(model.getReactionSet(), false)); } if (model.getMoleculeSet() != null) { cmlList.appendChild(cdkAtomContainerSetToCMLList(model.getMoleculeSet(), false)); } return cmlList; }
private CMLList cdkChemModelToCMLList(IChemModel model, boolean setIDs) { CMLList cmlList = new CMLList(); cmlList.setConvention("cdk:model"); if (useCMLIDs && setIDs) { IDCreator.createIDs(model); } if (model.getID() != null && !model.getID().equals("")) cmlList.setId(model.getID()); if (model.getCrystal() != null) { cmlList.appendChild(cdkCrystalToCMLMolecule(model.getCrystal(), false)); } if (model.getReactionSet() != null) { cmlList.appendChild(cdkReactionSetToCMLReactionList(model.getReactionSet(), false)); } if (model.getMoleculeSet() != null) { cmlList.appendChild(cdkAtomContainerSetToCMLList(model.getMoleculeSet(), false)); } return cmlList; }