private CMLCml cdkChemFileToCMLList(IChemFile file, boolean setIDs) { CMLCml cmlList = new CMLCml(); cmlList.setConvention("cdk:document"); if (useCMLIDs && setIDs) { IDCreator.createIDs(file); } if (file.getID() != null && !file.getID().equals("")) cmlList.setId(file.getID()); if (file.getChemSequenceCount() > 0) { Iterator<IChemSequence> sequences = file.chemSequences().iterator(); while (sequences.hasNext()) { cmlList.appendChild(cdkChemSequenceToCMLList(sequences.next())); } } return cmlList; }
private CMLCml cdkChemFileToCMLList(IChemFile file, boolean setIDs) { CMLCml cmlList = new CMLCml(); cmlList.setConvention("cdk:document"); if (useCMLIDs && setIDs) { IDCreator.createIDs(file); } if (file.getID() != null && !file.getID().equals("")) cmlList.setId(file.getID()); if (file.getChemSequenceCount() > 0) { Iterator<IChemSequence> sequences = file.chemSequences().iterator(); while (sequences.hasNext()) { cmlList.appendChild(cdkChemSequenceToCMLList(sequences.next())); } } return cmlList; }
private static void createIDsForChemFile(IChemFile file, List<String> tabuList) { if (tabuList == null) tabuList = ChemFileManipulator.getAllIDs(file); if (null == file.getID()) { chemFileCount = setID(CHEMFILE_PREFIX, chemFileCount, file, tabuList); } if (policy == OBJECT_UNIQUE_POLICY) { // start indices within a chem file always from 1 chemSequenceCount = 0; } for (IChemSequence chemSequence : file.chemSequences()) { createIDsForChemSequence(chemSequence, tabuList); } }