mdlWriter.writeMolecule(tocopy); } catch (Exception ex) { logger.error("Could not write molecule to string: ", ex.getMessage());
return; } else if (object instanceof IAtomContainer) { writeMolecule((IAtomContainer) object); return;
private void writeChemFile(IChemFile file) throws Exception { IAtomContainer bigPile = file.getBuilder().newInstance(IAtomContainer.class); for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(file)) { bigPile.add(container); if (container.getTitle() != null) { if (bigPile.getTitle() != null) bigPile.setTitle(bigPile.getTitle() + "; " + container.getTitle()); else bigPile.setTitle(container.getTitle()); } if (container.getProperty(CDKConstants.REMARK) != null) { if (bigPile.getProperty(CDKConstants.REMARK) != null) bigPile.setProperty(CDKConstants.REMARK, bigPile.getProperty(CDKConstants.REMARK) + "; " + container.getProperty(CDKConstants.REMARK)); else bigPile.setProperty(CDKConstants.REMARK, container.getProperty(CDKConstants.REMARK)); } } writeMolecule(bigPile); }