List<Integer> validOcc = rGroupDefinitions.get(r).matchOccurence(getRgroupQueryAtoms(r).size()); if (validOcc.size() == 0) { throw new CDKException("Occurrence '" + rGroupDefinitions.get(r).getOccurrence() + "' defined for Rgroup " + r + " results in no subsititute options for this R-group.");
public void setChemObject(IChemObject object) { if (object instanceof IRGroupQuery) { source = object; IRGroupQuery rgroupQuery = (IRGroupQuery)source; for (int i=0; i< rNumbers.size(); i++) { int r = rNumbers.get(i); JPanel rgrpPanel = panels.get(i); RGroupList rgrpList = rgroupQuery.getRGroupDefinitions().get(r); JTextField occurrenceField = (JTextField) (rgrpPanel.getComponent(1)); String occ=rgrpList.getOccurrence(); occurrenceField.setText(occ); JComboBox<?> restHBox = (JComboBox<?>) (rgrpPanel.getComponent(3)); boolean restH=rgrpList.isRestH(); String restHString= restH? GT.get("True"): GT.get("False"); restHBox.setSelectedItem(restHString); JComboBox<?> ifThenBox = (JComboBox<?>) (rgrpPanel.getComponent(5)); int ifThenR = rgrpList.getRequiredRGroupNumber(); String ifThenRString= ifThenR==0?GT.get("None"):"R"+ifThenR; ifThenBox.setSelectedItem(ifThenRString); } } else { throw new IllegalArgumentException("Argument must be a IRGroupQuery"); } }
String logLine = "M LOG" + MDLV2000Writer.formatMDLInt(1, 3) + MDLV2000Writer.formatMDLInt(rgrpNum, 4) + MDLV2000Writer.formatMDLInt(rgList.getRequiredRGroupNumber(), 4) + MDLV2000Writer.formatMDLInt(restH, 4) + " " + rgList.getOccurrence(); rootBlock.append(logLine).append(LSEP);
/** * Clones an RGroupList * * @param original * @return */ private static RGroupList makeClone(RGroupList original) { RGroupList clone = new RGroupList(original.getRGroupNumber()); try { clone.setOccurrence(original.getOccurrence()); clone.setRequiredRGroupNumber(original.getRequiredRGroupNumber()); clone.setRestH(original.isRestH()); List<RGroup> rgpList = new ArrayList<RGroup>(); for (RGroup r : original.getRGroups()) { rgpList.add(r); } clone.setRGroups(rgpList); } catch (CDKException e) { e.printStackTrace(); } return clone; } }
@Test public void testOccurrenceNull() throws CDKException { RGroupList rgrLst = new RGroupList(1); rgrLst.setOccurrence(null); Assert.assertEquals(rgrLst.getOccurrence(), RGroupList.DEFAULT_OCCURRENCE); }
@Test public void testOccurrenceCorrect() throws CDKException { RGroupList rgrLst = new RGroupList(1); rgrLst.setOccurrence("1, 3-7, 9, >11"); Assert.assertEquals(rgrLst.getOccurrence(), "1,3-7,9,>11"); }
Assert.assertEquals(val_1, 1); RGroupList rList = rGroupQuery.getRGroupDefinitions().get(val_1); Assert.assertEquals(rList.getOccurrence(), "0,1-3");
RGroupList rList = rGroupQuery.getRGroupDefinitions().get(2); Assert.assertEquals(rList.getRGroups().size(), 2); Assert.assertEquals(rList.getOccurrence(), "0,2"); Assert.assertEquals(rList.getRequiredRGroupNumber(), 11); Assert.assertFalse(rList.isRestH());