@Override public boolean areSubstituentsDefined() { List<IAtom> allRgroupAtoms = getAllRgroupQueryAtoms(); if (allRgroupAtoms == null) return false; for (IAtom rgp : allRgroupAtoms) { if (RGroupQuery.isValidRgroupQueryLabel(((IPseudoAtom) rgp).getLabel())) { int groupNum = Integer.valueOf(((IPseudoAtom) rgp).getLabel().substring(1)); if (rGroupDefinitions == null || rGroupDefinitions.get(groupNum) == null || rGroupDefinitions.get(groupNum).getRGroups() == null || rGroupDefinitions.get(groupNum).getRGroups().size() == 0) { return false; } } } return true; }
List<IAtom> allrGroupQueryAtoms = rGroupQuery.getAllRgroupQueryAtoms(); Assert.assertEquals(allrGroupQueryAtoms.size(), 2);
Assert.assertEquals(rGroupQuery.getRootStructure().getAtomCount(), 6); List<IAtom> allrGroupQueryAtoms = rGroupQuery.getAllRgroupQueryAtoms(); Assert.assertEquals(allrGroupQueryAtoms.size(), 1); RGroupList rList = rGroupQuery.getRGroupDefinitions().get(1);
Assert.assertEquals(rGroupQuery.getRootStructure().getAtomCount(), 7); for (IAtom at : rGroupQuery.getAllRgroupQueryAtoms()) { if (at instanceof PseudoAtom) { Assert.assertEquals(((PseudoAtom) at).getLabel(), "R1");
Assert.assertEquals(rGroupQuery.getRootAttachmentPoints().size(), 4); List<IAtom> rGroupQueryAtoms = rGroupQuery.getAllRgroupQueryAtoms(); Assert.assertEquals(rGroupQueryAtoms.size(), 4); Assert.assertEquals(rGroupQueryAtoms.size(), 1); for (IAtom at : rGroupQuery.getAllRgroupQueryAtoms()) { if (at instanceof PseudoAtom) { Assert.assertTrue(RGroupQuery.isValidRgroupQueryLabel(((PseudoAtom) at).getLabel()));