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Searched refs:getAtomByID (Results 1 – 9 of 9) sorted by relevance

/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/
H A DSMILESWriterTest.java376 …ond(2, 6).setBondStereoElement(new Atom[]{f.getAtomByID(1), f.getAtomByID(2), f.getAtomByID(6), f.… in testDoubleBondSupport4()
377 …nd(7, 8).setBondStereoElement(new Atom[]{f.getAtomByID(12), f.getAtomByID(7), f.getAtomByID(8), f.… in testDoubleBondSupport4()
408 …nd(1, 2).setBondStereoElement(new Atom[]{f.getAtomByID(11), f.getAtomByID(1), f.getAtomByID(2), f.… in testDoubleBondSupport7()
409 …ond(3, 4).setBondStereoElement(new Atom[]{f.getAtomByID(2), f.getAtomByID(3), f.getAtomByID(4), f.… in testDoubleBondSupport7()
H A DFragmentTest.java45 fm.createBond(frag.getAtomByID(1), frag.getAtomByID(2), 1); in testAddBond()
127 assertEquals("ID 10 gets atom1", atom1, frag.getAtomByID(10)); in testGetAtomByID()
128 assertEquals("ID 20 gets atom2", atom2, frag.getAtomByID(20)); in testGetAtomByID()
129 assertNull("ID 42 is not present", frag.getAtomByID(42)); in testGetAtomByID()
138 fm.createBond(frag.getAtomByID(2), frag.getAtomByID(4), 2); in testFindBond()
139 fm.createBond(frag.getAtomByID(1), frag.getAtomByID(2), 1); in testFindBond()
140 fm.createBond(frag.getAtomByID(1), frag.getAtomByID(3), 3); in testFindBond()
161 fm.createBond(frag.getAtomByID(1), frag.getAtomByID(2), 1); in testGetChainLength()
166 fm.createBond(frag.getAtomByID(2), frag.getAtomByID(3), 1); in testGetChainLength()
171 fm.createBond(frag.getAtomByID(2), frag.getAtomByID(4), 1); in testGetChainLength()
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H A DComponentProcessorTest.java128 int parityBefore = f.getAtomByID(2).getAtomParity().getParity(); in testDLStereochemistryLOnAminoAcid()
131 assertEquals(parityBefore, f.getAtomByID(2).getAtomParity().getParity()); in testDLStereochemistryLOnAminoAcid()
140 int parityBefore = f.getAtomByID(2).getAtomParity().getParity(); in testDLStereochemistryDOnAminoAcid()
143 assertEquals(parityBefore, -f.getAtomByID(2).getAtomParity().getParity()); in testDLStereochemistryDOnAminoAcid()
154 assertEquals(null, f.getAtomByID(2).getAtomParity()); in testDLStereochemistryDLOnAminoAcid()
173 int parityBefore = f.getAtomByID(2).getAtomParity().getParity(); in testDLStereochemistryLOnCarbohydrate()
185 int parityBefore = f.getAtomByID(2).getAtomParity().getParity(); in testDLStereochemistryDOnCarbohydrate()
188 assertEquals(parityBefore, f.getAtomByID(2).getAtomParity().getParity()); in testDLStereochemistryDOnCarbohydrate()
198 int parityBefore = f.getAtomByID(2).getAtomParity().getParity(); in testDLStereochemistryInvertedNaturalOnCarbohydrate1()
201 assertEquals(parityBefore, f.getAtomByID(2).getAtomParity().getParity()); in testDLStereochemistryInvertedNaturalOnCarbohydrate1()
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/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/
H A DFragment.java196 Atom getAtomByID(int id) { in getAtomByID() method in Fragment
207 Atom a = getAtomByID(id); in getAtomByIDOrThrow()
466 Atom a =getAtomByID(b.getTo()); in getIntraFragmentIncomingValency()
471 Atom a =getAtomByID(b.getFrom()); in getIntraFragmentIncomingValency()
H A DBuildResults.java125 Atom outAtom =fragment.getAtomByID(id); in getAtomByIdOrThrow()
H A DFragmentManager.java247 Atom getAtomByID(int id) { in getAtomByID() method in FragmentManager
249 Atom a = f.getAtomByID(id); in getAtomByID()
264 Atom a = getAtomByID(id); in getAtomByIDOrThrow()
H A DStereochemistryHandler.java775 if (carbohydrate.getAtomByID(atom.getID())!=null){ in assignCarbohydratePrefixStereochem()
H A DStructureBuildingMethods.java1319 if (frag.getAtomByID(atom2.getID()) != null) {//check other atom is actually in the fragment! in findBondsToUnSaturate()
H A DComponentProcessor.java1416 …Atom anomericCarbon = carbohydrateFrag.getAtomByID(carbohydrateFrag.getIdOfFirstAtom() + Integer.p… in processCarbohydrates()
1428 …Atom potentialCarbonyl = carbohydrateFrag.getAtomByID(carbohydrateFrag.getIdOfFirstAtom() + Intege… in processCarbohydrates()