@Override public int getAttachPointNum() { return pseudo.getAttachPointNum(); }
@Override public int getAttachPointNum() { return pseudo.getAttachPointNum(); }
/** * Determine if an atom is an attach point. * * @param atom potential attach point atom * @return the atom is an attachment point */ private boolean isAttachPoint(IAtom atom) { return atom instanceof IPseudoAtom && ((IPseudoAtom) atom).getAttachPointNum() > 0; }
@Override public int getAttachPointNum() { return pseudo.getAttachPointNum(); }
@Override public int getAttachPointNum() { return pseudo.getAttachPointNum(); }
if (pseudo.getAttachPointNum() > 0) { state.atomLabels.put(idx, "_AP" + pseudo.getAttachPointNum()); } else { if (!"*".equals(pseudo.getLabel()))
@Test public void attachPoints() throws InvalidSmilesException { IAtomContainer mol = smipar.parseSmiles("**.c1ccccc1CC |$;;;;;;;;;_AP1$|"); assertThat(mol.getAtom(9), is(instanceOf(IPseudoAtom.class))); assertThat(((IPseudoAtom) mol.getAtom(9)).getAttachPointNum(), is(1)); }
@Test public void markushFragment() throws InvalidSmilesException { IAtomContainer mol = smipar.parseSmiles("**.c1ccccc1CC |m:1:2.3.4.5.6.7,Sg:n:8:m:ht,$R';;;;;;;;;_AP1$|"); List<Sgroup> sgroups = mol.getProperty(CDKConstants.CTAB_SGROUPS); // P-var and F-var assertThat(sgroups.size(), is(2)); // atom-labels assertThat(mol.getAtom(0), is(instanceOf(IPseudoAtom.class))); assertThat(((IPseudoAtom) mol.getAtom(0)).getLabel(), is("R'")); // attach-points assertThat(mol.getAtom(9), is(instanceOf(IPseudoAtom.class))); assertThat(((IPseudoAtom) mol.getAtom(9)).getAttachPointNum(), is(1)); assertThat(mol.getTitle(), is("")); }
int attachNum = ((IPseudoAtom) atom).getAttachPointNum(); if (attachNum > 0) attachPoints.add((IPseudoAtom) atom); int attachNum = atom.getAttachPointNum();
if (atom instanceof IPseudoAtom && ((IPseudoAtom) atom).getAttachPointNum() == 1) { begAttach = atom; break;
if (atom instanceof IPseudoAtom && ((IPseudoAtom) atom).getAttachPointNum() == 1) { begAttach = atom; break;
if (atom instanceof IPseudoAtom) { IPseudoAtom pAtom = (IPseudoAtom) atom; if (pAtom.getAttachPointNum() <= 0) { if (pAtom.getLabel().equals("*")) { int mass = unboxSafely(pAtom.getMassNumber(), 0);