/** * This method uses generateCoordinates, but it removes the hydrogens first, * lays out the structure and then adds them again. * * @throws CDKException if an error occurs * @see #generateCoordinates * @deprecated use {@link #generateCoordinates()} */ @Deprecated public void generateExperimentalCoordinates() throws CDKException { generateExperimentalCoordinates(DEFAULT_BOND_VECTOR); }
/** * This method uses generateCoordinates, but it removes the hydrogens first, * lays out the structure and then adds them again. * * @throws CDKException if an error occurs * @see #generateCoordinates * @deprecated use {@link #generateCoordinates()} */ @Deprecated public void generateExperimentalCoordinates() throws CDKException { generateExperimentalCoordinates(DEFAULT_BOND_VECTOR); }
/** * Tests case where calling generateExperimentalCoordinates threw an NPE. * * @cdk.bug 1269 */ @Test(timeout = 5000) public void testBug1269() throws Exception { SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance()); String smiles = "O=C(O)[C@H](N)C"; // L-alanine, but any [C@H] will do IAtomContainer mol = sp.parseSmiles(smiles); SDG.setMolecule(mol); SDG.generateExperimentalCoordinates(new Vector2d(0, 1)); }