/** * Constructor for the EffectiveAtomPolarizabilityDescriptor object */ public EffectiveAtomPolarizabilityDescriptor() { pol = new Polarizability(); }
private static double[] listpolarizability(IAtomContainer container, int[][] dmat) throws CDKException { int natom = container.getAtomCount(); double[] polars = new double[natom]; Polarizability polar = new Polarizability(); for (int i = 0; i < natom; i++) { IAtom atom = container.getAtom(i); try { polars[i] = polar.calculateGHEffectiveAtomPolarizability(container, atom, false, dmat); } catch (Exception ex1) { throw new CDKException("Problems with assign Polarizability due to " + ex1.toString(), ex1); } } return polars; }
private static double[] listpolarizability(IAtomContainer container, int[][] dmat) throws CDKException { int natom = container.getAtomCount(); double[] polars = new double[natom]; Polarizability polar = new Polarizability(); for (int i = 0; i < natom; i++) { IAtom atom = container.getAtom(i); try { polars[i] = polar.calculateGHEffectiveAtomPolarizability(container, atom, false, dmat); } catch (Exception ex1) { throw new CDKException("Problems with assign Polarizability due to " + ex1.toString(), ex1); } } return polars; }
/** * A unit test for JUnit with n,n-dimethyl ethylendiamine */ @Test public void testCalculateBondPolarizability_IAtomContainer_IBond() throws Exception { Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("NCCN(C)(C)"); double result = pol.calculateBondPolarizability((IAtomContainer) mol, mol.getBond(0)); Assert.assertFalse(Double.isNaN(result)); }
/** * A unit test for JUnit */ @Test public void testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom() throws Exception { Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("NCCN(C)(C)"); double result = pol.getPolarizabilitiyFactorForAtom(mol, mol.getAtom(0)); Assert.assertFalse(Double.isNaN(result)); result = pol.getPolarizabilitiyFactorForAtom(mol, mol.getAtom(3)); Assert.assertFalse(Double.isNaN(result)); }
/** * A unit test for JUnit with methane */ @Test public void testCalculateKJMeanMolecularPolarizability() throws Exception { double testResult = 2.61; Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("C"); double result = pol.calculateKJMeanMolecularPolarizability(mol); Assert.assertEquals(testResult, result, 0.01); }
/** * A unit test for JUnit with Isopentyl iodide */ @Test public void testcalculateGHEffectiveAtomPolarizability_Isopentyl_iodide() throws Exception { double testResult = 8.69; /* from thesis Wolfgang Hanebeck, TUM */ Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("C(C)(C)CCI"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(5), 100, true); Assert.assertEquals(testResult, result, 0.01); }
/** * A unit test for JUnit with Ethyl chloride */ @Test public void testcalculateGHEffectiveAtomPolarizability_Ethyl_chloride() throws Exception { double testResult = 4.62; /* from thesis Wolfgang Hanebeck, TUM */ Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("CCCl"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(2), 100, true); Assert.assertEquals(testResult, result, 0.01); }
/** * A unit test for JUnit with Ethoxy ethane */ @Test public void testcalculateGHEffectiveAtomPolarizability_Ethoxy_ethane() throws Exception { double testResult = 5.21; /* from thesis Wolfgang Hanebeck, TUM */ Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("CCOCC"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(2), 100, true); Assert.assertEquals(testResult, result, 0.01); }
/** * A unit test for JUnit with Allyl bromide */ @Test public void testcalculateGHEffectiveAtomPolarizability_Allyl_bromide() throws Exception { double testResult = 6.17; /* from thesis Wolfgang Hanebeck, TUM */ Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("C=CCBr"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(3), 100, true); Assert.assertEquals(testResult, result, 0.01); }
/** * A unit test for JUnit with Allyl mercaptan */ @Test public void testcalculateGHEffectiveAtomPolarizability_Allyl_mercaptan() throws Exception { double testResult = 6.25; /* from thesis Wolfgang Hanebeck, TUM */ Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("C=CCS"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(3), 100, true); Assert.assertEquals(testResult, result, 0.01); } }
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges(); GasteigerPEPEPartialCharges pepe = new GasteigerPEPEPartialCharges(); Polarizability pol = new Polarizability(); StabilizationCharges stabil = new StabilizationCharges(); StructureResonanceGenerator gRI = new StructureResonanceGenerator();
/** * A unit test for JUnit with n,n-dimethyl ethylendiamine */ @Test public void testCalculateGHEffectiveAtomPolarizability_IAtomContainer_IAtom_Int_Boolean() throws Exception { double[] testResult = {4.73, 6.92}; Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("NCCN(C)(C)"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(0), 100, true); Assert.assertEquals(testResult[0], result, 0.01); result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(3), 100, true); Assert.assertEquals(testResult[1], result, 0.01); }
/** * A unit test for JUnit with Ethanolamine */ @Test public void testcalculateGHEffectiveAtomPolarizability_Ethanolamine() throws Exception { double[] testResult = {4.26, 3.60}; /* * from thesis Wolfgang Hanebeck, * TUM */ Polarizability pol = new Polarizability(); SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = sp.parseSmiles("NCCO"); double result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(3), 100, true); Assert.assertEquals(testResult[1], result, 0.01); result = pol.calculateGHEffectiveAtomPolarizability(mol, mol.getAtom(0), 100, true); Assert.assertEquals(testResult[0], result, 0.01); }
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges(); GasteigerPEPEPartialCharges pepe = new GasteigerPEPEPartialCharges(); Polarizability pol = new Polarizability(); StabilizationCharges stabil = new StabilizationCharges(); StructureResonanceGenerator gRI = new StructureResonanceGenerator();
Polarizability pol = new Polarizability(); counter = 0; for (int i = 0; i < molecule.getAtomCount(); i++) {
Polarizability pol = new Polarizability(); counter = 0; for (int i = 0; i < molecule.getAtomCount(); i++) {