/** * Constructor for the BondPartialTChargeDescriptor object. */ public BondPartialTChargeDescriptor() { peoe = new GasteigerMarsiliPartialCharges(); pepe = new GasteigerPEPEPartialCharges(); }
/** * calculate the electronegativity of orbitals sigma. * * @param ac IAtomContainer * @param atom atom for which effective atom electronegativity should be calculated * * @return piElectronegativity */ public double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom) { return calculateSigmaElectronegativity(ac, atom, maxI, maxRS); }
/** * Constructor for the Electronegativity object. * * @param maxIterations The maximal number of Iteration * @param maxResonStruc The maximal number of Resonance Structures */ public Electronegativity(int maxIterations, int maxResonStruc) { peoe = new GasteigerMarsiliPartialCharges(); maxI = maxIterations; maxRS = maxResonStruc; }
/** * Constructor for the BondPartialPiChargeDescriptor object. */ public BondPartialPiChargeDescriptor() { pepe = new GasteigerPEPEPartialCharges(); }
/** * calculate the electronegativity of orbitals pi. * * @param ac IAtomContainer * @param atom atom for which effective atom electronegativity should be calculated * * @return piElectronegativity */ public double calculatePiElectronegativity(IAtomContainer ac, IAtom atom) { return calculatePiElectronegativity(ac, atom, maxI, maxRS); }
/** * Constructor for the BondSigmaElectronegativityDescriptor object. */ public BondSigmaElectronegativityDescriptor() { electronegativity = new Electronegativity(); }
/** * Constructor for the EffectiveAtomPolarizabilityDescriptor object */ public EffectiveAtomPolarizabilityDescriptor() { pol = new Polarizability(); }
/** * Constructor for the PiElectronegativityDescriptor object */ public PiElectronegativityDescriptor() { electronegativity = new PiElectronegativity(); }
/** * Constructor for the StabilizationPlusChargeDescriptor object */ public StabilizationPlusChargeDescriptor() { stabil = new StabilizationCharges(); }
/** * Sets initial charges for atom types. * +1 for cationic atom types * -1 for anionic atom types * carboxylic oxygen -0.5 * phosphorylic oxygen -0.66 * sulfanilic oxygen -0.5 * or to formal charge (which must be determined elsewhere or set manually) * polycations are not handled by this approach * *@param atomContainer AtomContainer *@return AtomContainer with set charges *@exception Exception Description of the Exception */ public IAtomContainer setCharges(IAtomContainer atomContainer) throws Exception { atomContainer = setInitialCharges(atomContainer); return atomContainer; }
/** * Constructor for the Electronegativity object. * * @param maxIterations The maximal number of Iteration * @param maxResonStruc The maximal number of Resonance Structures */ public PiElectronegativity(int maxIterations, int maxResonStruc) { peoe = new GasteigerMarsiliPartialCharges(); pepe = new GasteigerPEPEPartialCharges(); maxI = maxIterations; maxRS = maxResonStruc; }
/** * Constructor for the PartialSigmaChargeDescriptor object */ public PartialSigmaChargeDescriptor() { peoe = new GasteigerMarsiliPartialCharges(); }
/** * calculate the electronegativity of orbitals sigma. * * @param ac IAtomContainer * @param atom atom for which effective atom electronegativity should be calculated * * @return piElectronegativity */ public double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom) { return calculateSigmaElectronegativity(ac, atom, maxI, maxRS); }
/** * Constructor for the PartialPiChargeDescriptor object */ public PartialPiChargeDescriptor() { pepe = new GasteigerPEPEPartialCharges(); }
/** * calculate the electronegativity of orbitals pi. * * @param ac IAtomContainer * @param atom atom for which effective atom electronegativity should be calculated * * @return piElectronegativity */ public double calculatePiElectronegativity(IAtomContainer ac, IAtom atom) { return calculatePiElectronegativity(ac, atom, maxI, maxRS); }
/** * Constructor for the SigmaElectronegativityDescriptor object */ public SigmaElectronegativityDescriptor() { electronegativity = new Electronegativity(); }
/** * Constructor for the Electronegativity object. * * @param maxIterations The maximal number of Iteration * @param maxResonStruc The maximal number of Resonance Structures */ public PiElectronegativity(int maxIterations, int maxResonStruc) { peoe = new GasteigerMarsiliPartialCharges(); pepe = new GasteigerPEPEPartialCharges(); maxI = maxIterations; maxRS = maxResonStruc; }
/** * Constructor for the BondPartialSigmaChargeDescriptor object. */ public BondPartialSigmaChargeDescriptor() { peoe = new GasteigerMarsiliPartialCharges(); }
/** * Constructor for the PartialTChargePEOEDescriptor object */ public PartialTChargePEOEDescriptor() { peoe = new GasteigerMarsiliPartialCharges(); pepe = new GasteigerPEPEPartialCharges(); }
/** * Constructor for the Electronegativity object. * * @param maxIterations The maximal number of Iteration * @param maxResonStruc The maximal number of Resonance Structures */ public Electronegativity(int maxIterations, int maxResonStruc) { peoe = new GasteigerMarsiliPartialCharges(); maxI = maxIterations; maxRS = maxResonStruc; }