/** * Gets the polarizabilitiyFactorForAtom. * *@param atomContainer AtomContainer *@param atom atom for which the factor should become known *@return The polarizabilitiyFactorForAtom value */ public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom) { IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); return getKJPolarizabilityFactor(acH, atom); }
/** * Gets the polarizabilitiyFactorForAtom. * *@param atomContainer AtomContainer *@param atom atom for which the factor should become known *@return The polarizabilitiyFactorForAtom value */ public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom) { IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); return getKJPolarizabilityFactor(acH, atom); }
/** * calculate bond polarizability. * *@param atomContainer AtomContainer *@param bond Bond bond for which the polarizabilitiy should be calculated *@return polarizabilitiy */ public double calculateBondPolarizability(IAtomContainer atomContainer, IBond bond) { double polarizabilitiy = 0; IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); if (bond.getAtomCount() == 2) { polarizabilitiy += getKJPolarizabilityFactor(acH, bond.getBegin()); polarizabilitiy += getKJPolarizabilityFactor(acH, bond.getEnd()); } return (polarizabilitiy / 2); }
double bond; polarizabilitiy += getKJPolarizabilityFactor(acH, atom); for (int i = 0; i < acH.getAtomCount(); i++) { if (!acH.getAtom(i).equals(atom)) { bond = distanceMatrix[atomIndex][i]; if (bond == 1) { polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i)); } else { polarizabilitiy += (Math.pow(0.5, bond - 1) * getKJPolarizabilityFactor(acH, acH.getAtom(i)));
/** * calculate bond polarizability. * *@param atomContainer AtomContainer *@param bond Bond bond for which the polarizabilitiy should be calculated *@return polarizabilitiy */ public double calculateBondPolarizability(IAtomContainer atomContainer, IBond bond) { double polarizabilitiy = 0; IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); if (bond.getAtomCount() == 2) { polarizabilitiy += getKJPolarizabilityFactor(acH, bond.getBegin()); polarizabilitiy += getKJPolarizabilityFactor(acH, bond.getEnd()); } return (polarizabilitiy / 2); }
double bond; polarizabilitiy += getKJPolarizabilityFactor(acH, atom); for (int i = 0; i < acH.getAtomCount(); i++) { if (!acH.getAtom(i).equals(atom)) { bond = PathTools.breadthFirstTargetSearch(acH, startAtom, acH.getAtom(i), 0, influenceSphereCutOff); if (bond == 1) { polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i)); } else { polarizabilitiy += (Math.pow(0.5, bond - 1) * getKJPolarizabilityFactor(acH, acH.getAtom(i)));
double bond; polarizabilitiy += getKJPolarizabilityFactor(acH, atom); for (int i = 0; i < acH.getAtomCount(); i++) { if (!acH.getAtom(i).equals(atom)) { bond = PathTools.breadthFirstTargetSearch(acH, startAtom, acH.getAtom(i), 0, influenceSphereCutOff); if (bond == 1) { polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i)); } else { polarizabilitiy += (Math.pow(0.5, bond - 1) * getKJPolarizabilityFactor(acH, acH.getAtom(i)));
polarizabilitiy += getKJPolarizabilityFactor(acH, atom); for (int i = 0; i < acH.getAtomCount(); i++) { if (!acH.getAtom(i).equals(atom)) { bond = distanceMatrix[atomIndex][i]; if (bond == 1) { polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i)); } else { polarizabilitiy += (Math.pow(0.5, bond - 1) * getKJPolarizabilityFactor(acH, acH.getAtom(i)));
/** * calculates the mean molecular polarizability as described in paper of Kang and Jhorn. * *@param atomContainer AtomContainer *@return polarizabilitiy */ public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer) { double polarizabilitiy = 0; IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); for (int i = 0; i < acH.getAtomCount(); i++) { polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i)); } return polarizabilitiy; }
/** * calculates the mean molecular polarizability as described in paper of Kang and Jhorn. * *@param atomContainer AtomContainer *@return polarizabilitiy */ public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer) { double polarizabilitiy = 0; IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); for (int i = 0; i < acH.getAtomCount(); i++) { polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i)); } return polarizabilitiy; }