/** * 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; }
throw new CDKException("Could not build HOSECode from atom " + i + " due to " + ex1.toString(), ex1); hoseCode = removeAromaticityFlagsFromHoseCode(hoseCode);
throw new CDKException("Could not build HOSECode from atom " + i + " due to " + ex1.toString(), ex1); hoseCode = removeAromaticityFlagsFromHoseCode(hoseCode);
/** * 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; }
@Override public void calculateCharges(IAtomContainer container) throws CDKException { try { this.setInitialCharges(container); } catch (Exception exception) { throw new CDKException("Could not calculate Gasteiger-Marsili PEPE charges: " + exception.getMessage(), exception); } } }
@Override public void calculateCharges(IAtomContainer container) throws CDKException { try { this.setInitialCharges(container); } catch (Exception exception) { throw new CDKException("Could not calculate Gasteiger-Marsili PEPE charges: " + exception.getMessage(), exception); } } }