Implement logD calculation method

[AATDev21]

We need to implement calculation method for logD - a distribution coefficient widely used to measure the lipophilicity of ionizable compounds, where the partition is a function of the pH. LogD is a better descriptor of the lipophilicity of a molecule, because the majority of known drugs contain ionisable groups and are likely to be charged at physiological pH, while logP only correctly describes the partition coefficient of neutral (uncharged) molecules. For non-ionizable compounds LogP = LogD throughout pH range, whereas for ionizable compounds LogD takes into account the partition of both ionized and non-ionized forms (see picture below).

Prediction of logD is more difficult, as it involves both estimation of logP and estimation of acid and base pKa constants of the compound. We have already a method for logP calculation. For pKa recently implemented Lee-Crippen SMARTS pKa calculation method can be used.