[Joelib-help] calculating properties

[Wayne V. <vol...@re...>]

I grabbed JOELib-bin-20031117 and some data from the nci database, as I
wanted to compare property calculations from JOELib to other
calculators.  I queried for all structures that had an experimental log
P associated with them, 3576 structures came back.
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I saw a number of discrepancies between what's calculated by JOELib and
what was recorded in the NCI dataset.  For example :
- In 16% of the cases # of rotational bonds disagreed
- In ~29% of the cases, Number_of_HBA2 disagreed with the number of
acceptors in the nci database
- In ~1% of the cases, Number_of_HBD1 disagreed with the number of
donors in the nci database
- JOELib logP had a correlation of 0.64 with the experimental log P
values; KOW & acd labs predictions in nci had correlations of 0.98 and
0.92
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Below is a snippet of the code I'm using-before I look any further at
the reasons for the differences noted above, could you let me know if
I'm using the library correctly?
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Thanks,
Wayne
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public class test {
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    public test() {
    }
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    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws Exception {
        SimpleReader sdfile =3D new SimpleReader(args[0]);
        JOEMol mol =3D new JOEMol();
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        PrintStream out =3D new PrintStream(new
FileOutputStream("out.dat"));
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        DescResult LogP =3D null;
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        out.println("E_NSC\tjoe_logP\tkow_LogP\texp_logP\tacd_logP");
        while (sdfile.readNext(mol)) {
            //System.out.println(mw.getDoubleValue(mol));
            LogP =3D DescriptorHelper.instance().descFromMol(mol, =
"LogP");
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            String kow_LogP =3D convert(mol.getData("E_LOGP"));
            String exp_LogP =3D convert(mol.getData("E_LOGP/2"));
            String acd_LogP =3D convert(mol.getData("E_LOGP/3"));
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            String nsc =3D mol.getData("E_NSC").toString();
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            out.print(nsc + "\t" + LogP  + "\t" + kow_LogP + "\t");
            out.println(exp_LogP + "\t" + acd_LogP);
        }
    }
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    static String convert(joelib.data.JOEGenericData in) {
        String result =3D "";
        if (in !=3D null) {
            result =3D in.toString().trim().substring(0,
in.toString().indexOf(' '
, 1));
        }
        if (result =3D=3D null) {
            return "";
        } else {
            return result;
        }
    }
}
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The "convert" function is used to clean off spaces & a zero appended to
the field containing the predicted log p values.  I don't know why the
sd file dump from the nci has that.
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