Need XML tags definitions and options for descriptors

User 8052c55234

16-07-2014 15:58:11


I am missing XML documentation files for fingerprint descriptors. I would like to see all the options which exists to adapt it to our project.

Is there any document on this way?


I actually specifically need an equivalent tag in <StandardizerConfiguration Version="0.1">
        <Actions> to the API options:Hydrogenize.convertExplicitHToImplicit(m); which is different than <RemoveExplicitH ID="RemoveExplicitH" Groups="target"/>

But we need to test other differents options.

By advance, thank you


ChemAxon e08c317633

17-07-2014 10:53:16

Please upload your XML configuration file here, and specify the standardizer actions you want to use. Pick the standardizer actions from this list:

User 8052c55234

17-07-2014 11:12:17



I would like to reproduce the API command hereafter with xml andperhaps increased different possibilities to avoid any differences:

I saw differences when I simply do :


            // General (Daylight conform) aromatization.
            // Call ambigous aromatization method


            // Keep the largest fragment
            final Molecule [] frags = m.convertToFrags();
            Molecule largestFrag = frags[0];
            for (int i = 1; i < frags.length; i++) {
               if (frags.getAtomCount() > largestFrag.getAtomCount()) {
                  largestFrag = frags;
            // Dehydrogenize read structure
            //Convert explicit Hydrogen atoms of the molecule to implicit.
            //Same as convertExplicitHToImplicit(m, MolAtom.LONELY_H | MolAtom.WEDGED_H).
            //Besides lonely and wedged H atoms, bound (to non-Hydrogen atom and
            //without Hydrogen bond), non-isotope, neutral, non-radical,
            //non-mapped H atoms are also removed


             // Print info
        //     System.err.println("Read mol: " + inputBuilder.size() + " name: " + largestFrag.getName());
            // Instantiate default descriptor parameters and descriptors        
            FP_EC ecfp = new FP_EC ();

            // Generate descriptors for the molecule

            txtBit = ecfp.fpBinary();

User 8052c55234

17-07-2014 13:49:11



ok, I've got it:

The API command Hydrogenize.convertExplicitHToImplicit(largestFrag);

is equivalent in an xml file as:

<RemoveExplicitH ID="RemoveExplicitH" Lonely="true" Wedged="true"/>



ChemAxon e08c317633

17-07-2014 14:27:59

Yes, that's right. For more explicit hydrogen removal options see