Need XML tags definitions and options for descriptors

Hello,

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

Regards

Please upload your XML configuration file here, and specify the standardizer actions you want to use. Pick the standardizer actions from this list: https://docs.chemaxon.com/display/standardizer/Standardizer+Actions

ello,

 

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.
            m.aromatize(MoleculeGraph.AROM_GENERAL);
                
            // Call ambigous aromatization method
            m.aromatize(MoleculeGraph.AROM_AMBIGUOUS);
            

           

            // 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
            Hydrogenize.convertExplicitHToImplicit(largestFrag);
            
            
           
                 
             largestFrag.setName(m.getProperty("EntryID"));

                        

             // 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
            ecfp.doFP(largestFrag);   

            txtBit = ecfp.fpBinary();

Hello,

 

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"/>

 

Regards

Yes, that's right. For more explicit hydrogen removal options see https://docs.chemaxon.com/display/standardizer/Remove+Explicit+Hydrogens