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Need XML tags definitions and options for descriptors
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seijo

Joined: 30 Jul 2010
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Link to postPosted: Wed Jul 16, 2014 4:58 pmPost subject: Need XML tags definitions and options for descriptors Reply with quote

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

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
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Link to postPosted: Thu Jul 17, 2014 11:53 amPost subject: Reply with quote

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

seijo

Joined: 30 Jul 2010
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Link to postPosted: Thu Jul 17, 2014 12:12 pmPost subject: Reply with quote

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[i].getAtomCount() > largestFrag.getAtomCount()) {
                  largestFrag = frags[i];
               }
            }
            
            // 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();

seijo

Joined: 30 Jul 2010
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Link to postPosted: Thu Jul 17, 2014 2:49 pmPost subject: Reply with quote

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

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
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Link to postPosted: Thu Jul 17, 2014 3:27 pmPost subject: Reply with quote

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

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