Hit Alignment off and SIMILARITY search mode

HItDisplayTool seems to ignore the ALIGNMENT_OFF option when using the SIMILARITY search option.  It always aligns to the query molecule.  Is there any way to force similarity to not align the result molecule?

    Molecule molecule = null;

    String alignTo = "CN1C2=C(N=CN2)C(=O)N(C)C1=O";
    HitColoringAndAlignmentOptions hco = new HitColoringAndAlignmentOptions();
    hco.setAlignmentMode(HitColoringAndAlignmentOptions.ALIGNMENT_OFF);

    MolHandler mh = new MolHandler(alignTo.getBytes());


    Molecule query = mh.getMolecule();


    MolHandler mh2 = new MolHandler(input);  // input is the target Molecule object


    Molecule target = mh2.getMolecule();


    MolSearchOptions mso = new MolSearchOptions(SearchConstants.SIMILARITY);


    HitDisplayTool hdt = new HitDisplayTool(hco, mso, null, query);


    molecule = hdt.getHit(target);

Hi John!

I have moved your issue to the JChem forum, because the HitdisplayTool belongs to the JChem. 
My colleagues will answer for you soon.

Regards,
Mate

 

Hi John,

 

We could reproduce this issue. It seems to be a bug, the alignment parameter is indeed ignored.

We will fix it in an upcoming release.

 

Best regards,

Szabolcs

Hi John,

thank you for reporting this issue. The fix will be delivered in version 5.11 expected to be released around 7th September 2012.

Kind regards,

Adrian

Thanks for following up.

Hi John,

I am wondering, if there is any specific reason not to align the result molecules? Do you have any suggestions that would be favorable to similarity functionalities?

Thank you,

Miklos