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support for D and T in formula
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mpustelnik

Joined: 02 Jul 2002
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Link to postPosted: Tue Mar 25, 2008 3:21 amPost subject: support for D and T in formula Reply with quote

Could you please add the support for common isotope alias i.e. D and T? Presently the call to from MoleculeGraph.getFormula() represents D as H. We have tested other chemical drawing tools and they display formula with D (ISIS Draw, ACD Labs sketch, Chemdraw).
Gyorgy
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Link to postPosted: Tue Mar 25, 2008 2:41 pmPost subject: Reply with quote

Please call the "isotopeFormula()" method of the ElementalAnalyser class. It will calculate the isotopic formula with D and T symbols by default.
mpustelnik

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Link to postPosted: Wed Mar 26, 2008 9:09 amPost subject: not expected results Reply with quote

We would like to see the alias i.e. D not [2H] which is more common in the other chemical drawing packages.
Gyorgy
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Link to postPosted: Wed Mar 26, 2008 11:54 amPost subject: Reply with quote

That's fine. The isotopeFormula() function of the ElementalAnalyser class just produces the formula using the D symbol as you wish it. That's the default behaviour.

MoleculeGraph.getFormula calculates the chemical formula and it does not distinguish isotopes. No isotopeFormula function is avaliable in the MoleculeGraph class, but there is the ElementalAnalyser class for this purpose.
Gyorgy
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Link to postPosted: Wed Mar 26, 2008 1:40 pmPost subject: Reply with quote

Just one remark. This functionality appeared first in version 5.0, maybe you have an older version...

Last edited by Gyorgy on Thu Mar 27, 2008 7:17 am; edited 1 time in total
mpustelnik

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Link to postPosted: Thu Mar 27, 2008 1:29 amPost subject: Reply with quote

What is the call to do this doing the jchem oracle cartridge? I tried jcf_evaluate(smiles,'isotopeformula') but this did not work.
Szabolcs
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Link to postPosted: Thu Mar 27, 2008 10:15 amPost subject: Reply with quote

You are right, that should be it, but it still uses the old default. We will fix it in the next minor release, 5.0.3., which is due in the middle of April.
Gyorgy
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Link to postPosted: Thu Mar 27, 2008 10:23 amPost subject: Reply with quote

Oh, are you calling the cartridge function? Now I understand. Unfortunately, the default behavior of the plugin (accessed by the cartridge) is different from the default behavior of the ElementalAnalyser class. We will change the default of the plugin as Szabolcs said and then it will work as you expect. We will provide an optional parameter for the plugin to generate the the old-style deuterium and tritium representation as well.
peter
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Link to postPosted: Thu Mar 27, 2008 10:41 amPost subject: Reply with quote

One minor remark about JChem Cartridge-related syntax:

jcf_evaluate returns number. For Chemical Terms expressions evaluating to strings, the jcf_evaluate_x function is available. Example:

Code:
select jcf_evaluate_x(structure, 'chemTerms:isotopeformula') from mytable
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