Re: [Cdk-devel] Help with PseudoAtom CO2H

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Hi John, 
thanks for the quick answer, and yes, I also came across 
efficientbits.blogspot minutes ago :-)

My input is sort-of a molfile, embedded into 
a Bruker MS/MS library file. And yes, I have 

	[...]
	A   57
	CO2H
	[...]
	M  END

So I am inclined to tell the authors to do the COOH explicitly, 
since this complicates everything downstream, unless you had 
a fix to expand CO2H to O=C-O-H in CDK itself. And still ...

Yours, 
Steffen

On Mo, 2016-12-05 at 11:28 +0000, John M wrote:
> Hi Steffen,
> 
> An interesting question that I've actually been thinking about
> recently. Is the input from a Molfile? In short the answer is no it's
> not supported yet and it's better keep formats sane but it's
> potentially a useful feature to support. Explanation:
> 
> We support the semantically correct way of doing this which is with
> SGroups. Here the abbreviation is merely a display shortcut and the
> full atom representation is present, here's one from ChemDraw:
>  
> > Untitled Document-1
> >   ChemDraw12051610002D
> 
>   5  4  0  0  0  0  0  0  0  0999 V2000
>    -0.3572   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.3572    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
>     1.0717   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
>   3  4  2  0      
>   3  5  1  0      
>   1  3  1  0      
>   1  2  2  0      
> M  STY  1   1 SUP
> M  SLB  1   1   1
> M  SAL   1  3   3   4   5
> M  SBL   1  1   3
> M  SMT   1 CO2H
> M  SBV   1   3   -0.7145   -0.4125
> M  END
> More info here: http://efficientbits.blogspot.co.uk/2015/11/bringing-
> molfile-sgroups-to-cdk.html
> 
> I'm guessing you have something like this:
>  
> > Untitled Document-1
> 
>   ChemDraw12051610082D
> 
>   3  2  0  0  0  0  0  0  0  0999 V2000
>     0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  0      
>   1  3  2  0      
> A    2
> CO2H
> M  END
> It's a relatively common for tools to presume these are simply
> labelled super atoms. A little flexibility causes a lot of problem,
> It's gets a lot more fun with di and trivalent labels, e.g. PEG
> -CH2CH2O- or a peptide -Cys<. I've seen a few presentations recently
> where a SMILES like notation is used for peptides, although it kind
> of works it gets messy very quickly with gamma linked or modified
> peptides etc.
> 
> The canonical implementation of Molfile support is BIOVIA (from
> Accelrys (from Symyx (from MDL)). In their old tools (I can go back
> as far as Symyx draw 2.5) they actually read it in and automatically
> expand some simple abbreviations. I've learnt from Andrew Dalke this
> is what is known as 'Librarian Mode'. Curiously CO2H isn't supported
> but it's clearly unambiguous.
> 
> John
> 
> On 5 December 2016 at 08:54, Steffen Neumann <sne...@ip...>
> wrote:
> > Hi,
> > 
> > I have ported some code from CDK-1.3.5 to 1.5.14, and ran into the
> > NPE 
> > mentioned in https://sourceforge.net/p/cdk/mailman/message/32890027
> > /
> > 
> > So I added Isotopes.getInstance().configureAtoms(container);
> > and find for some molecules the PseudoAtom CO2H,
> > which seems to be a carboxyl group COOH.
> > 
> > Question: Should I coax the molfile/structure provider to change 
> > this into COOH, or can I teach CDK that this is actually 
> > nothing special, and (somehow) write a PseudoAtom() 
> > for this ? In the latter case, how would I do this ?
> > Pointers to the documentation with examples welcome :-)
> > 
> > Thanks in advance, 
> > Yours,
> > Steffen
> > 
> > java.lang.IllegalArgumentException: Cannot configure 
> > an unrecognized element: PseudoAtom(2107853606, CO2H,
> > Atom(2107853606,
> > S:CO2H, H:0, SP:0, 2D:[(21.7612, -17.5386)], AtomType(2107853606,
> > FC:0,
> > EV:1, Isotope(2107853606, Element(2107853606, S:CO2H, AN:0)))))
> > 
> > 
> > 
> > --
> > IPB Halle                    AG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle                       +49 (0) 345 5582 - 0           
> > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> > 
> > 
> > 
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IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409