Re: [Cdk-devel] CDK generates wrong formula

[Ralf T. <rta...@sc...>]

I just found that

a) the problem also occurs with SMILE strings
b) it seems like it was re-introduced, or got much worse with newer 
versions of CDK

rcdk_3.0.1 / rcdklibs_1.3.6.1 :

library(rcdk)
betaDGlucose1 <- "[C@H]1([C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)CO"

mols <- parse.smiles(betaDGlucose1)[[1]]
do.aromaticity(mols)
do.typing(mols)
do.isotopes(mols)
convert.implicit.to.explicit(mols)
get.mol2formula(mols)

cdkFormula:  C6H24O6 , mass =  192.1573 , charge =  0


rcdk_2.9.6  / rcdklibs_1.2.3

...

cdkFormula:  C6H12O6 , mass =  180.0634 , charge =  0


Regards,
Ralf.

On 09/19/2010 02:05 PM, Ralf Tautenhahn wrote:
> Hi Egon,
>
> Unfortunately, we see this problem with more than one file.
>
> Ralf.
>
> On 09/19/2010 01:21 PM, Egon Willighagen wrote:
>    
>> Hi Ralf,
>>
>> On Sun, Sep 19, 2010 at 10:15 PM, Ralf Tautenhahn<rta...@sc...>   wrote:
>>
>>      
>>> So it has twice as much hydrogens as it should have.
>>>
>>>        
>> Yeah, I have heard about such situations before... just wondering, is
>> this the only file that gives this problem?
>>
>> That would suggest it depends on the MDL molfile, which I would not
>> have expected...
>>
>> Egon
>>
>>
>>
>>      
>