Re: [Cdk-user] NullPointerException when generating SMILES From Fragments contai ning R atoms

[Egon W. <eg...@sc...>]

On Tuesday 06 January 2004 11:33, nic...@sy... wrote:
> When I try to generate SMILE from molecule object which contains an R-atom
> (pseudoAtom R), I obtain a NullPointerException message. If I do this via a
> MOL File, I obtain the following response:
>
> Exception in thread "main" java.lang.NullPointerException
>         at
> org.openscience.cdk.smiles.SmilesGenerator.generateMassString(SmilesGenerat
>o r.java:1387)
>
> This kind of File works:
>
>   CDK
>
>   2  1  0  0  0  0  0  0  0  0999 V2000
>     0.5878   -0.6893    0.3173 O   0  0  0  0  0  0  0  0  0  0  0  0
>     0.0784   -1.2284    0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  1  0  0  0
>
> But this doesn't works:
>
>   CDK
>
>   2  1  0  0  0  0  0  0  0  0999 V2000
>     0.5878   -0.6893    0.3173 R   0  0  0  0  0  0  0  0  0  0  0  0
>     0.0784   -1.2284    0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  1  0  0  0
>
> Is anybody have a solution to create SMILE From molecule which contains
> R-atoms ?

SMILES has a '*' element... this could be used for pseudo atoms... If that 
sounds reasonable, then I'll make the appropriate changes in the source 
code...

Egon