[Cdk-devel] CDK generates wrong formula

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

Dear CDK developers,

I have problems generating the correct formula using the attached molfile.

The formula (r)CDK generates here is C35H128N3O21P3S,
the actual formula would be C35H64N3O21P3S.

So it has twice as much hydrogens as it should have.

Any idea why this might happen ?

I am using rcdk 2.9.23, with rcdklibs_1.3.4.2.

Can anybody reproduce this problem using CDK directly ?

Thanks,
Ralf.

      library(rcdk)

      mol <- load.molecules("45002.mol")[[1]]

      do.aromaticity(mol)
      do.typing(mol)
      do.isotopes(mol)

      convert.implicit.to.explicit(mol)

      formula <- get.mol2formula(mol ,charge=0)

     ## Here it generates formula: C35H128N3O21P3S, instead of 
C35H64N3O21P3S.



  > sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
   [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rcdk_2.9.23      iterators_1.0.3  png_0.1-1        fingerprint_3.2
[5] rcdklibs_1.3.4.2 rJava_0.8-4