[Joelib-devel] LogP and MolarRefractivity

[<chr...@ba...>]

Hi all,

I have a question regarding the descriptors LogP and MolarRefractivity:

If I calculate these descriptors for the molecule Oc1ccccc1OC  (which is also
used
in the class GroupContributionTest) using a 3D-structure (see file "tst.sdf"
attached at the end of the mail)
with the command:

convert.sh +d tst.sdf

I get the following wrong results:

>  <MolarRefractivity>
4.3751E1
>  <LogP>
2.2822


But if I delete all H-Atoms by using:
convert.sh -h +d tst.sdf

I get the following results,
which are correct according to the information in GroupContributionTest:

>  <MolarRefractivity>
3.46588E1
>  <LogP>
1.4007999999999998

My question is: Why do I get the wrong results, if I do not delete the H-Atoms?
Do I am on the save side, if I always delete H-Atoms when using a
group contribution method??
(For the "PolarSurfaceArea" it seems, that it doesn't matter if I use "-h" or
not.....)

(By the way, I've used version 2003-08-04)

All the best and thank you very much in advance,
Christoph Niederalt
_________________________________________
Bayer Technology Services GmbH
PT-AS-CS
Leverkusen, K  9
Tel.: +49 (0)214 30 75414
Fax:  +49 (0)214 30 64801
E-Mail:  chr...@ba...
Internet :  http://www.bayertechnology.com

tst.sdf:
===snip===
Model1
  Cerius2 01120415373D 1   1.00000
Structure written by MSI Cerius2 SD Exporter
 17 17  0  0  0  0  0  0  0  0999 V2000
    1.0524   -1.7053   -0.0293 C   0  0  0  0  0  0
    2.1287   -1.6085   -0.0417 H   0  0  0  0  0  0
    0.2023   -0.5743    0.0099 C   0  0  0  0  0  0
    0.6723    0.7567    0.0358 O   0  0  0  0  0  0
   -1.1895   -0.7709    0.0242 C   0  0  0  0  0  0
   -2.0332    0.3430    0.0629 O   0  0  0  0  0  0
   -1.7189   -2.0726   -0.0001 C   0  0  0  0  0  0
   -2.7901   -2.2293    0.0108 H   0  0  0  0  0  0
   -0.8683   -3.1781   -0.0387 C   0  0  0  0  0  0
   -1.2814   -4.1784   -0.0573 H   0  0  0  0  0  0
    0.5140   -2.9945   -0.0532 C   0  0  0  0  0  0
    1.1714   -3.8540   -0.0831 H   0  0  0  0  0  0
    2.0823    0.9796    0.0217 C   0  0  0  0  0  0
   -3.0188    0.1062    0.0707 H   0  0  0  0  0  0
    2.2712    2.0723    0.0457 H   0  0  0  0  0  0
    2.5572    0.5287    0.9194 H   0  0  0  0  0  0
    2.5320    0.5731   -0.9095 H   0  0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  1 11  2  0  0  0
  3  4  1  0  0  0
  3  5  2  0  0  0
  4 13  1  0  0  0
  5  6  1  0  0  0
  5  7  1  0  0  0
  6 14  1  0  0  0
  7  8  1  0  0  0
  7  9  2  0  0  0
  9 10  1  0  0  0
  9 11  1  0  0  0
 11 12  1  0  0  0
 13 15  1  0  0  0
 13 16  1  0  0  0
 13 17  1  0  0  0
M  END
$$$$