Dear All,
I made some progress with calculating tanimoto coefficient. I learn't to so it
from
command line in my ubuntu machine. I was able to do it for two molecules with
the
following command
PROMPT> babel mysmiles.smi mymols.sdf -ofpt
When I tried it for larger set, 1 (mysmiles.smi) vs 8(mymols.sdf), the
following
error pops up
=================================================
*** Open Babel Warning in ReadMolecule
WARNING: Problems reading a MDL file
Cannot read atom and bond count
Expected standard 6 character atom and bond count
==================================================
Can any expert explain what went wrong ?
I suppose, problem lies in grouping of 8 molecules into single mymols.sdf file.
This is how grouped mymols.sdf file looks like
================================
[ OpenBabel12221015072D
23 22 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................
.................................................................
2.6281 -18.1511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
...................
...................
22 23 1 0 0 0 0
M END
$$$$
$$$$ ] 7 times
OpenBabel12221015072D
25 24 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................
.................................................................
6.7196 -7.5210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
...................
...................
24 25 1 0 0 0 0
M END
$$$$
==================================
Any help is much appreciated
Thanks
Chak
chakrava...@....res.in wrote:
> Hi,
>
> I am new to openbabel. I came to know of open babel recently and want to use
> it for
> my academic work.
>
> Here is my Query:
>
> I want to calculate tanimoto coefficient (similarity score) of two lipid
> molecules
> but could not find step-by-step procedure to do so in open babel
> documentation.
>
> What I have done so far:
>
> I converted .sdf files of two lipids into SMILES string and obtained
> fingerprints
> (FP2) of SMILES string. FP2 of one of the molecules looks like this -
>
> 00000000 01000000 00000000 00000400 00080000 00000000
> 00000000 00000000 00000000 00000080 00000000 40010000
> 00000000 00800000 00000000 00080008 00000000 00000000
> 01402000 00000001 00000000 10000010 03000000 00000010
> 00000000 00000000 00000000 00000000 00000000 00040000
> 00020000 00000000
>
> Now, I would like to compare two such fingerprints (actually more than two)
> and
> calculate their similarity score. Can someone advice me how to do it ?
>
> Thanks in Advance
> Chak
>
> PS: I am new to openbabel and Linux. Till now, I used openbabel GUI in
> windows.
> Even though I have installed openbabel in my ubuntu, I have not used it.
>
>
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