Dear All,
I tried chris technique of holding ctrl to input more than one file. It helps,
but,
I did not get desired output.
Here is my input and output.
========================================================
Input:
[ 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
$$$$
$$$$ ] 7 times
OpenBabel12221015072D
25 24 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................
.................................................................
6.7196 -7.5210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
...................
...................
24 25 1 0 0 0 0
M END
$$$$
=====================================================
Output:
>
> Tanimoto from first mol = 0.869565
Possible superstructure of first mol
=====================================================
Any suggestions are welcome
Thank you Floriane and Chris !!
Chak
From: Chris Morley <c.morley@ga...> - 2011-01-24 10:34
When there are only a small number of molecules, fpt format will give
you what you want; you are nearly there.
In the GUI, select sdf for the input format and ftp for the output.
Open the sdf file with the pattern molecule, then open the sdf file with
all the other molecules you want to compare to it, holding CTRL as you
leave the open dialog (which allows more than one input file).
Click Convert, and you will get a list of the Tanimoto coefficients
between the first molecule and each of the rest, using the default FP2
fingerprint.
On the command line (Windows or Linux):
obabel patternmol.sdf othermols.sdf -ofpt
Chris
chak...@n..res.in wrote:
> 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
>
> chak 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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