On 01/02/2011 09:49, Chris Morley wrote:
On 01/02/2011 07:12, Andrew Dalke wrote:
On Jan 31, 2011, at 8:15 PM, cha...@ncbs.res.in wrote:
I noticed that molecules such as Myristic acid and Palmitic acid have
same similarity score of 1, ... I am thinking of modifying Tanimoto
score to other
>Just a small comment...
>Since Open Babel 2.3.0, it is possible to describe each of the set
>bits using the "s" output option, e.g.
Ah, nice feature.
Then one can build a dictionary of fragment<->bit mappings for a given input
set along FP2 generation, including detection of ambiguous mappings
Just a small comment...
Since Open Babel 2.3.0, it is possible to describe each of the set
bits using the "s" output option, e.g.
C:\Users\Noel>obabel -:"CCC(=O)Cl" -ofpt -xs
>
0 6 1 6 <670>
0 6 1 6 1 6 <260>
0 8 2 6 <623>
0 8 2 6 1 6 <329>
0 8 2 6 1 6 1 6 <652>
0 17 <17>
0 17 1 6 <328>
0 17 1 6
Hi,
FP2 is a Daylight type fingerprint. See 6.1.2 of
http://www.daylight.com/dayhtml/doc/theory/theory.finger.html for an
explanation.
FP2 generates fragments up to 7 bonds length or shorter if a ring is
encountered. The fragments are then hashed to the first 1021 bits of the 1024
bit space F
Dear All,
Thank you Chris for your help. It works well after removing .
I am curious to know what goes behind the open babel program. In particular, I
want
to understand two things
1. How FP2 is generated and what each digit in FP2 stands for.
2. How two FP2's are compared and Tanimoto scor
I read the discussion on Blue Obelisk immediately after posting. But in
fact the problem was that the sdf was malformed (extra lines). OB will
read titles with , but the -f option, which skips molecules,
doesn't like it.
Chris
On 25/01/2011 16:45, Noel O'Boyle wrote:
> Regarding the use o
Regarding the use of in the title, Chris, you might want to read
http://blueobelisk.shapado.com/questions/what-is-the-minimum-needed-to-correctly-identify-records-in-an-sd-file.
It seems that this is not allowed by the spec...
- Noel
2011/1/25 Chris Morley :
> Your file othermol.sdf was a pr
Your file othermol.sdf was a proper sdf file but the molecules all had a
title "". The use of the delimiter string as a title is not good
practice and confused OpenBabel. I'll see if I can correct this, but if
you change the titles to Mol1, Mol2, etc. and name PatternMol, the
command below
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
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
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
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
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