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.
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,
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
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
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
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
