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
Hi Dan,
Regarding (1) the relevant section in the docs is at
http://openbabel.org/docs/2.3.0/Fingerprints/fingerprints.html. I
think that the section on Similiarity Searching answers this question.
Question (2) is about searching for exact matches. Currently the only
way to do this is matching
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
Dan
You can look for an exact match in a large dataset using fastsearch format.
Index the data file (which must not be compressed):
obabel datset.xxx -ofs
Do an exact structure search:
obabel dataset.fs -O out.yyy -s SMILES exact
where the SMARTS string can be replaced by a
On Jan 24, 2011, at 4:42 AM, Noel O'Boyle wrote:
Hi Dan,
Regarding (1) the relevant section in the docs is at
http://openbabel.org/docs/2.3.0/Fingerprints/fingerprints.html. I
think that the section on Similiarity Searching answers this question.
Question (2) is about searching for exact
Hi,
On Fri, Jan 14, 2011 at 04:27:53PM -0500, Geoffrey Hutchison wrote:
Browsing openbabel-2.3.0/src/charges seems to confirm that
'none' is not a charge option.
Is there another way to ignore the charges ?
At the moment, not from the user utilities, no. I just added a none option
to
If the charges in the input file are all zero then the output file
will contain nonzero gasteiger partialcharges.
Hmm. That would be a bug. I'll take a look.
-Geoff
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