Hi Jeff,
Think I solved the majority of my problems by going to sleep! I am using
babel, here is the command line:
babel test1_0001.fs results.txt -SZINC29589833.pdbqt -aat0.2
which does output the hits into a file, and the first line is the tanimoto
score. That is definitely useable.
Is there a way to get just the scores, as when you use the -ofpt option
without the fastsearch index?
i.e. babel test1_0001.sdf ZINC29589833.sd -ofpt --title "" --append
EMOL_VERSION_ID gives me
>25284 Tanimoto from 10018 = 0.0357143
From: Jeff Janes [mailto:jeff.ja...@gmail.com]
Sent: Tuesday, September 24, 2013 10:47 PM
To: Brian Moldover
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] search a fastsearch database
On Tue, Sep 24, 2013 at 7:26 PM, Brian Moldover <moldov...@gmail.com> wrote:
I have what might be a silly (i.e. it's late) question.
I created a fastsearch database of ~1 million structures to get tanimoto
scores against a single structure. The results look like: > Tanimoto from
first mol = 0.0533981. How can I get the subject structure name to print
from the fastsearch database so I know what I'm hitting?
Can you show us the actual code you are using? I can't tell what language
bindings you are using, or if you are using the obabel command line, or
something else.
If the fs index was built from an sdf and you are using obabel, you can add
something like:
--title "" --append NAME
to the command line, where NAME is the name of the property which you
consider to be the structure's name.
Cheers,
Jeff
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