write of fs index incomplete

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write of fs index incomplete

Phil Evans
Hello,

I have a SD file which contains 244 000 entries.  When I attempt to
build a Fast Search index with

babel infile.sdf outfile.fs ---errorlevel 4

I get 9 audit messages, and then

 It took 7.5 minutes
104444 molecules converted
9 audit log messages

How can I determine:
-which SD is causing the problem?
-what might be the cause?

Or, alternatively, can I concatenate a bunch of small .fs files
together (in an attempt to try to find the problem file by isolating
it)?

Last, is a .fs file portable across OSes?

Thanks much, very much appreciate OpenBabel.
Phil

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Re: write of fs index incomplete

Chris Morley-3
On 28/09/2010 23:34, Phil Evans wrote:

> Hello,
>
> I have a SD file which contains 244 000 entries.  When I attempt to
> build a Fast Search index with
>
> babel infile.sdf outfile.fs ---errorlevel 4
>
> I get 9 audit messages, and then
>
>   It took 7.5 minutes
> 104444 molecules converted
> 9 audit log messages

Error message logging is turned off during indexing, so there is no
useful information there.
>
> How can I determine:
> -which SD is causing the problem?
> -what might be the cause?

This might give some information::
   babel  infile.sdf  -osdf  -f 104443  -l 104446

>
> Or, alternatively, can I concatenate a bunch of small .fs files
> together (in an attempt to try to find the problem file by isolating
> it)?
It is possible to build fs indexes to only some of the molecules in
the datafile, by using --filter, -f and -l options during the
preparation of the index.
>
> Last, is a .fs file portable across OSes?
No. This is a job for the future, possibly using FPB format
http://code.google.com/p/chem-fingerprints/
>
> Thanks much, very much appreciate OpenBabel.

Chris

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