difficulty reading from fastsearch index

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difficulty reading from fastsearch index

David Rose-9
Hi:

  I have had several instances where I build a fastsearch index
without any apparent trouble but then can't search it without an
error.  I finally have a small example of this problem that I can
post, using a 10 molecule smi file ( ten.smi) as input:

$ cat ten.smi
C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC
n1c([nH]c(cc1c1ccccc1)=O)c1ccc(cc1)Br
n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1
C1(/[CH]2[CH]3\C(=C4/CC(C)(C)NC(C4)(C)C)C=C[CH]3[CH]1C=C2)=C1/CC(C)(C)NC(C1)(C)C
n1c(c2ccc(C(=O)O)cc2)ccc(c1)CCCCC
N1(C(CN(CC1=O)C(=O)C1CCCCC1)=O)CCc1ccccc1
S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O
c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1
c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC

# file looks OK...build index:

$ babel ten.smi -ofs
This will prepare an index of ten.smi and may take some time...
 It took 0 seconds
10 molecules converted
37 audit log messages


$ ls -lt ten.fs
-rw-r--r--   1 rose  staff  1564 Nov 15 12:51 ten.fs

#  looks OK, no errors, fs file exists and has stuff in it.   Try a search:

$ babel ten.fs -ifs -s'Nc2nc(c1ccccc1)nc3ccccc23' out.smi
==============================
*** Open Babel Error  in ReadChemObject
  Difficulty reading from index ten.fs

0 molecules converted
1 errors 1 audit log messages

As I said, I run into this a lot.  In the past I assumed there was
some formatting problem in my input file that I couldn't find, and
I've been able to work around it by creating the file in a somewhat
different way.  With this small file there isn't any obvious place for
such an error to hide.  Any ideas what is going on?

This is on a PowerPC Apple XServe running OS X Server 10.4

Thanks,
David Rose
Cambridge, MA

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Re: difficulty reading from fastsearch index

Chris Morley-2
David Rose wrote:

> Hi:
>
>   I have had several instances where I build a fastsearch index
> without any apparent trouble but then can't search it without an
> error.  I finally have a small example of this problem that I can
> post, using a 10 molecule smi file ( ten.smi) as input:
>
> $ cat ten.smi
> C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC
> n1c([nH]c(cc1c1ccccc1)=O)c1ccc(cc1)Br
> n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1
> C1(/[CH]2[CH]3\C(=C4/CC(C)(C)NC(C4)(C)C)C=C[CH]3[CH]1C=C2)=C1/CC(C)(C)NC(C1)(C)C
> n1c(c2ccc(C(=O)O)cc2)ccc(c1)CCCCC
> N1(C(CN(CC1=O)C(=O)C1CCCCC1)=O)CCc1ccccc1
> S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
> c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O
> c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1
> c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC
>
> # file looks OK...build index:
>
> $ babel ten.smi -ofs
> This will prepare an index of ten.smi and may take some time...
>  It took 0 seconds
> 10 molecules converted
> 37 audit log messages
>
>
> $ ls -lt ten.fs
> -rw-r--r--   1 rose  staff  1564 Nov 15 12:51 ten.fs
>
> #  looks OK, no errors, fs file exists and has stuff in it.   Try a search:
>
> $ babel ten.fs -ifs -s'Nc2nc(c1ccccc1)nc3ccccc23' out.smi
> ==============================
> *** Open Babel Error  in ReadChemObject
>   Difficulty reading from index ten.fs
>
> 0 molecules converted
> 1 errors 1 audit log messages
>
> As I said, I run into this a lot.  In the past I assumed there was
> some formatting problem in my input file that I couldn't find, and
> I've been able to work around it by creating the file in a somewhat
> different way.  With this small file there isn't any obvious place for
> such an error to hide.  Any ideas what is going on?
>
> This is on a PowerPC Apple XServe running OS X Server 10.4
>
It looks as if the fs file header is not being read properly. This is a
binary file and the code may not have properly accounted for system
differences. (I have never had these difficulties o my Windows system.)
Could you send me a copy of the ten.fs that doesn't work?

Chris

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Re: difficulty reading from fastsearch index

Geoffrey Hutchison

On Nov 16, 2007, at 3:44 AM, Chris Morley wrote:

> It looks as if the fs file header is not being read properly. This  
> is a
> binary file and the code may not have properly accounted for system
> differences. (I have never had these difficulties o my Windows  
> system.)
> Could you send me a copy of the ten.fs that doesn't work?

My one worry here is that PowerPC Macs use a different byte order than  
Intel machines (Windows or otherwise).

Cheers,
-Geoff

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Re: difficulty reading from fastsearch index

Makio Tamura
I reproduced exactly the same problem on my x86 64bit RedHat Linux.

From this past post ---Problem using fs index file--- (http://n4.nabble.com/Problem-using-fs-index-file-td958832.html#a958832), I find that the problem may be caused by incompatible binary operation on 64 bit machine.

If the binary operation on 64bit machine is the cause of this problem, I would be wondering whether there might be any plan to fix this problem?  Or I appreciate that there could be some way to circumvent the error.

Makio
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Re: difficulty reading from fastsearch index

Chris Morley-3
Makio Tamura wrote:

> I reproduced exactly the same problem on my x86 64bit RedHat Linux.
>
>>From this past post ---Problem using fs index file---
> (http://n4.nabble.com/Problem-using-fs-index-file-td958832.html#a958832), I
> find that the problem may be caused by incompatible binary operation on 64
> bit machine.
>
> If the binary operation on 64bit machine is the cause of this problem, I
> would be wondering whether there might be any plan to fix this problem?  Or
> I appreciate that there could be some way to circumvent the error.

This is a problem that really needs investigating, but I do not have a
64-bit machine. I cannot see any constructs that I know will cause
problems but if you were able to identify what aspect of the code is
failing I might be able to take it further.

Noel is getting set up with 64bit builds and may be able to help.

There was a another bug unconnected with 64 bit which had similar
symptoms. Are you using the lastest version 2.2.3 which does not
suffer from this?

I don't think this has a bug report. Could you add one?
http://sourceforge.net/tracker/?group_id=40728&atid=428740

Chris

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Re: difficulty reading from fastsearch index

Makio Tamura
Chris

I posted this problem on the Bugs report (http://sourceforge.net/tracker/?func=detail&aid=2955101&group_id=40728&atid=428740).  I am using the version 2.2.3, the latest one up until on Feb. 19 2010, and encounter the problem.

Unfortunately, I am not that skilful to identify codes that may cause the error and can only provide the error message:  “Open Babel Error  in ReadChemObject”….

Makio
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Re: difficulty reading from fastsearch index

Noel O'Boyle
Administrator
I've updated the bug report. Unfortunately, I couldn't reproduce the
problem on 64-bit Windows, but I found another problem - only 2
molecules were converted on either 64-bit or 32-bit if -ofs (but all
ten if -osmi).

Chris, could you look into this?

- Noel

On 19 February 2010 18:36, Makio Tamura <[hidden email]> wrote:

>
> Chris
>
> I posted this problem on the Bugs report
> (http://sourceforge.net/tracker/?func=detail&aid=2955101&group_id=40728&atid=428740).
> I am using the version 2.2.3, the latest one up until on Feb. 19 2010, and
> encounter the problem.
>
> Unfortunately, I am not that skilful to identify codes that may cause the
> error and can only provide the error message:  “Open Babel Error  in
> ReadChemObject”….
>
> Makio
>
> --
> View this message in context: http://n4.nabble.com/difficulty-reading-from-fastsearch-index-tp958967p1562052.html
> Sent from the openbabel-discuss mailing list archive at Nabble.com.
>
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> Try the new software tools for yourself. Speed compiling, find bugs
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>

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