fast index search on linux

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fast index search on linux

Andy D P
Hi,
I have installed openbabel 2.2.3 on an ubuntu 10.04 machine via the apt installer but I am having problems substructure searching an indexed database viz:
> babel VS_Library_full.fs -ifs -s'N#Cc1c(Cl)cccc1' results.smi
==============================
*** Open Babel Error  in ReadChemObject
  Difficulty opening VS_Library_full.sd

0 molecules converted
1 errors 19 audit log messages


(note it is trying to open an sd file not an fs file)

Searching an sd file with this smiles string works fine.  Also, under windows and openbabel 2.2.3, searching this same .fs file works OK using the command prompt and this command. 
The obvious solution here is to use windows but I need to write a shell script to search through a lot of molecules and really need to get it working on linux.  What should I be doing here?
thanks,
Andy



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Re: fast index search on linux

Tim Vandermeersch


On Wed, May 12, 2010 at 5:23 PM, macc_200 <[hidden email]> wrote:
Hi,
I have installed openbabel 2.2.3 on an ubuntu 10.04 machine via the apt installer but I am having problems substructure searching an indexed database viz:
> babel VS_Library_full.fs -ifs -s'N#Cc1c(Cl)cccc1' results.smi
==============================
*** Open Babel Error  in ReadChemObject
  Difficulty opening VS_Library_full.sd

0 molecules converted
1 errors 19 audit log messages


(note it is trying to open an sd file not an fs file)

Searching an sd file with this smiles string works fine.  Also, under windows and openbabel 2.2.3, searching this same .fs file works OK using the command prompt and this command. 
The obvious solution here is to use windows but I need to write a shell script to search through a lot of molecules and really need to get it working on linux.  What should I be doing here?

Have you tried recreating the index on linux. I'm not sure if these binary files are portable across platforms. Others know more about this though.
 
thanks,
Andy



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Re: fast index search on linux

Noel O'Boyle
Administrator
Hi Andy,

Could you clarify where the .fs file came from, and whether the original sd file is present?

- Noel

On 12 May 2010 18:42, Tim Vandermeersch <[hidden email]> wrote:


On Wed, May 12, 2010 at 5:23 PM, macc_200 <[hidden email]> wrote:
Hi,
I have installed openbabel 2.2.3 on an ubuntu 10.04 machine via the apt installer but I am having problems substructure searching an indexed database viz:
> babel VS_Library_full.fs -ifs -s'N#Cc1c(Cl)cccc1' results.smi
==============================
*** Open Babel Error  in ReadChemObject
  Difficulty opening VS_Library_full.sd

0 molecules converted
1 errors 19 audit log messages


(note it is trying to open an sd file not an fs file)

Searching an sd file with this smiles string works fine.  Also, under windows and openbabel 2.2.3, searching this same .fs file works OK using the command prompt and this command. 
The obvious solution here is to use windows but I need to write a shell script to search through a lot of molecules and really need to get it working on linux.  What should I be doing here?

Have you tried recreating the index on linux. I'm not sure if these binary files are portable across platforms. Others know more about this though.
 
thanks,
Andy



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Re: fast index search on linux

Andy D P
In reply to this post by Tim Vandermeersch
Thanks Tim, this has solved the problem.  As you suggested, you need to make the .fs file on the same architecture you are running Openbabel


From: Tim Vandermeersch <[hidden email]>
To: macc_200 <[hidden email]>
Cc: [hidden email]
Sent: Wed, 12 May, 2010 18:42:09
Subject: Re: [Open Babel] fast index search on linux



On Wed, May 12, 2010 at 5:23 PM, macc_200 <[hidden email]> wrote:
Hi,
I have installed openbabel 2.2.3 on an ubuntu 10.04 machine via the apt installer but I am having problems substructure searching an indexed database viz:
> babel VS_Library_full.fs -ifs -s'N#Cc1c(Cl)cccc1' results.smi
==============================
*** Open Babel Error  in ReadChemObject
  Difficulty opening VS_Library_full.sd

0 molecules converted
1 errors 19 audit log messages


(note it is trying to open an sd file not an fs file)

Searching an sd file with this smiles string works fine.  Also, under windows and openbabel 2.2.3, searching this same .fs file works OK using the command prompt and this command. 
The obvious solution here is to use windows but I need to write a shell script to search through a lot of molecules and really need to get it working on linux.  What should I be doing here?

Have you tried recreating the index on linux. I'm not sure if these binary files are portable across platforms. Others know more about this though.
 
thanks,
Andy



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Re: fast index search on linux

lirong wang
In reply to this post by Andy D P
I have tried to run on linux, create .fs file on linux platform and run
search, it works fine.

lirong


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