Question about file conversion

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Question about file conversion

Brendan M. O'Boyle
Hello,

I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf files for manipulation with Schrodinger software.

I installed the OpenBabel first and then I am using iBabel.  I put in the SMILES string under the convert header and then use that to prepare an sdf file.

However, the file is zero bytes and there is something wrong with the conversion even though a file is generated.

Is this a common problem?

Thank you,
Brendan
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Re: Question about file conversion

mwojcikowski
Hi,

That is a wild guess, since you gave us near to zero information, but what is the first line of your .smi file? If it's not valid smiles, then the reader will give up, since it has finish reading the file on first line. Valid smiles file is: "smiles string, white-space and name", like "c1ccccc1 benzene" 

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Maciek Wójcikowski
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2016-05-09 4:35 GMT+02:00 Brendan M. O'Boyle <[hidden email]>:
Hello,

I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf files for manipulation with Schrodinger software.

I installed the OpenBabel first and then I am using iBabel.  I put in the SMILES string under the convert header and then use that to prepare an sdf file.

However, the file is zero bytes and there is something wrong with the conversion even though a file is generated.

Is this a common problem?

Thank you,
Brendan
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Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
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Re: Question about file conversion

Chris Swain
In reply to this post by Brendan M. O'Boyle
You need to have the SMILES string(s) in a plain text file.

It should look like this

c1ccccc1
c1ccccc1F
C1CCCCC1
CCCC(=O)Cl

and ideally you should name it something like myfile.si or myfile.smiles

Enter the path to the file in the input file field.

Cheers,
Chris

>
> Message: 1
> Date: Sun, 8 May 2016 19:35:30 -0700
> From: "Brendan M. O'Boyle" <[hidden email]>
> Subject: [Open Babel] Question about file conversion
> To: <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello,
>
> I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf files for manipulation with Schrodinger software.
>
> I installed the OpenBabel first and then I am using iBabel.  I put in the SMILES string under the convert header and then use that to prepare an sdf file.
>
> However, the file is zero bytes and there is something wrong with the conversion even though a file is generated.
>
> Is this a common problem?
>
> Thank you,
> Brendan
>
>


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