Re: [Open Babel] Question about file conversion

[Chris Swain]

You need to have the SMILES string(s) in a plain text file.

It should look like this

c1c1
c1c1F
C1C1
(=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" 
> Subject: [Open Babel] Question about file conversion
> To: 
> Message-ID: 
> 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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Re: [Open Babel] Question about file conversion

[Maciek Wójcikowski]

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 "c1c1
benzene"


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-05-09 4:35 GMT+02:00 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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