Re: [Open Babel] Use of wild card characters in iBabel GUI

[<chr...@bt...>]

I notice from the command line you use

m -gen3D

but iBabel outputs

m --gen3D

And according to the babel help it should be m --gen3D

Also try clicking the "Use Terminal" checkbox on the bottom left of the GUI and see what happens.

I'll also investigate further

Chris




On 18 Feb 2011, at 15:14, ope...@li... wrote:

> Message: 5
> Date: Wed, 16 Feb 2011 11:33:19 -0800
> From: Felix Grun <fg...@uc...>
> Subject: [Open Babel] Use of wild card characters in iBabel GUI ?
> To: ope...@li...
> Message-ID: <ADE...@uc...>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi,
> 
> I'd like to use iBabel 3.0beta and Open Babel 2.3.0 running on my iMac OSXv10.6 to batch convert .mol files to .pdbqt files for virtual docking.
> 
> If I change directory to a desktop folder containing my structures, I can successfully use "babel" from the terminal to batch convert using the wild card character * for the input file. 
> 
> biologix:~ farpelix$ cd /Users/farpelix/Desktop/Docking/Ligands/Mol_Files/
> biologix:~ farpelix$ babel -imol *.mol -opdbqt -m -gen3D
> 
> However when I use the GUI in iBabel, I cannot use wild card characters in the File Input field. Instead I get an "OpenAndSetFormat" error message in the terminal as follows:
> 
> /usr/local/bin/babel  -imol   '/Users/farpelix/Desktop/Docking/Ligands/Mol_Files/*.mol'  -opdbqt   '/Users/farpelix/Desktop/Docking/Ligands/PDBQT/ligand.pdbqt'     -m    --gen3D 
> 
> -bash: ?: command not found
> biologix:~ farpelix$ /usr/local/bin/babel  -imol   '/Users/farpelix/Desktop/Docking/Ligands/Mol_Files/*.mol'  -opdbqt   '/Users/farpelix/Desktop/Docking/Ligands/PDBQT/ligand.pdbqt'     -m    --gen3D   
> ==============================
> *** Open Babel Error  in OpenAndSetFormat
>  Cannot open /Users/farpelix/Desktop/Docking/Ligands/Mol_Files/*.mol
> 0 molecules converted
> 1 errors
> 
> What is the correct syntax for using wild card characters in iBabel, or do I need to change any settings for babel ?
> 
> Any help would be appreciated. Thanks.
> 
> Felix Grun