Re: [Open Babel] Limits on number of input files

[Noel O'B. <bao...@gm...>]

Hello Michael,

Regarding the GUI, I'll let Chris answer.

File names with spaces require quotation marks around them. This is a
feature of the Windows command line, not babel. You will have a
similar problem on Linux, except that the spaces will need to be
escaped instead.

I'm sure there's a way to do what you want using the Windows command
line, but for me it's easier to use Python. If you install the Python
module, the following code should work:

import pybel
import glob

smiles = []
for molfile in glob.glob("*.mol"):
    mol = pybel.readfile("mol", molfile).next() # Assuming a single molecule
    mol.title = molfile
    smiles.append(mol.write("smi"))
print >> open("result.smi", "w"), "".join(smiles)

- Noel

2009/2/27 Michael Fisher <mf...@ta...>:
> I’ve started using the OpenBabel GUI.  I have two directories with .mol
> files I want to get SMILES strings for.  One has about 3500 files, the other
>>13000.  There appears to be an input file limit of about 700 files.
>  Obviously, I could do 700 at a time, but I then have to concatenate all the
> files (at least twenty for the big directory).  Am I right that there’s a
> limit?  Is there a way to get around it?
>
>
>
> FYI, the filenames contain numerous spaces, periods and commas, so the
> command line version of babel (which I’ve tried) crashes.  Also, I’m
> presently stuck doing this in Windows XP.  If I switch to Fedora, will the
> command line version ignore punctuations?  Will there still be a limit on
> input files in the GUI?
>
>
>
> Mike
>
>
>
> ________________________________
> IMPORTANT NOTICE: TAKASAGO DISCLAIMER This e-mail may be confidential and/or
> subject to legal privilege, and is for the use of the intended addressee
> only. Any unauthorized use, dissemination, or copying of the information in
> this message is strictly prohibited. If you have received this message in
> error, please notify the sender immediately and delete this message.
>
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>