> Thank you for the speedy replies. I attached an example 2D SDF file.
Well, you can verify for yourself that 3D generation works, e.g.:
% obabel ~/Desktop/CHEMBL100358.sdf --gen3d -O CHEMBL.sdf
# waiting.. .. ..
% cat CHEMBL.sdf
It works fine from the command-line.
Hope that helps,
-Geoff
-
Geoff and Noel,
Thank you for the speedy replies. I attached an example 2D SDF file.
Wallace
On Fri, Nov 22, 2013 at 4:28 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > my $filename = $id . '.sdf';
> > open (OUT, ">temp.sdf");
> >
> my $filename = $id . '.sdf';
> open (OUT, ">temp.sdf");
> print OUT @sdfdata;
> close OUT;
> $obConversion->ReadFile($obMol, "temp.sdf”);
This just seems weird. Even if you have a bunch of data, you don’t need to sa
Hi Wallace,
I'm not much good with Perl, but for those folks who are, could you
provide a complete Perl script that reproduces the problem. The
smaller the script the better. For example, at the moment I can easily
blame everything on what everything is in @sdfdata. Also please note
that ReadFile
Dear All,
Once again, I apologize for my utter lack of experience, but I was hoping
y'all could help me out with a problem I've been having. Using OpenBabel in
Perl, I have been trying to convert several 2D SDF files to 3D. The process
appears to be stuck somewhere between the 'Do' and 'WriteFile'
Hi all,
when using OBConformerSearch I get a ton of logging messages and I do not
see an option how to turn them off. Where Can I turn these messages off?
Thank you.
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According to Google, this has come up on the list before:
http://www.mail-archive.com/openbabel-discuss@lists.sourceforge.net/msg02727.html
HTH,
- Noel
On 22 November 2013 09:32, Pascal Muller wrote:
> Hi,
>
>
>
>
>> I have some multi-molecule SDF files from ZINC and simply want to filter
>> t
Hi,
I have some multi-molecule SDF files from ZINC and simply want to filter
> them down to keep only those with a molecular weight < 1000 and rotatable
> bonds < 20.
>
I use a python script for this. If it suits you, adjust for the file name
and file format you are using:
#!/usr/bin/python
im
Thanks! that worked.
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