On Oct 9, 2012, at 1:58 PM, David van der Spoel wrote:
> So is there any defined plan for what goes into 2.4 and when it should
> be ready?
...
> I can live with a development version as well (trunk?) for a while but
> since we're considering linking openbabel in with gromacs at some stage
> (
On 2012-10-09 19:44, Geoff Hutchison wrote:
>> Apparently it did more than just that and fixed some issue
>> along the way.
>>
>> Geoff, could this be considered for maintenance release?
>
> Not as-is. It changes API / ABI, so it must be confined for trunk. There are
> usually bugs like this which
> Apparently it did more than just that and fixed some issue
> along the way.
>
> Geoff, could this be considered for maintenance release?
Not as-is. It changes API / ABI, so it must be confined for trunk. There are
usually bugs like this which are fixed by 2.x releases which cannot be fixed by
To be honest, I rarely use OBConversion directly - that's why I wrote
Pybel. Instead, I would do:
import pybel
mols = [pybel.readfile("mol2", filename).next() for filename in
["a.mol2", "b.mol2"]]
output = pybel.Outputfile("sdf", "ab.sdf")
for mol in mols:
output.write(mol)
output.close()
-
Thanks a lot Noel.
I just looked through the Pybel code. Assuming I wanted to do all that
directly I could do the following (ignoring any safe guards for the
moment), right?
import openbabel as ob
conv = ob.OBConversion()
conv.SetInAndOutFormats('mol2', 'sdf')
m1 = ob.OBMol()
m2 = ob.OBMol()
Sorry for posting this twice. This was already answered on 04/10/12.
-Original Message-
From: chjjmp [mailto:pra...@ccdc.cam.ac.uk]
Sent: 04 October 2012 12:04
To: openbabel-discuss@lists.sourceforge.net
Subject: [Open Babel] Splitting multimol2 file with OpenBabel without changing
bond
Hello Hannes,
You need to use the readfile method for reading, and Outputfile class
for writing. If you cannot figure it out, post some code here and I
will correct it.
- Noel
On 8 October 2012 11:08, Hannes Loeffler wrote:
> Hi,
>
> how would I do the following in Python?
>
> babel -imol2 a.mo
Hi,
I am using OpenBabel to split a multimol2 file into separate mol2 files
(i.e. one mol2 file per compound). I use the following command:
babel my_ligands.mol2 ligandPart.mol2 -m
such that each single ligand mol2 file will be called ligandPart1.mol2,
ligandPart2.mol2, etc
The issue is that f
On Mon, Oct 08, 2012 at 10:55:12AM +0200, David van der Spoel wrote:
> Hi,
>
> sorry to be a pain but I found another few pathetic cases (chemistry has
> a lot of them). Azulene C10H8 is a merged 5 and 7 ring, purely CH:
>
> % babel -ipdb azulene.pdb -oinchi ---errorlevel
> 2===
Hi,
how would I do the following in Python?
babel -imol2 a.mol2 b.mol2 -osdf ab.sdf
Obviously I need to convert two mol2 files and combined them in a
single sdf.
Thanks,
Hannes.
--
Scanned by iCritical.
--
Don't let
Hi,
I am Using OpenBabel for converting one file format to other. I am getting
> the desired output. Along with it I am getting following displayed on my
> command line:
>
> 1 molecule converted
> 14 audit log messages 1 debugging messages
>
> I dont want it to be displayed on the CMD. Any sugges
On Tue, Oct 09, 2012 at 09:01:08AM +0200, David van der Spoel wrote:
> On 2012-10-08 21:08, Reinis Danne wrote:
> > On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote:
> >> On 2012-10-08 19:11, Reinis Danne wrote:
> >>> On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel
On 2012-10-08 21:08, Reinis Danne wrote:
> On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote:
>> On 2012-10-08 19:11, Reinis Danne wrote:
>>> On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote:
>
> It adds TWO H for InChi output, not for SDF output, but it
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