A sidepoint from GPU development - and directly related to Geoff's
earlier point.
Perhaps multicore awareness is the way to go...
In the most reductionist of approaches -- you could launch n threads
(instead of one) and have each generate a conformer each since these
are really independent proces
On 6 July 2012 19:46, Geoff Hutchison wrote:
> > Is there an torsion angle energy minimizer in open babel?
>
> Not per-se. There are multiple general force fields with minimizers, and
> you could set up constraints to just minimize torsions and not anything
> else.
>
>
Interesting.
So, in a nuts
Hi there,
Is there an torsion angle energy minimizer in openbabel?
Based on some of the rotatable bond conformer generation work I suspect
there is. But I cannot seem to find it.
Many Thanks.
-
Jean-Paul Ebejer
Early Stage Researcher
Hi there,
I have checked out and successfully built openbabel from the svn repository
(trunk).
$ obabel -V
Open Babel 2.3.90 -- Jun 30 2012 -- 12:38:05
But when I try to generate conformers using:
obabel ./astex_1g9v/ligand_babel3d.sdf -O/tmp/test.sdf --conformer --nconf
10 --writeconformers --
On 31 May 2012 03:56, Geoff Hutchison wrote:
>
> On May 29, 2012, at 11:23 AM, JP wrote:
>
> > This value of 1A in the steric filter is not available from the command
> line, correct?
>
> No, there isn't (yet) a way to set that. The current SVN trunk now has an
&g
On 29 May 2012 15:25, Geoff Hutchison wrote:
> Some of the generated conformers look really ugly (in terms of close
> atoms/steric clashes).
> I have placed a selected subset at: http://imgur.com/a/LgJqL
>
> Is that to be expected in RMSD scoring -- because I have not used --score
> energy? (I tr
Hi there OpenBabels!
I am generating conformers for
molecule C(=O)(O)C(C)(C)Oc1ccc(cc1)CC(=O)Nc1cc(cc(c1)C)C using the
--conformer option (and --writeconformers, otherwise I get only one
conformer written to file) in the following manner :-
obabel ligand_babel3d.sdf -O conf2.sdf --conformer --nco
. I'll file a bug...
>
> On 25 May 2012 11:09, JP wrote:
>> Hi there OpenBabel,
>>
>> I have mass tested the obabel 2.3.1 depiction code, and all looks
>> awesome with the exception of:
>>
>> obabel -:"c1cn2cc(CC(=O)NCC(NCC([O-])=O)=O)nc2s1" -
Hi there OpenBabel,
I have mass tested the obabel 2.3.1 depiction code, and all looks
awesome with the exception of:
obabel -:"c1cn2cc(CC(=O)NCC(NCC([O-])=O)=O)nc2s1" -O test.svg
Any idea why this innocuous looking molecule produces no co-ordinates
in the svg file?
[...snip...]
Note tha
Hello everyone,
I would like to calculate the energy of a molecule (using the mmff94 force
field). I do *not* want to do minimization, just read off the energy value
programatically.
I see that there is an "energy" attribute in pybel -- but the documentation
at
http://openbabel.org/docs/dev/UseT
Researcher
On 9 December 2011 17:55, JP wrote:
> yes Geoff, this does help *a lot* - especially considering the call from
> the command line.
>
> One more question and a suggestion please.
>
> Q: The weighted rotor conformer gives only one conformer (lowest energy)?
> What hap
yes Geoff, this does help *a lot* - especially considering the call from
the command line.
One more question and a suggestion please.
Q: The weighted rotor conformer gives only one conformer (lowest energy)?
What happens when you specify the num of conformers to say 50 ?
S: Also a suggestion oba
Hi there
I would like to generate a fixed number of conformers for particular
molecules.
I have read through http://openbabel.org/dev-api/group__conformer.shtml -
is there more documentation about this?
(There is nothing in the excellent bible -
http://openbabel.org/docs/current/)
Specifically,
Using OpenBabel 2.3.1, on Ubuntu Linux 10.10
Using the attached *seemingly unsuspect and correct* sdf file - zzz.sdf.
Converting this file to smiles:
$ obabel zzz.sdf -osmi -Ozzz.smi
2 molecules converted
Gives us the expected and correct result:
$ more zzz.smi
C[C@@H](N)C(=O)OAla1
C[C@
Morley wrote:
> On 11/11/2011 09:38, JP wrote:
>
>> Is it possible to have a transparent background (or user specified) when
>> converting to an svg?
>> The choice of black and white looks very arbitrary.
>>
>
> Well, minimalist. So to bring some color back to
Is it possible to have a transparent background (or user specified) when
converting to an svg?
The choice of black and white looks very arbitrary.
I can only find this in the options:
b black background
The default is white. The atom colors work with both.
-
Jean-Paul Ebejer
Early Stage Rese
Yo OpenBabels,
Any ideas why the following
> babel test.mol2 test.sdf
babel: cannot write output format!
Open Babel 2.3.0 -- Nov 1 2010 -- 11:33:23
Usage: babel [-i] [-o]
Try -H option for more information.
test.mol2 exists, is correct,and the same command line with the same
files work on an
...
On 3 June 2011 19:02, Craig A. James wrote:
> On 6/3/11 12:56 AM, JP wrote:
>>
>> Hi there,
>>
>> Using OpenBabel 2.3.0, is there a way how to split a molecule file
>> (e.g. sdf) into chunks?
>>
>> I can imagine two different modes of action:
>>
work with smaller
files (e.g. when submitting multiple jobs on a cluster), or for
testing of products.
Cheers
JP
--
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap
That is probably because you got the messages digest.
In the original email those prices were marked as Euros.
On 24 March 2011 17:18, christophersw...@btconnect.com <
christophersw...@btconnect.com> wrote:
> Noel,
>
> I think you need to be a little more explicit with the currency :-)
>
> Chr
Right - but you forgot to mention the OS you are using (architecture and
version please)
On 22 March 2011 17:15, wrote:
>
> Dong Li
>
>
>
> --
> Enable your software for Intel(R) Active Management Technology to meet the
Maybe; you have a different version number than NoB than?
Details!Details!
On 18 March 2011 13:53, Bradley Calhoun wrote:
> I have to wonder then what the difference is. I ran the code again to make
> sure, and the program sat for 30 minutes without any progress.
>
> I added a few other molec
l have to try
> the development version and regenerate the bindings (-DRUN_SWIG=ON).
>
> - Noel
>
> On 12 March 2011 16:07, JP wrote:
> > Noel,
> > What version of OB does this script run against?
> > I am having problems with pybel.ob.OBAlign():
> >>
> >
spread_values = calculate_spread(molecules_file)
> File "./calculate_spread.py", line 24, in calculate_spread
> align = pybel.ob.OBAlign()
> AttributeError: 'module' object has no attribute 'OBAlign'
Thanks
JP
On 7 March 2011 13:48, Noel O'Boyle wrote:
&g
+1000 Karma Awesomeness Factor O'Boy.
(PS Should this go somewhere with the docs?)
On 7 March 2011 13:48, Noel O'Boyle wrote:
> Hi JP,
>
> Please find attached a Python script that calculates the RMSD for a
> set of conformers versus a set of crystal structures. RMSD i
Any ideas where I can find an example/documentation on how to calculate RMSD
values
for two molecules which are chemically the same (but have different
conformers) - using pybel ?
Many Thanks
--
What You Don't Know About D
Just out of curiosity - did the Molcore project fly eventually?
(
http://baoilleach.blogspot.com/2009/08/molcore-new-beginning-for-openbabel-and.html
)
Doesn't seem so from the links in NoB post...
--
Special Offer-- Downl
Friday evening query: Using pybel/Openbabel: is there a way to get the
largest physical length of a whole molecule? (basically the largest
pairwise distance between the atoms in the molecules)...
Many Thanks
JP
this happens since my mol2 file contains dummy atoms and I am
fine with that. All the warnings are "distracting" in this particular case.
Thanks
JP
--
Increase Visibility of Your 3D Game App & Earn a Chance To
wrote:
> JP,
>
> Noel's summary below is, in my opinion, dead on: The molfile has problems:
> 1) there's a 4 coordinate neutral nitrogen
> 2) it's missing the "M END" line (maybe it's also missing the M CHG
> line that would fix the nitrogen?)
>
perfectly fine, please redirect your query
elsewhere
d) None of the above, the OS/hardware is playing tricks on you
I appreciate any help and any light you can shed.
Cheers
JP
PS These two frameworks are really great!! well done everyone!!
1hww.mol
Description: Binary data
1hww.smiles
Description
file
Invalid bond specification, atom numbers or bond order are wrong.
0 molecules converted
1 warnings 2 audit log messages
I can see no problems with it... (atom numbers and bonds look OK too)
Many Thanks
JP
--
Centralized
babel co2h.smi co2h.mol2
babel co2h.mol2 co2h-broken.smi
You can also do (for comparison):
babel co2h.smi co2h.sdf
babel co2h.sdf co2h-not-broken.smi
You will notice that co2h-not-broken.smi has the correct double bond (=)
while co2h-broken.smi does not.
Cheers
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