On 31 May 2012 03:56, Geoff Hutchison ge...@geoffhutchison.net 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
improved filter
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?
rect x=0% y=0% width=100%
on Windows. I'll file a bug...
On 25 May 2012 11:09, JP jeanpaul.ebe...@inhibox.com 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 -O test.svg
Any idea why this innocuous
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,
Researcher
On 9 December 2011 17:55, JP jeanpaul.ebe...@inhibox.com 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
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
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 :-)
Chris
On
Right - but you forgot to mention the OS you are using (architecture and
version please)
On 22 March 2011 17:15, dong_...@sbcglobal.net wrote:
Dong Li
--
Enable your software for Intel(R) Active Management
the development version and regenerate the bindings (-DRUN_SWIG=ON).
- Noel
On 12 March 2011 16:07, JP jeanpaul.ebe...@inhibox.com wrote:
Noel,
What version of OB does this script run against?
I am having problems with pybel.ob.OBAlign():
Traceback (most recent call last):
File
(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 baoille...@gmail.com wrote:
Hi JP,
Please find attached a Python script that calculates
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
+1000 Karma Awesomeness Factor O'Boy.
(PS Should this go somewhere with the docs?)
On 7 March 2011 13:48, Noel O'Boyle baoille...@gmail.com 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
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...
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Special Offer--
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
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is 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
greg.land...@gmail.com 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?)
OpenBabel takes the bad mol file
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 and thanks,
JP
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