It doesn't work because it's an invalid SMILES. Should either be
OCC(O)CO or [H]OCC(O[H])CO[H].
I appreciate that an error message would be nice...
- Noel
On 6 February 2012 18:27, Thomas Womack wrote:
> If I have a file glycerol.smi containing
>
> HOCC(OH)COH
>
> and issue
>
> % obabel glycero
If I have a file glycerol.smi containing
HOCC(OH)COH
and issue
% obabel glycerol.smi -osmiles -xK
0 molecules converted
% obabel -V
Open Babel 2.3.1 -- Jan 25 2012 -- 15:40:47
then it doesn't produce an INCHI key.
If I remove the hydrogens from the SMILES string, it does.
I think there shou
Also, I should add, you should see whether your PHP is using safe
mode. As described at
http://php.net/manual/en/ini.sect.safe-mode.php#ini.safe-mode-exec-dir
, safe mode can be used to restrict what directories one can execute
programs from.
-David
On Mon, Feb 6, 2012 at 11:51 AM, David Hall w
are the environment variables correct? As in, to run it on the
command line, do you have special PATH or other settings? If so, you
should use http://www.php.net/putenv to put those variables into the
PHP script.
-David
On Tue, Jan 31, 2012 at 4:25 AM, Sangeetha Subramaniam
wrote:
> Dear All,
On 03/02/2012 16:56, KC soh wrote:
> I read that openbabel can read png to mol but would it be possible to then
> export the mol as png/svg/jpg formats? Is there somewhere i can find out
> how to do it with the C++ implementation?
Could you clarify what you are looking for?
OpenBabel can read (a
Hello,
I have a program (written in C#) that uses OpenBabel. This program call
optimisation routines.
I wan't to use it on a USB key without to make the installation of openbabel
on the machine.
I have not found to make it work.
I don't know which parts of the library I have to copy on my key
Dear All,
Can someone help me to run babel for file conversion in PhP.
Here is what I want to do:
"babel -ismi compound.smi -osdf -0 com_3d.sdf --gen3d"
This runs fine in command as well as in shell, but not in PHP. There is no
problem with file permission.
Can someone please help.
PS:I see t
