On Fri, Sep 16, 2011 at 8:33 AM, Nina Jeliazkova
wrote:
>
>
> On 16 September 2011 09:29, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
>
>>
>>
>> On Thu, Sep 15, 2011 at 12:33 PM, Fredrik Wallner wrote:
>>
>>> Hi again,
>>> (I realized i forgot to cc the list in my last reply)
>>> 15
On Thu, Sep 15, 2011 at 12:33 PM, Fredrik Wallner wrote:
> Hi again,
> (I realized i forgot to cc the list in my last reply)
> 15 sep 2011 kl. 12:29 skrev Martin Guetlein:
>
> On Thu, Sep 15, 2011 at 12:21 PM, Fredrik Wallner wrote:
>
>> Hi,
>>
>> Since the fp2 fingerprint is a path-based hashed f
Hi everyone, I have this application where I need to introduce custom atom
types.
The problem is I also need to perform sub-structure isomorphism and without
real atom types, that poses a problem in matching the sub-structure.
Is there a way to add an atom type(atomic number) during run time?
Th
After testing it out on your system, it seems to be that "make
install" fails if using EIGEN2 and the Python bindings (this is
already reported at
http://sourceforge.net/tracker/?func=detail&aid=3399341&group_id=40728&atid=428742).
I need to fix this.
If not using Eigen2, then it all works fine fo
Ah, thanks!
Igor
On Thu, 2011-09-15 at 11:04 -0400, Geoffrey Hutchison wrote:
> > Actually, I used WriteString() when I got that extra newline character:
> >
> > my $inchi = $obinchi->WriteString($obmol);
>
> my $inchi = $obinchi->WriteString($obmol, true); # trim final whitespace
>
> Hope th
> Actually, I used WriteString() when I got that extra newline character:
>
> my $inchi = $obinchi->WriteString($obmol);
my $inchi = $obinchi->WriteString($obmol, true); # trim final whitespace
Hope that helps,
-Geoff
Actually, I used WriteString() when I got that extra newline character:
my $inchi = $obinchi->WriteString($obmol);
Igor
On Thu, 2011-09-15 at 10:18 -0400, Geoffrey Hutchison wrote:
> On Sep 15, 2011, at 8:33 AM, Noel O'Boyle wrote:
>
> > I understand what you're saying, but that is on purpose.
On Sep 15, 2011, at 8:33 AM, Noel O'Boyle wrote:
> I understand what you're saying, but that is on purpose. The library
> API is geared towards converting files, rather than returning string
> representations for further processing.
There is, of course OBConversion::WriteString(&mol, true), whic
Ah, I see what you mean.
Thanks,
Igor
On Thu, 2011-09-15 at 13:33 +0100, Noel O'Boyle wrote:
> I understand what you're saying, but that is on purpose. The library
> API is geared towards converting files, rather than returning string
> representations for further processing.
>
> - Noel
>
> On
I understand what you're saying, but that is on purpose. The library
API is geared towards converting files, rather than returning string
representations for further processing.
- Noel
On 15 September 2011 13:22, Igor Filippov wrote:
> Speaking of InChI and InChIKey - I noticed that InChIKey cal
Speaking of InChI and InChIKey - I noticed that InChIKey calculated
through libopenbabel (via a Perl script in my case) seems to end with a
carriage return. Surely the library should return just the InChI or
InChIKey string without "\n" stuck at the end?
Igor
On Thu, 2011-09-15 at 08:07 -0400, Ch
On 05/09/2011 19:27, Ken Smith wrote:
In response to this, I have made a few changes to the way OpenBabel
calculates InChI.
> E.g. for a proton [H+], I get:
>
> InChI=1S/H/q+1
> (ASSFXGJQJOXDAB-UHFFFAOYSA-N)
>
> But I *think* I should be getting:
>
> InChI=1S/p+1
> (GPRLSGONYQIRFK-UHFFFAOYSA-N)
Done.
1) I purged any previous version of python-babel (either manually
installed or via apt-get).
2) I added the local python libraries folder to LD_LIBRARY_PATH (I had
previously added the local OpenBabel path)
3) I modified all the relevant lines at CMakeCache.txt in the build
directory.
Hi again,
(I realized i forgot to cc the list in my last reply)
15 sep 2011 kl. 12:29 skrev Martin Guetlein:
> On Thu, Sep 15, 2011 at 12:21 PM, Fredrik Wallner wrote:
> Hi,
>
> Since the fp2 fingerprint is a path-based hashed fingerprint, there is no
> such list.
>
> But the bit at positon i
One Python is 2.6, the other is 2.7. You need to decide which you want
to use as you can't compile against 2.7 and then use the 2.6 one. Can
you check all Python related variables in CMakeCache to see whether
they point to the version you want to use (and then "touch
openbabel-python.i" and recompi
Debian 6.0.2 64-bit.
Yes, I have OpenBabel installed globally using apt-get because there are
several packages that depend on it. I also have it locally. PYTHONPATH
now points to the locally installed version, but I was getting the same
error before defining the environmental variable PYTHONPAT
Hi,
I would like to have the corresponding fragment for each bit of the fp2
fingerprint.
Using the -s param (as described by Noel here:
http://forums.openbabel.org/Need-help-in-calculationg-tanimoto-coefficient-td3233604.html)
is not very practical for what I want to do, I would prefer a list of 1
On 15 September 2011 10:37, Miro Moman wrote:
> So, I do not understand what is wrong. Is this a bug?
What operating system? Do you have other versions of Open Babel
installed. Also, what is the result of testing the installation as
described in the install instructions:
http://openbabel.org/docs
So, I do not understand what is wrong. Is this a bug?
On 09/14/2011 02:50 PM, Geoff Hutchison wrote:
>> How do I know if Swig is actually being used?
> The development version doesn't include any scripting modules, so if it's
> even attempting to compile/link, then it's using swig.
>
> -Geoff
-
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