I've never heard about ChemJSON before, but...
Where does it say which one's C1 and which one's H7? All I can tell
from this is all atoms are linked with the same type of bond (1 stands
for aromatic perhaps?) What do you draw if the -0.932892 is missing
from the json the client sent you?
It's great, Noel, but... no MCS in OpenBabel? :(
I completely agree that my implementation is not perfect but it does
work within some reasonable limits...
Igor
On 12/4/2012 12:48 PM, Craig James wrote:
Very nice ... thanks for doing this. Things like this should be
available in the OB
Wow - I never realized there are API documentation for 2.3.x branch -
thank you Chris! I just always went through the front page -
openbabel.org and didn't know there is backdoor to the more recent docs.
Igor
On Wed, 2012-08-29 at 09:50 -0400, Chris Morley wrote:
On 28/08/2012 16:58, Jaehong
Dear colleagues,
Is it possible to set a bond as wavy or to check if it has wavy
attribute in OB similar to SetWedge() and IsWedge()?
Best regards,
Igor
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:56 -0400, Tim Vandermeersch wrote:
Hi,
On Tue, Jul 31, 2012 at 11:50 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Answering my own email - it seems if I surround lines 303 and 304 in
tools/obabel.cpp with:
#if defined(USING_DYNAMIC_LIBS)
...
#endif
I will get
This is very helpful - thank you!
I was able to make a static libopenbabel on OS X 10.5 with eigen3 and
edited plugin.cpp.
Unfortunately there seem to be more problems with MinGW build - I'm
getting the following error - perhaps someone knows what to do:
[ 79%] Built target openbabel
[ 79%]
First of - congratulations on the paper! This gives us a way to give OB
developers their due by citing the publication.
I have found a few examples of Substances from Pubchem where OB 2.3.0
gives segfault - my guess is due to the presence of a dummy atom - e.g.
6361218
-OEChem-04171109372D
Fantastic, thank you!
Igor
On Tue, 2011-10-11 at 13:07 -0400, My Th wrote:
O , 2011-10-11 12:52 -0400, Igor Filippov [Contr] rakstīja:
First of - congratulations on the paper! This gives us a way to give OB
developers their due by citing the publication.
I have found a few examples
6. CIR
what's wrong with CIR?
Igor
On Tue, 2011-04-05 at 11:36 -0400, qiancheng shen wrote:
Dear Geoffrey,
I appreciate your help very much ! Thank you for your time.
At first I thought it is a very simple problem, so I am
confident to find such a tool when a chemist
Benoit,
I don't think OpenBabel supports it out of the box.
There are other free/open solutions - OPSIN from Peter Murray-Rust,
converts IUPAC names into structures, and CIR - converts anything into
anything as long as it's one of 100 million molecules in our database:
, Noel O'Boyle wrote:
You need to cast it to the specific subclass first. Try calling
$newad = toSetData($ad)
and then
if ($newad $newad-GetAlias() eq Xx)
- Noel
On 21 March 2011 15:06, Igor Filippov [Contr] filipp...@mail.nih.gov wrote:
Dear Colleagues,
I need to implement in Perl
Dear Colleagues,
I need to implement in Perl a procedure which is C++ looks like the
following:
AliasData *ad;
ad = (AliasData *) a-GetData(OBGenericDataType::SetData);
if (ad != NULL ad-GetAlias() == Xx)
This is what I have at the moment and it does not work unfortunately:
Works like a charm, this is exactly what I needed!
Thanks,
Igor
On Wed, 2010-12-15 at 10:27 -0500, Geoffrey Hutchison wrote:
I've never seen this before, but it looks like libopenbabel is now
printing warning messages on stderr:
==
*** Open Babel Warning in
I've never seen this before, but it looks like libopenbabel is now
printing warning messages on stderr:
==
*** Open Babel Warning in CreateCisTrans
Error in cis/trans stereochemistry specified for the double bond
I think this is wrong - a library should not spit
I was just going to say RTFM, but to my shock and surprise the manual
actually does say cmake ../src!!!
http://openbabel.org/docs/2.3.0/Installation/install.html#compiling-open-babel
John, you should use cmake ../ I have no slightest idea who put
cmake ../src on the above page, it's just plain
://www.cmake.org/Wiki/CMake_FAQ#Out-of-source_build_trees)
- Noel
On 9 December 2010 19:48, Igor Filippov [Contr] filipp...@mail.nih.gov
wrote:
Hmmm, looks like the instructions published on that website are a bit
tricky:
tar zxf openbabel-2.3.0.tar.gz
mv openbabel-2.3.0 src
mkdir build
cmake
I would be very interested in this too, if it's possible in a general
case.
Best regards,
Igor
On Tue, 2010-11-30 at 05:48 -0500, Hans De Winter wrote:
All,
I'm using the OB C++ API and I wwas wondering whether there is a way
to retrieve bot Kekule structure from an aromatic system (if
Duan,
Looks like you need to install boost. On my Fedora 13 system the
necessary package is boost-devel.
Hope this helps,
Igor
On Fri, 2010-11-12 at 03:18 -0500, 段宝根 wrote:
Hi,
I want to install openbabel_2.3.0 in linux OS, but some errors are
found in the course of compiling.
attaching make.out output of make.
Igor
On Thu, 2010-10-21 at 20:25 -0400, Tim Vandermeersch wrote:
On Thu, Oct 21, 2010 at 1:35 AM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Wed, Oct 20, 2010 at 4:29 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Tim,
I'll take
/wiki/CMake
but it's so terse I cannot figure out how to use this information for a
project that does not use cmake itself. And I'm not a cmake expert at
all unfortunately...
Igor
On Sat, 2010-10-16 at 10:23 -0400, Tim Vandermeersch wrote:
On Fri, Oct 15, 2010 at 11:40 PM, Igor Filippov [Contr
passed, 41 tests failed out of 56
Far cry from 100% PASS on dynamically linked babel.
Igor
On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wrote:
Hi,
On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Tim,
Thanks, I can build my executable per your
get
the following:
27% tests passed, 41 tests failed out of 56
Far cry from 100% PASS on dynamically linked babel.
Igor
On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wrote:
Hi,
On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Tim
work for static builds yet. Only the babel
executable with all plugins.
Igor
On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wrote:
Hi,
On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Tim,
Thanks, I can build my executable per your
It builds nicely on Fedora 12, x64 system.
Some points:
1) When building with -DBUILD_SHARED=no one needs to make sure static
zlib exists somewhere (libz.a) otherwise the error message which cmake
gives is somewhat confusing.
2) build/lib is full of dynamic libs (.so) even with BUILD_SHARED=no.
Was there some significant change in how libopenbabel should be linked?
It was working fine with 2.2.3 release.
Igor
On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote:
Thanks. Corrected in r3897.
Chris
On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
I've run into a problem with an SD
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