Hi Geoff,
On Wed, Apr 1, 2020 at 5:59 PM Geoffrey Hutchison
wrote:
> 3) Handling of unpsecified stereochemistry in SMILES-SDF roundtrip test
>
> Using the SDF file format for the rountrip tests is also problematic.
> Although we correctly write out unspecified atom stereo parities, these are
>
Hi,
Some notes from Geoff regarding the topic:
I'm not sure. We save the constraints before doing anything:
> https://github.com/openbabel/openbabel/blob/master/src/distgeom.cpp#L176
>
> The original code for CheckStereoConstraints was here:
>
Hi,
Here are all the cases I found:
Testing: [C-4].[Si+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
std::string::npos (FAIL)
[C-4] not found in [CH4-4].[SiH4+4]
Testing: [C-4].[Co].[W+4]
/home/tim/openbabel/test/canonmultitest.cpp:50: canon.find(smiles) !=
Hi,
Are there any examples of disconnected SMILES that have this problem? IIRC,
a canonical code is created for each fragment individually and these are
later sorted to create the entire canonical order. A quick look at the code
confirms this but I'll try to test some cases tonight to see if this
molecules and
compare the results to get a better view (with more confidence) of what
would actually change.
Tim
On Mon, Feb 17, 2014 at 6:41 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
Hi,
Are there any examples of disconnected SMILES that have this problem?
IIRC, a canonical code
On Thu, Dec 13, 2012 at 4:25 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
On 12/12/2012 18:15, Tim Vandermeersch wrote:
Hi,
On Wed, Dec 12, 2012 at 5:55 PM, Geoffrey Hutchison geo...@pitt.edu
mailto:geo...@pitt.edu wrote:
On Dec 12, 2012, at 11:44 AM, Noel O'Boyle wrote
Hi,
On Wed, Dec 12, 2012 at 5:55 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
On Dec 12, 2012, at 11:44 AM, Noel O'Boyle wrote:
I can't find it on the Daylight website, or in the OpenSMILES spec,
but Roger has told me (the classic appeal to authority argument)
...
Certainly Daylight's
Hi,
I have commented out the code that caused the compile problems.
However, I have no idea why the OBMinimizingEnergyConformerScore and
OBMinimizingRMSDConformerScore classes Geoff added were removed. Also
I added virtual destructors again but did not make them pure virtual.
I get a link error
Hi,
On Tue, Aug 28, 2012 at 12:36 AM, My Th rei4...@gmail.com wrote:
P , 2012-08-27 23:22 +0200, Tim Vandermeersch rakstīja:
Hi,
I have commented out the code that caused the compile problems.
However, I have no idea why the OBMinimizingEnergyConformerScore
Hi,
On Mon, Jul 23, 2012 at 4:07 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
On 22/07/2012 23:35, Tim Vandermeersch wrote:
Hi,
The problem seems to be in src/fingerprints/finger3.cpp:
//Each bit represents a single substructure; no need for
confirmation when substructure searching
Hi,
I've created a fastsearch index using the FP2, FP3, FP4 MACCS
fingerprints. When I do a substructure search without fingerprints (in
a 10K file), I get 647 hits. With FP2 I also get these hits. However
with the other fingerprints I get more hits. These hits include
molecules that do not have
and MACCS only 12. Is there something I'm missing
here. If the bits simply represent a substructure, the fingerprint
screening should return all possible molecules containing the query.
Thanks in advance,
Tim
On Sun, Jul 22, 2012 at 11:48 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
Hi
Hi,
On Mon, Jul 2, 2012 at 10:09 PM, ovalerio omar.valerio-min...@ichec.ie wrote:
See test/mmff94validate.cpp and the comments at the top. The easiest
to grab is:
MMFF94_dative.mol2
MMFF94_opti.log
Okay I will definitely have a look at that one. Thanks.
surprising. I'll be
Hi,
Deleting the copying of the molecule should be no problem since the
ferrocene specific code is also gone. This code was added to make the
canonicalization of ferrocene-like structures possible. Since it
requires 10! labelings to be analysed, it took forever to find the
canonical labeling.
Hi Noel,
On Sat, Feb 18, 2012 at 8:27 PM, Noel O'Boyle baoille...@gmail.com wrote:
Hey Tim,
I hope all is well with you.
Someone was just asking me whether this is possible to enumerate
tautomers with OB (for ligand preparation for docking), and I've just
discovered your tautomerism code
Hi,
The OBChiralData isn't used anymore. Also the functions
OBAtom::IsClockwise, and OBAtom::IsAntiClockwise are obsolate.
Instead, you should serialize the OBCisTransStereo and
OBTetrahedralStereo data objects. See
http://openbabel.org/api/2.3/group__stereo.shtml for the new
stereochemistry
Hi,
I'm working on adding support for tautomers to openbabel. There is now
an initial commit in trunk with an algorithm to enumerate tautomers
and to find the canonical tautomer. This is based on Roger Sayle's
algorithm: http://www.daylight.com/meetings/emug99/Delany/taut_html/index.htm
There is
Hi Noel,
On Tue, Aug 16, 2011 at 1:43 PM, Noel O'Boyle baoille...@gmail.com wrote:
Hi Tim,
Following up on the report by Robert Kiss, I see that isotopes are not
differentiated in the symmetry classes returned by FindSymmetry (using
OBGraphSym):
obabel -:[C@](Br)(I)([12CH3])[14CH3] -osmi
On Sun, Jun 26, 2011 at 12:38 PM, nms_uk noureddine...@yahoo.com wrote:
Can openbabel build a molfile given a graph data structure representing a
molecule?
If so, Which function/module can do that?
Assuming you have a graph data structure, you first convert the
vertices to OBAtom objects. This
On Sat, Apr 16, 2011 at 10:04 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
On 16/04/2011 20:10, Tim Vandermeersch wrote:
Hi,
I have two local commits with some polishing changes for the depiction
code and svg format. The first just makes the lines thicker and sets
the linecap and linejoin
the w option to bring it back.
Do you know how to fix the unit test? I can't seem to find the right
options for OBConversion::AddOption.
Thanks,
Tim
- Noel
On 16 April 2011 18:30, Tim Vandermeersch tim.vandermeer...@gmail.com wrote:
Hi,
While working with Molsketch, I noticed the stereo
On Sat, Apr 16, 2011 at 7:50 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Sat, Apr 16, 2011 at 7:38 PM, Noel O'Boyle baoille...@gmail.com wrote:
Looking at the unittest I can see why it fails.
I changed the mol format writer so that it does not use wedge/hash
bond designations
On Sat, Apr 16, 2011 at 7:55 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Sat, Apr 16, 2011 at 7:50 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Sat, Apr 16, 2011 at 7:38 PM, Noel O'Boyle baoille...@gmail.com wrote:
Looking at the unittest I can see why it fails
20:10, Tim Vandermeersch tim.vandermeer...@gmail.com wrote:
Hi,
I have two local commits with some polishing changes for the depiction
code and svg format. The first just makes the lines thicker and sets
the linecap and linejoin to round. The before and after results can be
seen in the first
On Thu, Oct 28, 2010 at 5:54 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Dear Ernst-George,
I was able to compile OB on MinGW - though not the static library which
was my original goal. Please see the comments in this bug report,
perhaps they will resolve the problem for you:
On Mon, Oct 25, 2010 at 8:16 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Dear All,
I'm not able to get a static compilation (-DBUILD_SHARED=no) on either
OSX or Windows (MinGW). On OSX it fails at 81% building babel.o, on
MinGW at 23% building mcdlutil.obj. If anyone was
On Sat, Oct 23, 2010 at 11:45 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Oct 21, 2010, at 4:46 AM, Fred Ludlow wrote:
For what I'm doing I can live with both of those, so I think I'll try doing
it this way first - if it works and you think having disconnected matching's
against it.
Igor
On Mon, 2010-10-18 at 16:09 -0400, Tim Vandermeersch wrote:
On Mon, Oct 18, 2010 at 9:49 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
Tim,
Something still not working for me -
Here is what I do:
g++ -fopenmp -g -O3 -g -O2 -I/usr/local/ -D_LIB -D_MT
/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-Bstatic
-Wl,-rpath,/usr/local/lib:
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]
filipp...@mail.nih.gov wrote:
It builds nicely on Fedora 12, x64 system.
Some points:
1
don't 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
Hi,
The continuous build script now updates only one revision at a time.
This should allow to find the commit(s) that break unit tests faster.
This is especially useful for developers using git that use git svn
dcommit to push several commits at once to the svn repo.
The new continuous_0_2.cmake
On Sun, Oct 17, 2010 at 6:04 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
On Oct 17, 2010, at 11:59 AM, Tim Vandermeersch wrote:
Hi,
The continuous build script now updates only one revision at a time.
This should allow to find the commit(s) that break unit tests faster
On Fri, Oct 15, 2010 at 11:40 PM, Igor Filippov [Contr]
filipp...@mail.nih.gov wrote:
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
On Sat, Oct 16, 2010 at 8:35 PM, Craig A. James cja...@emolecules.com wrote:
Can someone give me a quick tutorial or point me to documentation on how to
run the entire test set? make test doesn't seem to do anything, and the
shell scripts in the test directory don't seem to do the trick.
On Sat, Oct 16, 2010 at 8:42 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Sat, Oct 16, 2010 at 8:35 PM, Craig A. James cja...@emolecules.com wrote:
Can someone give me a quick tutorial or point me to documentation on how to
run the entire test set? make test doesn't seem to do
On Wed, Oct 13, 2010 at 8:58 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
3429680: [Li+251] 24639246
3429701: [ClH+276] 24639289
3429702: [n+251]1(C)c1 24639291
These are an easy fix to the SMILES reader. Currently, we only take single
digits for charge. Now I think the
On Thu, Oct 14, 2010 at 5:31 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 22 September 2010 14:33, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
The automorphism based version was not usable for general use since
there were memory issues. The automorphism search is actually memory
Hi,
Here are the results from the shuffle (10x) test for the 5 million
compounds in the eMolecules database. In general the results are good
and only 33 canonicalization errors remain which should be easy to
fix.
Process stops: 3429680, 3429701, 3429702, 3429717, 3429742, 3429767,
3429887, ...
On Tue, Oct 12, 2010 at 3:14 AM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Mon, Oct 11, 2010 at 7:16 PM, Craig A. James cja...@emolecules.com wrote:
On 10/11/10 8:52 AM, Tim Vandermeersch wrote:
I still need to figure out how to deal with metallocene compounds
where there are 8
Hi,
On Mon, Oct 11, 2010 at 2:42 AM, Craig A. James cja...@emolecules.com wrote:
Here are the results of another 1.2 million SMILES shuffle tests. Each
shuffle is 20 randomized versions of one SMILES (so 24 million
canonicalizations total).
Most, maybe all of these are repeates of
On Mon, Oct 11, 2010 at 6:24 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
In general, performance is good for relase now. The canonconsistent
test completes in 30 seconds here. Converting cansmi-roundtrip.smi to
can takes 16 seconds, to smi takes 8 so canonical coding takes about
50%
On Mon, Oct 11, 2010 at 7:20 PM, Craig James craig_ja...@emolecules.com wrote:
This is a cross-post from the OpenBabel-devel mailing list.
On 10/11/10 8:52 AM, Tim Vandermeersch wrote:
I still need to figure out how to deal with metallocene compounds
where there are 8 or more neighbors
On Mon, Oct 11, 2010 at 7:16 PM, Craig A. James cja...@emolecules.com wrote:
On 10/11/10 8:52 AM, Tim Vandermeersch wrote:
I still need to figure out how to deal with metallocene compounds
where there are 8 or more neighbors with the same symmetry class. I
already have a hack to handle
Hi,
Two weeks ago, I added some changes to the cmake build system to
improve static building. There is no documentation for this yet but
I'll give an overview in this mail. I'll add the complete version to
the docs/wiki.
* Linux
There are two use cases for static building which determine the
Hi,
On Thu, Oct 7, 2010 at 12:25 AM, Craig A. James cja...@emolecules.com wrote:
On 10/6/10 9:58 AM, Tim Vandermeersch wrote:
I was looking through the new canon.cpp code, and it looks like a
huge improvement over the original, and the tests we've been
running are confirming
On Tue, Oct 5, 2010 at 2:21 AM, Craig A. James cja...@emolecules.com wrote:
On 10/4/10 2:10 PM, Noel O'Boyle wrote:
Hello all,
Back on the 19/03/2009 I emailed to this list with the subject
Canonical SMILES performance about a test set of around 18000
PubChem 3D structures. I did the
On Tue, Oct 5, 2010 at 5:52 AM, Craig A. James cja...@emolecules.com wrote:
Here's another molecule with two different canonical SMILES. In this case,
the molecule is very simple:
http://www.emolecules.com/image?db=549id=513261width=500height=500
[C@@H]([...@h](CO)O)([C@@H](CO)O)O
Hi,
On Tue, Oct 5, 2010 at 11:51 PM, Craig A. James cja...@emolecules.com wrote:
Hi Tim,
I was looking through the new canon.cpp code, and it looks like a huge
improvement over the original, and the tests we've been running are
confirming this. This is a big step forward.
But I noticed
On Mon, Sep 27, 2010 at 9:42 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
I struggle with CMake, so I'll ask here to avoid depressing myself any
further.
First, running CMake on a fresh SVN download fails to find wxWidgets
on my system, although it is found by the existing version. Why is
Hi,
We now have continuous build for OB on linux (ubuntu 9.04, 64bit). It
checks every 5 minutes to see if there are new commits. It doesn't run
when there are no new commits so 5 minutes seems a reasonable
interval. It is set up to run 24/7
http://my.cdash.org/index.php?project=Open+Babel
# should be the starting SMILES with stereo
Whatever you think of the merits of preserving chiral stereochemistry
in a 0D mol file, this was working until the 31 file update on Sunday
(http://my.cdash.org/index.php?project=Open+Babeldate=2010-09-19).
- Noel
On 20 September 2010 21:23, Tim
Hi,
FindStereogenicUnits doesn't detect square planar centers yet. It
would not be hard to add this but I'm not sure how to decide when an
atom should be tetrahedral or square planar. I currently have a short
list of atoms that are sp AFAIK: Rh, Ir, Pd, Pt, Au. There are also
metals like Ni that
On Mon, Sep 20, 2010 at 10:15 AM, Noel O'Boyle baoille...@gmail.com wrote:
Hi Tim,
Last night's build had some problems with pytest_sym and smiles_test.
Looks like debugging messages left in the code:
e.g. http://my.cdash.org/testDetails.php?test=3016547build=98883
Yes, this fixed in svn
Hi,
Here are some comments regarding my commits from yesterday.
The type used to represent automorphisms has been changed from
std::vector std::mapunsigned int, unsigned int to std::vector
std::pairunsigned int, unsigned int . This makes a huge difference
in performance but might require small
On Sun, Sep 19, 2010 at 7:53 PM, Noel O'Boyle baoille...@gmail.com wrote:
testkekule.py has identified a regression due to recent changes in
canonicalisation. The following smiles strings represent the same
molecule, a benzene with three C-14s in a row:
obabel -:[14cH]1[14cH][14cH]ccc1 -ocan
to the list once this code is in svn.
Tim
Gert
On Sep 15, 2010, at 4:46 PM, Tim Vandermeersch wrote:
Are you using OB trunk? If so, the canonical coding algorithm is slow
at the moment but this should be improved in the next couple of days.
Tim
On Thu, Aug 12, 2010 at 5:41 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
base class?) Then the original OBConversion gets destroyed. It tries
to delete the source again as part of delete pLineEndBuf but it has
already been deleted. If we had access to the destructor we could fix
Hi,
Can we set a release date? How about next Monday? Is everyone back
from vacation?
There is a wiki page with the 2.3 projects here:
http://openbabel.org/wiki/Version_2.3_Projects
I'll mainly be working on documentation, fixing some bugs and other
small code changes like opaque pointers,
Did you call OBForceField::GetCoordinates after minimizing? The
forcefield works on a copy of the molecule so you have to get the
updated coordinates explicitly.
On Sun, Aug 1, 2010 at 12:44 AM, N David Brown hubd...@googlemail.com wrote:
..whoops, that's FOR_ATOMS_OF_MOL of course, just a typo
On Sat, Jul 31, 2010 at 1:40 AM, David Lonie lonieda...@gmail.com wrote:
On Fri, Jul 30, 2010 at 1:06 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
Hans De Winter and Silicos whipped up a 2-page quick reference PDF intended
to be printed double-sided on one sheet of paper. They wish to
On Thu, Jul 22, 2010 at 3:58 PM, Noel O'Boyle baoille...@gmail.com wrote:
Hello Tim,
I've just been checking OBAlign in trunk and writing the doxygen docs.
There's just one missing feature - would it be possible for you to
alter the isomorphism mapper so that it can take an OBBitVec as a
On Mon, Jul 12, 2010 at 6:14 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Jul 8, 2010, at 12:24 PM, Tim Vandermeersch wrote:
It seems that the OBMol::FindChiralCenters() has been commented out in
the latest development code. Is there a reason for this or do I just
miss something
On Thu, Jul 8, 2010 at 5:58 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Thu, Jul 8, 2010 at 5:46 PM, Hans De Winter
hans.dewin...@silicos.com wrote:
Dear,
It seems that the OBMol::FindChiralCenters() has been commented out in
the latest development code. Is there a reason
On Mon, Jul 5, 2010 at 5:56 PM, Craig A. James cja...@emolecules.com wrote:
On 7/2/10 4:44 AM, Tim Vandermeersch wrote:
Hi,
I have put the old aromaticity algorithm back since unit tests were
failing. I tried to debug the problem but didn't get far. When Craig
has time to look at this, I
Hi,
While checking if the spectrophore code builds on windows I noticed
the charge methods (qeq and qtie) require the error function erf. This
is not standard and MSVC doesn't have it but boost does. I'm changing
the build system to find boost and use it when available. Otherwise,
the charge
Hi,
A few questions regarding the next release: Are we releasing 2.2.4 or
2.3? Are there any new features? Do we want to include Noel's Kabsch
alignment?
There are probably more people interested in this and I don't think
there is a wiki page for coordination yet.
Tim
Hi,
I have put the old aromaticity algorithm back since unit tests were
failing. I tried to debug the problem but didn't get far. When Craig
has time to look at this, I can merge this again.
Although electron counting isn't the problem with the failing unit
test, Craig has a point. There should
On Thu, Jul 1, 2010 at 11:02 AM, Noel O'Boyle baoille...@gmail.com wrote:
On 30 June 2010 16:44, Geoffrey Hutchison ge...@geoffhutchison.net wrote:
bliss. bliss is GPLv2 and available from
http://www.tcs.hut.fi/Software/bliss/. My code also has a dependency
on Eigen2.
I'm not thrilled at the
On Thu, Jul 1, 2010 at 3:56 PM, Konstantin Tokarev annu...@yandex.ru wrote:
Hi,
I think geometry optimization steps have slightly different nature than
set of molecular conformers, and possibility to distinguish this data
types in software using OB (e.g., Avogadro) will be useful. Also, there
On Thu, Jul 1, 2010 at 4:39 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 1 July 2010 15:36, Tim Vandermeersch tim.vandermeer...@gmail.com wrote:
On Thu, Jul 1, 2010 at 3:56 PM, Konstantin Tokarev annu...@yandex.ru wrote:
Hi,
I think geometry optimization steps have slightly different nature
On Wed, Jun 23, 2010 at 7:43 PM, Craig A. James cja...@emolecules.com wrote:
On 6/23/10 9:44 AM, Tim Vandermeersch wrote:
Sorry to keep nagging, but the remaining test failure seems to be real
bug: http://my.cdash.org/testDetails.php?test=2416695build=76838
It says that babel -ismi -osmi
On Wed, Jun 23, 2010 at 6:02 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 23 June 2010 01:37, Tim Vandermeersch tim.vandermeer...@gmail.com wrote:
On Tue, Jun 22, 2010 at 11:08 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum greg.land
On Tue, Jun 22, 2010 at 10:06 AM, Noel O'Boyle baoille...@gmail.com wrote:
On 22 June 2010 03:31, Craig A. James cja...@emolecules.com wrote:
On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
The changes
On Tue, Jun 22, 2010 at 12:05 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 22 June 2010 09:06, Noel O'Boyle baoille...@gmail.com wrote:
On 22 June 2010 03:31, Craig A. James cja...@emolecules.com wrote:
On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey
On Tue, Jun 22, 2010 at 4:31 AM, Craig A. James cja...@emolecules.com wrote:
On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
The changes are in svn trunk. The current test set (aromatics.smi,
attype.00.smi
On Tue, Jun 22, 2010 at 6:28 PM, Craig A. James cja...@emolecules.com wrote:
On 6/21/10 2:49 PM, Tim Vandermeersch wrote:
The LSSR algorithm is simple:
for S in (3, 4, 5, 6, ...)
find all rings of size S, add to LSSR
if all cyclic atoms and bonds are included in at
least one
Hi Greg,
On the openbabel devel mainling list there was discussion about the
Largest Set of Smallest Rings (LSSR). RDKit calls this symmetric SSSR
I think. Craig proposed an algorithm to directly select this LSSR from
the found rings. This doesn't work for all cases though.
Most of these
On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi Tim,
On Tue, Jun 22, 2010 at 9:34 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On the openbabel devel mainling list there was discussion about the
Largest Set of Smallest Rings (LSSR). RDKit calls
On Tue, Jun 22, 2010 at 11:08 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi Tim,
On Tue, Jun 22, 2010 at 9:34 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On the openbabel devel mainling
On Mon, Jun 21, 2010 at 6:43 PM, Craig A. James cja...@emolecules.com wrote:
The recent discussion of SSSR bugs prompted me to dig back through my emails
to one I wrote on 20 November 2007 to the BlueObelisk mailing list. Here it
is in its entirety.
Craig
On Mon, Jun 21, 2010 at 7:24 PM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
On Mon, Jun 21, 2010 at 6:43 PM, Craig A. James cja...@emolecules.com wrote:
The recent discussion of SSSR bugs prompted me to dig back through my emails
to one I wrote on 20 November 2007 to the BlueObelisk
On Fri, Jun 18, 2010 at 12:59 PM, Noel O'Boyle baoille...@gmail.com wrote:
Hello all,
There's a nightly build of doxygen available at
http://openbabel.org/dev-api. It uses Doxygen 1.7.0 and so it looks
quite a bit different. We can edit the style file if necessary to
change the defaults. The
On Fri, Jun 18, 2010 at 12:06 PM, Konstantin Tokarev annu...@yandex.ru wrote:
Recently OpenBabel was added to upstream tracker of linuxtesting.org
http://linuxtesting.org/upstream-tracker/versions/openbabel.html
This service generates header-based tests and checks API and ABI
compatibility
Hi,
Andrew has raised some important issues with outdated docs etc. I
think we should turn all wiki pages into in-source documentation
(using doxygen for example) that is updated nightly. The current wiki
is just not suited for maintainability IMHO, there is no real overview
of files. We can't
Hi,
Has anyone attempted building openbabel with the OpenSUSE build
service before? I tried it in ubuntu here but didn't get very far. I'm
now installing OpenSUSE, that should hopefully fix the problems I was
having.
I couldn't find openbabel so I created it. I can add users to
collaborate...
On Wed, Mar 31, 2010 at 10:23 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 31 March 2010 20:58, Tim Vandermeersch tim.vandermeer...@gmail.com wrote:
Hi,
Has anyone attempted building openbabel with the OpenSUSE build
service before? I tried it in ubuntu here but didn't get very far. I'm
On Mon, Mar 22, 2010 at 7:13 PM, Konstantin Tokarev annu...@yandex.ru wrote:
22.03.10, 18:56, Tim Vandermeersch tim.vandermeer...@gmail.com:
On Sun, Mar 21, 2010 at 12:48 PM, Konstantin Tokarev wrote:
Are there any perforamnce benchmark scripts for OB? E.g., I'd like to test
if OB
2010/3/23 Konstantin Tokarev annu...@yandex.ru:
23.03.10, 20:30, Tim Vandermeersch tim.vandermeer...@gmail.com:
On Mon, Mar 22, 2010 at 7:13 PM, Konstantin Tokarev wrote:
22.03.10, 18:56, Tim Vandermeersch :
On Sun, Mar 21, 2010 at 12:48 PM, Konstantin Tokarev wrote
On Sun, Mar 21, 2010 at 12:48 PM, Konstantin Tokarev annu...@yandex.ru wrote:
Are there any perforamnce benchmark scripts for OB? E.g., I'd like to test if
OB compiled by Intel is faster than by GCC or if -O3 optimization with Intel
is more effective than -O2
Are there specific parts of the
Hi,
On Wed, Mar 3, 2010 at 4:41 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Mar 3, 2010, at 10:31 AM, Noel O'Boyle wrote:
* test/graphsymtest.cpp: There are still some cases were this test
fails. However, it mainly has to do with N atoms becoming aromatic
On Wed, Mar 3, 2010 at 6:42 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Mar 3, 2010, at 12:40 PM, Tim Vandermeersch wrote:
Should we change this in the unit test (i.e. use the new smiles
string)?
I already changed it -- the aromatic SMILES is there. Any failures
Hi,
On Tue, Mar 2, 2010 at 10:21 PM, David Lonie lonieda...@gmail.com wrote:
On Tue, Mar 2, 2010 at 4:16 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
Is there some method to this that I'm missing? Would anyone object to
the change I propose?
The main requirement is that you don't
Hi,
On Sat, Feb 20, 2010 at 6:57 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
On Feb 20, 2010, at 12:18 PM, Tim Vandermeersch wrote:
best option for nitrogen. Detecting chiral (bridge-head) nitrogen
atoms seems complex...
Well, the starting place would be to check
Hi,
On Sat, Feb 20, 2010 at 4:22 PM, Noel O'Boyle baoille...@gmail.com wrote:
On 20 February 2010 13:35, Geoffrey Hutchison ge...@geoffhutchison.net
wrote:
http://my.cdash.org/index.php?project=Open%20Babel
Here's another failure. This is on the SMILES/SMARTS match test (i.e., all
of
On Tue, Oct 6, 2009 at 6:41 PM, Craig A. James cja...@emolecules.com wrote:
Noel O'Boyle wrote:
I'm trying to profile an optimization using MMFF94 (obminimize) using
OB22x and gprof as follows:
I'll second Geoff's recommendation of valgrind. It works on unmodified code,
and runs it in a
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