Hi,
While working with Molsketch, I noticed the stereo bond flags are not
written for many formats. I wrote a simple unit test for this and
committed this. Until recently, this was working. I'll try to find the
commit but if anyone has a clue please let me know.
Thanks,
Tim
-
ecify 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 wrote:
>> Hi,
>>
>> While working with Mol
On Sat, Apr 16, 2011 at 7:50 PM, Tim Vandermeersch
wrote:
> On Sat, Apr 16, 2011 at 7:38 PM, Noel O'Boyle 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 by d
On Sat, Apr 16, 2011 at 7:55 PM, Tim Vandermeersch
wrote:
> On Sat, Apr 16, 2011 at 7:50 PM, Tim Vandermeersch
> wrote:
>> On Sat, Apr 16, 2011 at 7:38 PM, Noel O'Boyle wrote:
>>> Looking at the unittest I can see why it fails.
>>>
>>> I changed t
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 pair of images:
Thicker lines before: http://imagebin.org/148554
On Sat, Apr 16, 2011 at 9:38 PM, Noel O'Boyle wrote:
> The C=O in http://imagebin.org/148555 should be symmetrical, I think.
I've added some additional rules to handle aldhydes and ketones
separately. The new results: http://imagebin.org/148565
Tim
> - Noel
>
> On 16
On Sat, Apr 16, 2011 at 10:04 PM, Chris Morley 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
>>
On Sun, Jun 26, 2011 at 12:38 PM, nms_uk 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 can be done using OB
Hi Noel,
On Tue, Aug 16, 2011 at 1:43 PM, Noel O'Boyle 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
> C(Br)(I)([12C
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,
On Thu, Nov 10, 2011 at 4:32 PM, David Lonie wrote:
> Hi list,
>
> In atom.h, there are the following three functions:
>
> //! \return the internal atom index (e.g., inside an OBMol)
> unsigned int GetIdx() const { return((int)_idx); }
> unsigned int GetIndex() const
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 imple
Hi Noel,
On Sat, Feb 18, 2012 at 8:27 PM, Noel O'Boyle 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 from last Novem
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. Th
Hi,
On Mon, Jul 2, 2012 at 10:09 PM, ovalerio 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 curious what
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
FP4 25 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
wrote:
> Hi,
Hi,
On Mon, Jul 23, 2012 at 4:07 PM, Chris Morley 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
>> c
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 wi
Hi,
On Tue, Aug 28, 2012 at 12:36 AM, My Th 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 and
>&g
Hi Benoit,
On Tue, Aug 28, 2012 at 3:10 PM, benoit-leblanc
wrote:
> Dear All,
>
> Sorry for the mess I've created. In fact I started to work from the
> latest stable version 2.3.1. And then we I got the SVN version in, I
> did not check that there was some update in between for the Conformer
> Se
Hi,
I'm working on an OBFormat for parsing SMILES using my new Smiley parser.
The initial tests look good but there is a specific problem regarding
aromatic nitrogens. When I read a molecule using the new format and write
out the caonical smiles, all aromatic nitrogens are written out as "[nH]".
D
Hi,
In OB trunk you can now find the new SmileyFormat. It reads SMILES using my
new Smiley parser (http://moldb.net/smiley.php). Since this is a single
header file, I've just included it in OB to avoid an additional dependency.
The main reason for doing this was to test my new parser but if we can
Hi,
I recently added the smiley test, this is still experimental and I have to
check it on more platforms etc. So don't worry about this one.
I have no idea why the MMFF94 test fails though. I assume you were not
wroking on the force field code?
Tim
On Thu, Nov 29, 2012 at 7:49 PM, David van de
Hi,
On Wed, Dec 12, 2012 at 5:55 PM, Geoffrey Hutchison 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 Dep
On Thu, Dec 13, 2012 at 4:25 PM, Chris Morley wrote:
> On 12/12/2012 18:15, Tim Vandermeersch wrote:
> > Hi,
> >
> > On Wed, Dec 12, 2012 at 5:55 PM, Geoffrey Hutchison > <mailto:geo...@pitt.edu>> wrote:
> >
> >
> > On Dec 12, 2012, at 1
Hi,
Ghemical should never be used. It was only used for testing the initial
implementation due to it's simplicity.
MMFF94 should be used for drug-like molecules. GAFF is also for
organic/biological molecules. UFF can be used for cases where MMFF94/GAFF
setup fails. There might be some cases where
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
tch on a few million 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 hav
Hi,
While implementing a test described by Craig for multi-fragment SMILES
canonicalization, I found this strange bug:
$ echo "[C-4]" | babel -ismi -ocan
[C-4]
1 molecule converted
16 audit log messages
$ echo "[C-4].C" | babel -ismi -ocan
C.[CH4-4]
1 molecule converted
14 audit log messages
T
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) !=
std::string
Hi,
While porting the depiction code to Helium, I've made a small improvement
to how aromatic rings are drawn. I've also updated the OpenBabel code to
include this improvement. Here is a simple before and after depiction:
http://www.moldb.net/timvdm/before.svg
http://www.moldb.net/timvdm/after.sv
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:
> https://github.com/openbabel/openbabel/blob/master/sr
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
> i
Hi,
Using openbabel trunk there are still a number of cases where highly
symmetric molecules can not be canonicalized. See my blog posts for
examples: http://timvdm.blogspot.com
To correctly select a minimum or maximum canonical labeling, I was
planning to implement the algorithm from the 1993 Ra
classes. This would mean symmetry classes are
topologically only (not regarding stereochemistry).
Tim
> - Noel
>
> 2009/9/28 Tim Vandermeersch :
>> Hi,
>>
>> Using openbabel trunk there are still a number of cases where highly
>> symmetric molecule
On Wed, Sep 30, 2009 at 10:02 AM, Noel O'Boyle wrote:
> 2009/9/29 Craig A. James :
>> Tim Vandermeersch wrote:
>>>
>>> On Tue, Sep 29, 2009 at 10:50 PM, Noel O'Boyle
>>> wrote:
>>>>
>>>> Nice work.
>>>> http://
On Tue, Sep 29, 2009 at 11:24 PM, Craig A. James wrote:
> Tim Vandermeersch wrote:
>>
>> On Tue, Sep 29, 2009 at 10:50 PM, Noel O'Boyle
>> wrote:
>>>
>>> Nice work.
>>> http://timvdm.blogspot.com/2009/09/automorphism-group-bliss.html
>&g
On Wed, Sep 30, 2009 at 3:47 PM, Noel O'Boyle wrote:
> A correction; it's not that it misses the initial conformation. It's
> that it doesn't include a torsion angle of 0. Which I think is
> definitely a bug.
yes, that would definitely be a bug. Can you fix this?
> 2009/9/30 Noel O'Boyle :
>> Th
On Mon, Oct 5, 2009 at 6:05 PM, Geoffrey Hutchison
wrote:
>> When a test fails (e.g. file formats not available), it still
>> continues and can easily segfault. Is it possible to make OB_ASSERT
>
> I think we'd want something like OB_FATAL for that case.
We have OB_REQUIRE for this:
void report_
On Tue, Oct 6, 2009 at 6:41 PM, Craig A. James 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 virtual machine
On Thu, Oct 15, 2009 at 12:28 AM, Igor Filippov [Contr]
wrote:
> TJ,
>
> Glad I was able to help :)
> As for myself I only needed libopenbabel-3.dll which I get with:
>
> ./configure --disable-dynamic-modules
> make
> make install
>
> Compilation of babel.exe breaks, but libopenbabel DLL contains
On Wed, Oct 14, 2009 at 6:09 PM, Jerome Pansanel
wrote:
> Hi,
>
> The FindChiralCenters() function has been disabled in mol.h and chiral.cpp.
> However, I'm using it in Mychem before to use the IsChiral() function. Does it
> mean that the function is useless ? Or is it replaced by another function
On Thu, Oct 22, 2009 at 11:51 PM, Craig A. James wrote:
> I'm baffled by the following, and can only assume I have some
> misunderstanding of how atom Idx's are stored.
>
> I asked for an SSSR using GetSSSR(), then take the first ring from the SSSR.
> Then I wanted something simple: one atom fr
Hi Craig,
On Wed, Nov 18, 2009 at 4:56 PM, Craig A. James wrote:
> Tim,
>
> I've run into a problem: OpenBabel add a hydrogen to any potentially-chiral
> carbon that doesn't have four bonds, for example, when it parses "ClC(Br)I"
> (but not "ClC(Cl)Br" since it can't be chiral). I'm pretty sur
On Wed, Nov 18, 2009 at 6:34 PM, Craig A. James wrote:
> Tim Vandermeersch wrote:
>>
>> Hi Craig,
>> ...
>> The new stereo code doesn't need these extra hydrogens. The added
>> hydrogens you are seeing are probably added in
>> OBMol2Cansmi::AddHydrog
Hi,
Sorry for the late reply but you are correct about the Van der Waals
interaction. I've just commited a corrected version to svn trunk with
correct analytical gradients. Thanks for the vdw.cpp file, this made
it very easy to check the energies.
Thanks,
Tim
On Sat, Dec 5, 2009 at 4:55 AM, Geof
Hi,
Molsketch 0.2.0 has just been released. It is a 2D chemistry editing
application and it uses openbabel for some of the underlying
functionality. It is still has some rough edges but I thought now
would be a good time to get some feedback.
The source package can be downloaded from sourceforge.
Hi,
On Sat, Feb 20, 2010 at 4:22 PM, Noel O'Boyle wrote:
> On 20 February 2010 13:35, Geoffrey Hutchison
> 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 these SMILES should match themselves w
Hi,
On Sat, Feb 20, 2010 at 6:57 PM, Geoffrey Hutchison
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
Hi,
On Tue, Mar 2, 2010 at 10:21 PM, David Lonie wrote:
> On Tue, Mar 2, 2010 at 4:16 PM, Geoffrey Hutchison
> 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 remove API. Otherwise, I think we
Hi,
On Wed, Mar 3, 2010 at 4:41 PM, Geoffrey Hutchison
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
>> and getting an ext
On Wed, Mar 3, 2010 at 6:42 PM, Geoffrey Hutchison
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
On Sun, Mar 7, 2010 at 6:46 PM, Igor Filippov wrote:
> Sure, I'd love to help out.
> But I do remember the last time I tried to help with MinGW compilation
> and everything worked fine with the svn snapshot, and did not work at
> all with the release. For some reason what's released is not the sam
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 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 code you want t
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:
>> > Are there any perforamnce benchmark scripts for OB? E.g., I'd like to test
>
2010/3/23 Konstantin Tokarev :
>
>
> 23.03.10, 20:30, "Tim Vandermeersch" :
>
>> On Mon, Mar 22, 2010 at 7:13 PM, Konstantin Tokarev wrote:
>> >
>> >
>> > 22.03.10, 18:56, "Tim Vandermeersch" :
>> >
>> >&g
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... (re
On Wed, Mar 31, 2010 at 10:06 PM, Konstantin Tokarev wrote:
>
>
> 31.03.10, 21:58, "Tim Vandermeersch" :
>
>> Hi,
>>
>> Has anyone attempted building openbabel with the OpenSUSE build
>> service before? I tried it in ubuntu here but didn't
On Wed, Mar 31, 2010 at 10:23 PM, Noel O'Boyle wrote:
> On 31 March 2010 20:58, Tim Vandermeersch 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'
Hi,
Here is my own attempt at an openbabel webservice:
http://openbabel.selfip.org/ It runs on some spare hardware here at
home so I don't know how the performance will be. It's not meant as a
complete API yet since there are only 3 apps but the main page has
instructions for contributors... :-)
On Fri, May 7, 2010 at 1:44 PM, Noel O'Boyle wrote:
> On 6 May 2010 17:29, Noel O'Boyle wrote:
>> Currently 2D structures go into the OBBuilder flat, and come out flat.
>> This is due to void Convert2DCoords(OBMol *obMolecule) which just does
>> a few little things like giving a push to wedge and
On Mon, May 17, 2010 at 11:22 AM, Noel O'Boyle wrote:
> Hi all,
>
> I would like to be able to const iterate over the atoms of a mol with,
> for example, FOR_CONST_ATOMS_OF_MOL or so. I am instead reduced to
> using "for (i=1; i<=mol.NumAtoms(); ++i)" which is very sad.
>
> I'm not quite sure how
On Mon, May 17, 2010 at 12:50 PM, Noel O'Boyle wrote:
> On 17 May 2010 11:19, Tim Vandermeersch wrote:
>> On Mon, May 17, 2010 at 11:22 AM, Noel O'Boyle wrote:
>>> Hi all,
>>>
>>> I would like to be able to const iterate over the atoms of a mol wi
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 gre
html (From another
project, far from finished but the general idea is there)
I see your point though. Having a default doxygen page as the main
portal is not a good idea.
Tm
> Just my two cents,
> Igor
>
> On Tue, 2010-06-08 at 12:59 -0400, Tim Vandermeersch wrote:
>> Hi,
>>
&
On Wed, Jun 9, 2010 at 3:33 PM, Noel O'Boyle wrote:
> On 8 June 2010 22:18, Noel O'Boyle wrote:
>> On 8 June 2010 17:59, Tim Vandermeersch wrote:
>>> Hi,
>>>
>>> Andrew has raised some important issues with outdated docs etc. I
>>
On Thu, Jun 10, 2010 at 10:22 PM, Noel O'Boyle wrote:
> Hi all,
>
> The built-in memory leak detection in MSVC2008 seems not to work (no
> line numbers), but I've found Visual Leak Detector to work amazingly
> well (given that I don't know what I'm doing):
> http://sites.google.com/site/dmoulding/
On Thu, Jun 10, 2010 at 10:33 PM, Noel O'Boyle wrote:
> On 10 June 2010 21:27, Tim Vandermeersch wrote:
>> On Thu, Jun 10, 2010 at 10:22 PM, Noel O'Boyle wrote:
>>> Hi all,
>>>
>>> The built-in memory leak detection in MSVC2008 seems not to work (no
On Tue, Jun 15, 2010 at 7:25 PM, Craig A. James wrote:
> On 6/15/10 10:12 AM, Geoffrey Hutchison wrote:
>> I think there are two classes of documentation:
>> 1) Developer-level docs (e.g., tutorials, API, etc.).
>>
>> 2) User-level tutorials.
>
> Right, I agree with Geoff. My comments about in-li
On Fri, Jun 18, 2010 at 12:59 PM, Noel O'Boyle 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 search box on
On Fri, Jun 18, 2010 at 12:06 PM, Konstantin Tokarev 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 between rele
Hi,
This mail turned out longer than I had expected. Some parts should
probably be in the docs so I'll copy them :-) My main question is:
Should I try to fix the recent SSSR bug (see link at the bottom).
Is anyone familiar with the SSSR code? Geoff's name is in the file but
I don't know if there
On Mon, Jun 21, 2010 at 6:12 PM, Geoffrey Hutchison
wrote:
>> Is anyone familiar with the SSSR code? Geoff's name is in the file but
>> I don't know if there have been many ring perception bugs in the past.
>
> I think there was one. I believe some parts of the code have also been
> contributed b
On Mon, Jun 21, 2010 at 6:43 PM, Craig A. James 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
>
>
>
>
> Andrew s
On Mon, Jun 21, 2010 at 7:24 PM, Tim Vandermeersch
wrote:
> On Mon, Jun 21, 2010 at 6:43 PM, Craig A. James 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 i
On Mon, Jun 21, 2010 at 11:14 PM, Craig A. James wrote:
> On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
>
>>> For most "ordinary" molecules, the LSSR is the same as the SSSR. The
>>> LSSR and
>>> SSSR only differ with "cage" structures, whe
On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
wrote:
>> The changes are in svn trunk. The current test set (aromatics.smi,
>> attype.00.smi & nci.smi) is not good though.
>
> By that, I assume you mean that the current test set is not sufficient for
> SSSR vs. LSSR? I can probably generate
On Tue, Jun 22, 2010 at 10:06 AM, Noel O'Boyle wrote:
> On 22 June 2010 03:31, Craig A. James wrote:
>> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
>>> wrote:
>>>>> The changes are in
On Tue, Jun 22, 2010 at 12:05 PM, Noel O'Boyle wrote:
> On 22 June 2010 09:06, Noel O'Boyle wrote:
>> On 22 June 2010 03:31, Craig A. James wrote:
>>> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>>>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
On Tue, Jun 22, 2010 at 4:31 AM, Craig A. James wrote:
> On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
>> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
>> wrote:
>>>> The changes are in svn trunk. The current test set (aromatics.smi,
>>>> atty
On Tue, Jun 22, 2010 at 6:28 PM, Craig A. James 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 at
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 extensio
On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum wrote:
> Hi Tim,
>
> On Tue, Jun 22, 2010 at 9:34 PM, Tim Vandermeersch
> wrote:
>>
>> On the openbabel devel mainling list there was discussion about the
>> Largest Set of Smallest Rings (LSSR). RDKit calls this sy
On Tue, Jun 22, 2010 at 11:08 PM, Tim Vandermeersch
wrote:
> On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum wrote:
>> Hi Tim,
>>
>> On Tue, Jun 22, 2010 at 9:34 PM, Tim Vandermeersch
>> wrote:
>>>
>>> On the openbabel devel mainling list there was dis
On Wed, Jun 23, 2010 at 6:02 PM, Noel O'Boyle wrote:
> On 23 June 2010 01:37, Tim Vandermeersch wrote:
>> On Tue, Jun 22, 2010 at 11:08 PM, Tim Vandermeersch
>> wrote:
>>> On Tue, Jun 22, 2010 at 9:59 PM, Greg Landrum
>>> wrote:
>>>> Hi T
On Wed, Jun 23, 2010 at 7:43 PM, Craig A. James 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=2416695&build=76838
>>>
>>&
Hi,
Currently all commandline tools implement argument parsing on their
own. Apart from code duplication this is also prone to errors (babel
is probably ok, the other tools could use improvement).
Does anyone know good candidate libraries to do this? They should be
cross-platform and ideally be s
Chris and I (at least) think that most of these
> tools such be incorporated into babel (or obabel) as operations.
>
> - Noel
>
> On 30 June 2010 14:54, Tim Vandermeersch wrote:
>> Hi,
>>
>> Currently all commandline tools implement argument parsing on their
>> o
On Thu, Jul 1, 2010 at 11:02 AM, Noel O'Boyle wrote:
> On 30 June 2010 16:44, Geoffrey Hutchison 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 idea of adding additional depe
On Thu, Jul 1, 2010 at 2:44 PM, Noel O'Boyle wrote:
> On 1 July 2010 12:17, Tim Vandermeersch wrote:
>> On Thu, Jul 1, 2010 at 11:02 AM, Noel O'Boyle wrote:
>>> On 30 June 2010 16:44, Geoffrey Hutchison wrote:
>>>>> bliss. bliss is GPLv2 and availabl
On Thu, Jul 1, 2010 at 3:56 PM, Konstantin Tokarev 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
> are relaxed
On Thu, Jul 1, 2010 at 4:39 PM, Noel O'Boyle wrote:
> On 1 July 2010 15:36, Tim Vandermeersch wrote:
>> On Thu, Jul 1, 2010 at 3:56 PM, Konstantin Tokarev wrote:
>>> Hi,
>>> I think geometry optimization steps have slightly different nature than
>>> set
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
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
--
On Sun, Jul 4, 2010 at 3:58 AM, Geoffrey Hutchison
wrote:
>> 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 have been many new features in trunk for 2.3, e.g., 2D depiction,
> im
On Mon, Jul 5, 2010 at 5:56 PM, Craig A. James 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 fa
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 model
there were errors in the file
(are these your weird boost errors?). It still compiles since we don't
use any of the constants though.
> On 5 July 2010 23:06, Tim Vandermeersch wrote:
>> Hi,
>>
>> While checking if the spectrophore code builds on windows I noticed
>>
On Thu, Jul 8, 2010 at 11:41 AM, Tim Vandermeersch
wrote:
> On Tue, Jul 6, 2010 at 10:12 AM, Noel O'Boyle wrote:
>> I hope you can get this to work. I tried using boost::erf and got
>> weird boost errors - presumably something I was doing wrong.
>
> I got it working her
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