Try the xyz format.
On 12 February 2013 16:26, David Lonie david.lo...@kitware.com wrote:
Hi list,
Is there a way to perceive bonds in a collection of atoms with obabel? I
looked though the documentation, but don't see an explicit operation for
this.
We thought maybe converting cml -- cml
Oops - looks like align.h is not wrapped in Perl. If you create the
bindings yourself, it's fairly easy to do it. See the references to
align.h in scripts/openbabel-python.i.
On 6 February 2013 13:01, ganoud durand_mor...@yahoo.fr wrote:
Dear All,
I try to make RMSD calculation from a perl
You need to provide the relevant code snippet. It could be several things.
- Noel
On 7 February 2013 06:14, andi ad...@mail.missouri.edu wrote:
Hi all,
I am running into a strange problem and just can't seem to find a cause.
What I am trying to do is pass a an OBMol to some function and
Rather than subclass have you considered attached GenericData of some sort?
- Noel
On 23 January 2013 18:58, Dhroso, Andi (MU-Student)
andi.dhr...@mail.missouri.edu wrote:
Hi everyone,
I have an application where I need to add additional information to
OBAtom, and OBBond so i decided to
Cannot initialize database is fixed by setting the environment
variable BABEL_DATADIR to point to the Open Babel data files,
typically installed in
C:\Users\noel\AppData\Roaming\OpenBabel-2.3.2\data. Setting this
correctly should sort out the problem.
- Noel
On 16 January 2013 22:31, Gaudreault,
2012 16:55, 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 Depict (http://www.daylight.com
The docs for OBMol operator+= are currently as follows:
//! Copies atoms and bonds but not OBGenericData
OBMol operator+=(const OBMol mol);
So, mola += molb adds molb to mola but does not copy the stereo or
residue info (among others). Is there a rationale for this?
Shouldn't mola = molb
Hi Geoff,
I've been implementing the SMILES valence model to set the number the
implicit hydrogens at the point of reading a SMILES string.
I've run into the problem that the current kekulization code (or at
least that invoked by the SMILES reader) does not take into account
the location of
On 11 December 2012 16:39, David van der Spoel sp...@xray.bmc.uu.se wrote:
On 2012-12-10 15:44, Geoffrey Hutchison wrote:
The SSSR of buckyball has changed. Can I just update the energy in the
appropriate test file?
Yes. You can do that manually or run ffmff94 -g to re-generate the test file.
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)
that For aromatic nitrogens in SMILES the number of implicit
hydrogens is always specified. [nH] and [nH+] indicate one, n, [n]
and [n+] indicate zero. That n and
Due to recent changes to the SSSR code, the exact SSSR returned has
changed (e.g. for cubane). I fixed the corresponding test failures
(which depended on the specific SSSR) but one remains.
The MMFF94 energy of buckyball has changed:
not ok 17 # calculated energy incorrect for molecule
The MMFF94 test fail is me. The change to SSSR order causes a fail -
I've yet to look into it.
On 29 November 2012 19:04, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
Hi,
I recently added the smiley test, this is still experimental and I have to
check it on more platforms etc. So
The OpenSMILES spec doesn't fully describe the Daylight valence model.
I'll get the full details from Roger, but in the meanwhile here's some
bullet points from a talk of his:
Daylight’s valence model for SMILES is that all aromatic nitrogens
have no implicit hydrogens by default. If a hydrogen
On 12 November 2012 20:43, Geoff Hutchison ge...@geoffhutchison.net wrote:
I just noticed that multipoles higher than dipole are not read in from
Gaussian log files, and neither are ESP points!
These are relatively new data. I added the support (e.g., quadrupoles) in the
core library, but
My only concern is that this adds to the complexity of maintaining the
bindings (or am I wrong about this? - is it the same?). For your own
purposes, could you not copy out the installed binding files (there
are just two), before rerunning against a different Python (no rebuild
of the entire OB
On 6 October 2012 20:08, Reinis Danne rei4...@gmail.com wrote:
On Mon, Oct 01, 2012 at 04:32:11PM -0400, Geoffrey Hutchison wrote:
If there are other changes or fixes on trunk that you'd like to see
resolved, speak now.
After discussion on ob-discuss I just committed r5034 (improve
bond
On 1 October 2012 21:32, Geoffrey Hutchison geo...@pitt.edu wrote:
I've merged in basically everything in trunk to the 2.3 branch. There are
some depiction fixes and the ASCII painter that Noel committed remaining, as
far as I can tell. Noel, please either merge these to the branch yourself,
I'm looking into it. As you say, it seems that some references to
HAVE_EIGEN2 have not been updated. The bindings need some extra code
to handle this.
- Noel
On 25 September 2012 11:13, Reinis Danne rei4...@gmail.com wrote:
On Tue, Sep 25, 2012 at 09:24:48AM +0100, Noel O'Boyle wrote
(mol.OBMol)
molb = pybel.readstring(smi, ClC(=O)CC)
molb.make3D()
align.SetTargetMol(molb.OBMol)
align.Align()
True
align.GetRMSD()
0.97250415028443593
On 27 September 2012 09:24, Noel O'Boyle baoille...@gmail.com wrote:
I'm looking into it. As you say, it seems that some references to
HAVE_EIGEN2
The release is coming up soon, and as far as I understand, we are not
necessarily supporting Eigen3 instead of Eigen2. Geoff?
Regarding the error message, what is the context? Is this compiling
the current trunk svn, with Eigen3 installed but not Eigen2. Best to
include the complete output of
Great. Whichever is fine by me.
On 2 September 2012 20:36, Chris Morley c.mor...@gaseq.co.uk wrote:
Geoff
Can I request a delay until at least September 22nd? The earlier date is
during my (rare) holidays away from home. I know the release has been
pending for some time, but issues always
On 23 June 2012 12:02, Chris Morley c.mor...@gaseq.co.uk wrote:
On 23/06/2012 10:29, Noel O'Boyle wrote:
It seems that libcurl would be a better choice for other operating
systems. HappyHttp is not even available as a Debian package, for
example, and *everything* is available as a Debian
On 11 June 2012 21:10, Noel O'Boyle baoille...@gmail.com wrote:
Sounds good.
Sorry - I just realised something that should make things easier.
Perhaps the best way to do this is actually via a ctest script as you
don't have to hardcode the compiler path. The one we use for our
nightly builds
requires a
bit of study and doesn't yield to a quick look.
Craig
On Fri, Jun 8, 2012 at 4:03 AM, Noel O'Boyle baoille...@gmail.com wrote:
I'm not going to spend any more time on this now, but as a brief
update, tautomer test will pass if the molecules are copied before
writing out as can. I can
Have you tried first of all compiling it as per the instructions?
http://openbabel.org/docs/dev/Installation/install.html#windows-msvc
Here is the command that ctest uses on my machine to compile
everything at the command-line:
C:\PROGRA~2\MICROS~1.0\Common7\IDE\VCExpress.exe openbabel.sln /build
configuration for Win 7 64 bit when it's
complete and may suggest a skeletal pom.xml that a developer could expand
on.
David
On 11 June 2012 20:41, Noel O'Boyle baoille...@gmail.com wrote:
Have you tried first of all compiling it as per the instructions?
http://openbabel.org/docs/dev
Hi Reinis,
Your r4832 (conformersearch.h: Fix -Wdelete-non-virtual-dtor) is
causing a warning when compiling the bindings with MSVC.
1C:\Tools\openbabel\trunk\include\openbabel/conformersearch.h(65) :
warning C4273: 'OpenBabel::OBConformerFilter::~OBConformerFilter' :
inconsistent dll linkage
1
Yes - it does. That's great. I've commited it in r4869.
- Noel
On 9 June 2012 16:05, My Th rei4...@gmail.com wrote:
S , 2012-06-09 14:59 +0100, Noel O'Boyle rakstīja:
Hi Reinis,
Your r4832 (conformersearch.h: Fix -Wdelete-non-virtual-dtor) is
causing a warning when compiling the bindings
I've edited the SMILES writer so that it doesn't add hydrogens to
chiral centers (and fixed the resulting problems)...but tautomer test
is still failing.
- Noel
On 30 May 2012 16:29, Craig James cja...@emolecules.com wrote:
Hi Tim,
When I reverted the SMILES canonicalizer (that is,
;
tautomers.push_back(conv.WriteString(mol));
in the functor allows the test to pass (along with a similar change
elsewhere in the test). The underlying problem should be identified
and fixed though.
- Noel
On 8 June 2012 10:15, Noel O'Boyle baoille...@gmail.com wrote:
I've edited the SMILES writer so
Hello all,
I just checked in code for two new SMILES canonicalisation schemes,
both based on the InChI's canonicalisation. This is something I've
been working on for a while and a paper is almost ready to submit.
-osmi -xU gives Universal SMILES, which gets the canonical labels from
the InChI
On 30 May 2012 16:29, Craig James cja...@emolecules.com wrote:
Hi Tim,
When I reverted the SMILES canonicalizer (that is,
SMIBaseFormat::WriteMolecule()) back so that it doesn't copy the molecule, I
solved the performance problem, but it causes the Tautomer Test to fail.
I've looked through
I've added two new SMILES output options:
(1) R - do not reuse bond symbols (e.g. c1c1Oc2c2). This is
currently in the OpenSMILES spec though I hope it will be removed.
(Note to self: check that it causes an error message if number of
rings 99.) This may be useful for people who want to
On 30 May 2012 00:06, Craig James cja...@emolecules.com wrote:
On Tue, May 29, 2012 at 2:42 PM, My Th rei4...@gmail.com wrote:
O , 2012-05-29 14:29 -0700, Craig James rakstīja:
I've confirmed absolutely on Ubuntu: Testing in the build directory
works. Testing with an installed OpenBabel
wrote:
I asked about cmake because newer versions should set env variables correctly
to use the build dir.
Geoff
On May 30, 2012, at 4:41 AM, My Th rei4...@gmail.com wrote:
T , 2012-05-30 09:26 +0100, Noel O'Boyle rakstīja:
On 30 May 2012 00:06, Craig James cja...@emolecules.com wrote
On 30 May 2012 16:10, Craig James cja...@emolecules.com wrote:
On Wed, May 30, 2012 at 7:59 AM, Noel O'Boyle baoille...@gmail.com wrote:
I've just confirmed what Craig was seeing. I have CMake 2.8.5.
I always install locally but once I added the installed lib directory
to the front
Now I've checked the tautomer tests, and it also fails with the stock
r4758, i.e. before I changed smilesformat.cpp.
$ bin/test_tautomer
/home/cjames/openbabel-2.3.x-r4758/source/test/tautomertest.cpp:76:
canonicalTautomers.size() == 1 [13 == 1] (FAIL)
I think there's something wrong
Looking at blame online, it seems that Tim made the change to allow
ferrocene structures to be normalised for the eMolecule
canonicalisation tests:
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/formats/smilesformat.cpp?r1=4033r2=4034;
IMO, structure normalisations
My own 2c is that I'd prefer Mercurial. Historically Git has not been
very nice to use on Windows (i.e. horrible and slow - problems of
msysgit's console). I see now that TortoiseGit may now be usable - if
so, that would solve some problems.
In any case, I would push stronger for Mercurial except
I don't remember if the SDF output code you are using in that version of
2.2.x ever made it to a release (I don't think so). In any case, it's not
correct, and was subsequently fixed. The 3 for a double bond stereo is
used to indicate unknown stereo - this is not quite clear in the spec (3 =
Cis
Can you provide some small example code that triggers this?
- Noel
On 16 May 2012 02:08, Craig James cja...@emolecules.com wrote:
This looks like a bug but I wanted to post it here before adding it to the
bug database. It's using some memory after freeing it.
This is output from valgrind.
unpleasant for us to have to
explain to a customer that they'd ordered hundreds of incorrect compounds
because OpenBabel doesn't handle cis/trans the way you'd expect.
Thanks,
Craig
On Sat, May 12, 2012 at 6:37 AM, Noel O'Boyle baoille...@gmail.comwrote:
Sorry - I got things backward
See also this thread:
http://www.mail-archive.com/blueobelisk-discuss@lists.sourceforge.net/msg00665.html
where Greg Landrum dissuades me from including stereo in 0D Mol file.
- Noel
On 14 May 2012 11:32, Noel O'Boyle baoille...@gmail.com wrote:
The issue is only regarding cis/trans
I usually run 3D generation as follows:
obabel -:OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H
]2CCC2=CC(=O)CC[C@]12C)F --gen3d -osdf
==
*** Open Babel Warning in OpenBabel::OBBuilder::CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
Hello all,
The current SMILES writer does not output cis/trans bond symbols for double
bonds in rings of size 12 or less. In the course of other work, I've come
across example of cis/trans bonds in rings of size 9 for example:
https://www.ebi.ac.uk/chembldb/compound/inspect/CHEMBL520004 versus
It's intentional, rather than a bug. I originally had some code in there to
support stereo in 0D SDF, but the format really doesn't support this
officially - it's supposed to be either 2D or 3D. It's all very well for
cis/trans, but it's not possible to store tet stereo without coordinates
(which
Sorry - I got things backward. It's storing the cis/trans stereochemistry
in a 0D format that's the problem. See the post and comments at
http://baoilleach.blogspot.com/2010/02/how-to-store-stereochemistry-in-mol.html
- Noel
On 12 May 2012 13:52, Noel O'Boyle baoille...@gmail.com wrote:
It's
IMO it's a trivial configuration issue. You should trust the nightly
builds. We always welcome more nightly builds (hint hint) of course if your
OS or g++ version is not listed. I'm happy to talk you through setting one
up, or else sshing in to do so.
- Noel
On 9 May 2012 22:23, Craig James
Can you confirm that this does not affect canonical labels for regular
molecules?
And just a matter of interest, what do you use the fragment canonical
labels for?
- Noel
On 4 May 2012 22:20, Craig James cja...@emolecules.com wrote:
I just checked in a simple but important change to
In the OB docs, there's an example C++ program. Can you edit this so that
it reproduces the problem? Also, are you including babelconfig.h as follows?
-DOPENBABEL2_INCLUDE_DIR=C:\Tools\openbabel\trunk\include;C:\Tools\openbabel\trunk\windows-vc2008\build\include
On 9 May 2012 13:22, David Lonie david.lo...@kitware.com wrote:
On Wed, May 9, 2012 at 7:42 AM, David Lonie david.lo...@kitware.comwrote:
On Wed, May 9, 2012 at 4:42 AM, Noel O'Boyle baoille...@gmail.comwrote:
In the OB docs, there's an example C++ program. Can you edit this so
The tests are run from the build directory so you need to do the
BABEL_LIBDIR, LD_LIBRARY_PATH and BABEL_DATADIR dance. The segfaults are
mainly from loading a file format, but not checking whether it is NULL or
not.
- Noel
On 9 May 2012 19:52, Craig James cja...@emolecules.com wrote:
I'm
If OB is not built with Eigen these classes are missing.
On 3 May 2012 11:42, David Lonie david.lo...@kitware.com wrote:
I'm having an issue compiling the latest avogadro, and it looks like an
issue with the new OBConformerSearch class. Can anyone reproduce? This is
with a fresh
Are you comparing 32-bit builds?
- Noel
On 1 May 2012 23:36, Richard West r.h.w...@gmail.com wrote:
Hi all,
I think that at some point between v 2.2.3 and the current svn trunk, the
result of OBAtom.GetAtomicNum() in Python changed from type 'int' to
'long'. Is this an intentional change to
wrote:
On Tue, Apr 17, 2012 at 7:56 AM, Noel O'Boyle baoille...@gmail.com
wrote:
Well, Geoff, if you're going to be working on this I've recently been
subjecting ChEMBL to some canonicalisation tests, and can supply a good
few
more test cases. I'll wrap them up and email them to you off list
Hello all,
I've had ASCII depiction on the brain for some time, and I finally
implemented it in Open Babel without any external dependencies. I've named
the format -oascii. It seems to work quite well, but naturally the more
columns you have available the better the resolution. Multimolecule
Hi Sergei,
This isn't a layout or coordinate generation problem though, just a
question of depictio, so there's no need for any changes to
mcdlutil.cpp.
We just need to render the double bond as a twisted double bond. See
Option 3 at
Hi all,
Just a note to say that I've enabled some support for subversion to
recognise bug names in log messages. Just prepend the # symbol to the
ID of a bug (or feature request etc), e.g. PR#1232 or bug #13123,
and graphical svn clients (notably TortoiseSVN on Windows, but others
should also)
Hi Chris,
Re:
http://openbabel.svn.sourceforge.net/viewvc/openbabel?view=revisionrevision=4718
I added --highlight as discussed in comments at
http://baoilleach.blogspot.com/2012/02/portrait-of-molecule-as-green.html.
I was also missing this. I originally planned to edit opisomorph.cpp
to add
Hello all,
As far as I can tell, there's no particular reason that the data files
be licensed under the GPL.
I'd like to see them (a) under data licenses, and (b) preferably CC0
so that others can use them without restriction. Clearly, this cannot
be done without the agreement of the original
Hi Chris,
Just FYI, I've been playing around with the SVG output to see whether
I could improve draggability for the 1000 molecule SVG discussed at
[1]. I didn't edit the OB code; I just wrote a Python script to
transform the SVG (see [2]).
(A) There was a suggestion in the comments at [1] that:
n 27 February 2012 09:48, Chris Morley c.mor...@gaseq.co.uk wrote:
On 26/02/2012 16:19, Noel O'Boyle wrote:
I've been looking at the opalign which I really like. There's one
issue remaining which I can't quite decide how to handle.
Basically, if you use --align -s substructure color -O
Hi Chris,
I've been looking at the opalign which I really like. There's one
issue remaining which I can't quite decide how to handle.
Basically, if you use --align -s substructure color -O myfile.svg
and your input structure is 2D everything is fine. However, if your
input structure is 3D, it
?
Thank you,
Gonzalo
On Sat, Feb 18, 2012 at 5:27 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
On 21 February 2012 20:08, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
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
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 November.
The code seems to implement Roger Sayle's recipe up until the
for grabbing all stereochemistry from CDX files.
In the 2.3.x effort, the stereochemistry code was completely rewritten.
If you are considering looking at the code, I suggest posting to the list, as
others (particularly Noel O'Boyle) can probably help.
-Geoff
On Feb 15, 2012, at 12:00 PM
On 4 January 2012 12:53, David Lonie lonieda...@gmail.com wrote:
On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison
ge...@geoffhutchison.net wrote:
On Jan 3, 2012, at 2:45 PM, David Lonie wrote:
beyond the trust radius. I didn't track down which is happening, but
switching to the Newton2Num
On 17 December 2011 04:46, Geoff Hutchison ge...@geoffhutchison.net wrote:
The weird thing is that IdentifyResidue can identify the first serine
without any problems; it just doesn't identify the second one. Also,
it will identify them both correctly if the --gen3d is omitted (or
more
See the section To obtain a fingerprint in the API docs:
http://openbabel.org/dev-api/classOpenBabel_1_1OBFingerprint.shtml#_details
On 14 December 2011 15:31, Marianne Seijo marianne.se...@epfl.ch wrote:
Hello,
I use the openbabel API and really exciting to the all the possibilities of
OB. I
On 7 December 2011 20:20, My Th rei4...@gmail.com wrote:
2011/12/7 Noel O'Boyle baoille...@gmail.com:
I'm afraid, it's not possible to ask disutils the location of the
site-packages folder (believe me, I have tried, googled, everything).
As a result, we have no choice. In any case
I'm afraid, it's not possible to ask disutils the location of the
site-packages folder (believe me, I have tried, googled, everything).
As a result, we have no choice. In any case, this simplifies
everything and I wouldn't change it back now. The user just needs to
add the lib directory to
On 2 November 2011 22:35, Chris Morley c.mor...@gaseq.co.uk wrote:
On 01/11/2011 02:27, Geoff Hutchison wrote:
On Oct 11, 2010, at 4:18 PM, Chris Morley wrote:
A simpler and more obvious model for this purpose has essentially a single
IMPVAL for each charge state of the molecule. (Only if
On 15 November 2011 17:22, Geoff Hutchison ge...@geoffhutchison.net wrote:
Geoff, what do you think about changing the way we do mailing list
moderation.
What do you think if we change things so that (a) we only moderate
once a week, and (b) we highlight the fact that members are not
Geoff, what do you think about changing the way we do mailing list moderation.
The GROMACS guy spoke at MIOSS last year. He said that one of the
reasons that the community was so vibrant was that the mailing list
from the start required registration. As a result, there were more
community members
Hi there,
I've checked in some code for Smarts tet stereo support. Previously
this was not working correctly. Now it supports all forms of tet
stereo involving 4-coordinate atoms (i.e. it works for ring closures
and so forth).
To support this, I've had to ensure that each atom records its
After a brief test, looks good to me on Windows/MSVC.
- Noel
On 22 October 2011 13:14, Vincent Favre-Nicolin
vinc...@users.sourceforge.net wrote:
Hi,
OK, I found a way to fix this, though the mysteries of tellg() and
seekg() in istream still elude me...
= I've commited to SVN the
/Users/cmayne/openbabel/build/openbabel/CMakeFiles
[100%] Built target _openbabel
/Applications/CMake 2.8-5.app/Contents/bin/cmake -E cmake_progress_start
/Users/cmayne/openbabel/build/openbabel/CMakeFiles 0
On Thu, Oct 13, 2011 at 10:03 AM, Noel O'Boyle baoille...@gmail.com wrote:
That should
at lower-left side and 5 - membered cycle at upper right.
It seems for me that Chris Morley asked me for such code some years ago...
-Original Message-
From: Noel O'Boyle [mailto:baoille...@gmail.com]
Sent: Friday, October 07, 2011 12:13 PM
To: Sergey V. Trepalin
Subject: Re: Some
On 5 October 2011 21:44, David Lonie lonieda...@gmail.com wrote:
On Wed, Oct 5, 2011 at 4:37 PM, Chris Morley c.mor...@gaseq.co.uk wrote:
The recent changes in OBUnitCell constantness mean that the SWIG
bindings do not compile in Visual C++ 9:
1..\..\..\scripts\java\openbabel-java.cpp(2945) :
On 6 October 2011 14:13, Chris Morley c.mor...@gaseq.co.uk wrote:
On 06/10/2011 10:03, Noel O'Boyle wrote:
Now on to how to avoid specifying the C# executable as an absolute
address.
Is there a problem with the current setup?
It would be better if it used the information
it like
InChICompareFormat would leave all the other InChIFormat options still
available on the command line for the enthusiasts, who would be sure to ask
for any options that haven't been implemented.
Chris
On 19/09/2011 11:21, Noel O'Boyle wrote:
Hi Chris,
What do you think about having
Hi Chris,
What do you think about having the InChIKey available as a separate
format? It seems like it's becoming increasingly popular to merit
this.
I can make the changes, if you agree.
- Noel
--
BlackBerryreg;
calculations (not
Tanimoto).
- Noel
On 16 September 2011 19:25, Chris Morley c.mor...@gaseq.co.uk wrote:
On 16/09/2011 14:32, Noel O'Boyle wrote:
Hi Chris,
Earlier in the year there were a couple of suggestions for conversion
features; one for splitting sdf files into chunks, and the other
Bump - another patch.
On 20 July 2011 20:29, Izhar Wallach izh...@cs.toronto.edu wrote:
I just noticed that my suggested code below has a bug...
currConf should hold the index of the current conformation and not a pointer
to it (because that memory address belongs to the source object).
So,
Hi Chris,
Earlier in the year there were a couple of suggestions for conversion
features; one for splitting sdf files into chunks, and the other for
using the filename as a descriptor. What do you think about these?
http://forums.openbabel.org/Split-SDF-file-in-chunks-td3570274.html
On 15 September 2011 11:48, Michael Banck mba...@gmx.net wrote:
Hi,
On Tue, Sep 13, 2011 at 01:50:47PM -0400, Geoffrey Hutchison wrote:
OK, I think it's more than overdue to release 2.3.1. We have a *lot*
of improvements in this release and it's time to get it out the door
and start in on
On 13 September 2011 19:51, Geoffrey Hutchison geo...@pitt.edu wrote:
The patch is correct. It just exposes some bugs in the SMARTS matcher
for stereochemistry. I'm 50% through resolving it. Can you hang on
another few days and I'll have it sorted?
OK, sounds good.
-Geoff
On second
On 14 September 2011 13:52, Geoffrey Hutchison geo...@pitt.edu wrote:
On second thoughts, I think I'll wait until after the release to sort
this out.
So I should revert (or not apply) the parsmarts patch for 2.3.1, correct?
Exactly. I think you've already reverted it on the trunk, so you
The patch is correct. It just exposes some bugs in the SMARTS matcher
for stereochemistry. I'm 50% through resolving it. Can you hang on
another few days and I'll have it sorted?
- Noel
On 13 September 2011 18:50, Geoffrey Hutchison geo...@pitt.edu wrote:
OK, I think it's more than overdue to
for windows too)
Thanks Igor and Noel, and great job Igor!
I will make a test in a larger database soon, and make an automaping
approach (with reactions) soon too. If ever need some code, do not hesitate
Really good and totally happy
Marianne
2011/9/1 Noel O'Boyle [via Open Babel
Hi Geoff,
pytest_sym has been failing since r4538. The Simplify rotation code
in builder.cpp part of r4538 must not be quite right. The test case
is:
obabel -:I/C=C/1\NC1 -oxyz --gen3d | bin/obabel -ixyz -ocan
Before r4538, it gives I/C=C\1/CN1; afterwards, it gives I[CH][C]1CN1.
It's not the
it will pass, sometimes fail:
AssertionError: u'I[CH][C]1CN1' != 'I/C=C\\1/CN1'
or
AssertionError: u'I/C=C\\1/CN1' != 'I/C=C/1\\CN1'
Reinis
O , 2011-08-30 16:15 +0100, Noel O'Boyle rakstīja:
Hi Geoff,
pytest_sym has been failing since r4538. The Simplify rotation code
in builder.cpp part
On 30 August 2011 16:21, Vincent Favre-Nicolin
vinc...@users.sourceforge.net wrote:
Le 30/08/2011 16:35, Noel O'Boyle a écrit :
For some time I have been using hashizume.cif (in
scripts/python/examples) to test the Python bindings. Some time ago,
the test started to fail due to the text below
On 17 August 2011 15:27, Geoffrey Hutchison ge...@geoffhutchison.net wrote:
Would it break the API to add another value for the enum
OBStereo::Winding? Current values are Clockwise and AntiClockwise: I'd
like to add Unknown.
Are you asking for 2.3 or trunk? For trunk the answer is no problem.
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)([12CH3])[14CH3]
It seems that this would be fixed if I added the isotope
You should use the development code. See
http://openbabel.org/docs/dev/Contributing/DevBestPractices.html#working-with-the-development-code
- Noel
On 7 July 2011 11:28, yuecaili yueca...@gmail.com wrote:
Hi all,
I encountered the same problem,
but I don't know how to remove fvisibility=hidden
Hi all,
Would it be okay to rename the GUI executable from OBGUI to obgui, in
keeping with the other exes?
- Noel
--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a
Would an easier fix be to simply replace
s += \n;
with
s += delimstr[0];
- Noel
On 2 July 2011 21:51, Jiahao Chen jia...@mit.edu wrote:
Hi all,
I am currently implementing some changes to the MOPAC file format
reader which requires use of the tokenize() function (the variant that
takes 3
On 16 June 2011 20:29, Geoffrey Hutchison ge...@geoffhutchison.net wrote:
I think we should put this up (see below), along with the Blue Obelisk
logo. Maybe at the bottom of the main page. It's rather large though -
I wonder if they have an SVG version...
Excellent! I think we can probably
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