The OpenBabel toolkit has the ability to generate canonical SMILES of
fragments. It's a key part of the SMILES generator. And it keeps the
context of each atom and writes partial aromaticity. For example, if you
have Oc1c1O, and you specify atoms 1,2, 7, and 8, it will write "OccO".
OBMol *pmo
Hi Noel,
On Thu, Mar 2, 2017 at 10:11 AM, Noel O'Boyle wrote:
> In the course of sorting out the handling of implicit Hs, I've found
> that the current SMILES writer writes hypervalent atoms from the
> organic subset in square brackets. E.g. Texas carbons:
>
> >obabel -:C(C)(C)(C)(C)C -osmi
> [C
It would be helpful if you could be very specific. Are you reading a file,
or creating a molecule via a C++ program? What sort of output are you
looking at, a particular file (like SMILES, SDF, or PDB)? The best way is
to give a concrete example with sample files that will allow others to
repeat yo
)" before I generate the
InChI, and it seems to solve the problem. Nothing like a good hack to come
back and bite me later!
Craig
On Wed, Oct 7, 2015 at 4:08 PM, Craig James wrote:
>
> On Wed, Oct 7, 2015 at 1:07 PM, Noel O'Boyle wrote:
>
>> Are you using the dev versi
On Wed, Oct 7, 2015 at 1:07 PM, Noel O'Boyle wrote:
> Are you using the dev version? If not, sounds like a problem I fixed
> earlier this year - see github closed issues from that period.
>
Noel, thanks for the suggestion. I downloaded and installed the latest code
from git, but it made no diffe
Can anyone shed some light on this? If I use Gen2D and then try to write
out an InChI, the stereo layer is wiped out.
#include
#include
#include
#include
#include
using namespace std;
using namespace OpenBabel;
/*--
* FU
On Mon, Apr 27, 2015 at 8:05 AM, Nana Sakisaka wrote:
>
> Please understand that I'm not going to destroy the original project.
> I want to say a simple sentence:
> The C++ library should be updated.
>
Again I ask: why? I'm not trying to be difficult or critical. Rather, I
think this is a perfec
On Mon, Apr 27, 2015 at 5:55 AM, Marcus D. Hanwell <
marcus.hanw...@kitware.com> wrote:
> On Sun, Apr 26, 2015 at 3:16 PM, Noel O'Boyle
> wrote:
> > Hi there,
> >
> > I propose moving the MSVC-specific 3rd party libs, dlls and include
> > files to a separate git submodule. Or perhaps just a separ
On Tue, Feb 10, 2015 at 12:23 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > I definitely remember reading discussion where Noel was mentioning a
> limit (that at this point can't be 1k atoms) but I can't find it since
> Sourceforge seems to be down for maintenance.
>
> There is an
On Tue, Dec 2, 2014 at 1:47 AM, Ernst-Georg Schmid <
ernst-georg.sch...@bayer.com> wrote:
> Hello,
>
> I'm using the following code to convert molfiles to PNG with
> Openbabel-2.3.2 on Ubuntu 14.04 LTS:
>
> typedef struct
> {
> size_t datasz;
> char data[1];
> } _PNG;
>
> extern "C" _PNG *
On Fri, Feb 14, 2014 at 12:03 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > I have a number of multimolecular complexes that I'm converting into
> canonical SMILES. Some of these molecules are carbon monoxide, and I am
> noticing that sometimes they are written as [C]=O, and some
On Mon, Feb 3, 2014 at 8:12 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > The presence of the hydrogen on the pyridinium nitrogen is critical for
> aromaticity.
>
> Yes, except there are decidedly users who feel that with SMILES, explicit
> hydrogens only need to be used in cases
Hey Geoff,
Congratulations! Well done.
Craig
On 30/10/2013 20:10, Geoffrey Hutchison wrote:
> > Dear everyone,
> >
> > My department voted recently to recommend me for tenure here at Pitt.
> While this still needs approval from the Dean, it’s essentially settled.
> >
> > Open Babel and Avogadro
On Wed, Oct 2, 2013 at 2:40 AM, Maciek Wójcikowski wrote:
> I'd like to bring the topic of release frequency of OpenBabel to the
> table. Since OB was migrated to the GitHub its development has speed up
> noticeably. Last release 2.3.2 was almost one year ago, and I think it's
> good time to discu
Does anybody remember disabling chirality features for SMARTS matching
somewhere around version 2.3.2? I have a vague memory that using '@' for a
tetrahedral center was just broken and gave wrong answers prior to Tim's
work, so it was disabled and SMARTS were matched as though they had no
chiral m
Maybe I'm overlooking the obvious, but how do you run all of the tests for
OpenBabel? I dug around the web, in the source code, etc. but can't find
anything that describes how to launch all tests. Isn't there something
like the "make test" that comes with most systems?
Thanks,
Craig
On Mon, Jul 22, 2013 at 5:28 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> Huh. Try this patch.
>
Thanks, that works.
Craig
>
> -Geoff
>
--
See everything from the browser to the database with AppDynamic
I'm trying to push some bug fixes and thought it might be good to compile
and test first ;-)
When I try to compile, I get this:
[ 27%] Building CXX object src/CMakeFiles/openbabel.dir/distgeom.o
In file included from /emi/openbabel-2.3.x-dev/source/src/distgeom.cpp:22:
/emi/openbabel-2.3.x-dev/so
If anyone familiar with the stereo code (Tim?) has a minute, this bug that
I just added has me stuck:
https://sourceforge.net/p/openbabel/bugs/885/
It's something in the stereo code that's referencing deallocated
OBGenericData.
Thanks,
Craig
time ago, and Tim's recent changes to the stereo code fixed whatever
OB bug caused SetDimension(2) to be needed for SMILES parsing.
Thanks,
Craig
>
> - Noel
>
> On 18 June 2013 19:48, Craig James wrote:
> > (forgot to cc list the first time...)
> >
> >
> >
From3D(mol, stereoUnits);
CisTransFrom3D(mol, stereoUnits);
break;
default:
TetrahedralFrom0D(mol, stereoUnits);
CisTransFrom0D(mol, stereoUnits);
break;
}
}
... but who knows? I'll have to dig into it a bit more...
I'm getting different InChI strings from obabel than when I invoke the
InChI format directly from C++ code. It looks like it has to do with
options ... but my code isn't setting any I/O options for the InChI
writer. Here's the output from my test program:
ERROR: incorrect InChI:
expected:
'InC
After struggling for two days to get my own swig Perl wrappers to work, I
decided to start with OpenBabel's and work backwards. However, I can't
even get OpenBabel's perl bindings to work. It seems to be the exact same
problem: it can't find the plug-ins.
One detail. The default configuration in
On Wed, Jun 12, 2013 at 7:51 AM, Craig James wrote:
>
>
> On Wed, Jun 12, 2013 at 2:21 AM, Noel O'Boyle wrote:
>
>> If you're using the development source, you will need to create the
>> bindings with SWIG. For once (!) this *is* in the docs :-)
>&g
>
With Eigen2 installed, my compile fails. It seems to be this bug:
http://sourceforge.net/p/openbabel/bugs/823/
My version of Eigen is the standard one distributed with Ubuntu. Do I need
to compile Eigen from source?
Thanks,
Craig
> - Noel
>
> On 12 June 2013 02:21, Craig Jam
NCLUDE_DIR EIGEN2_VERSION_OK)
Is there a way to make cmake fail when this happens? If I specify
-DPERL_BINDINGS=TRUE (or any other language binding) and a requirement
can't be met, it would be more useful to quit with a fatal error than to
keep going.
Thanks,
Craig
>
> - Noel
&
Trying to get the Perl bindings to work...
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel-2.3.x-dev
-DPERL_BINDINGS=TRUE ../source
make -j4
su
make install
So far so good. But trying to install:
$ cd scripts
$ make install
Install the project...
-- Install configuration:
utput of ldd on the various
> library files? This shows which libraries will be dynamically loaded,
> or whether they cannot be found.
>
> - Noel
>
> On 4 April 2013 16:20, Craig James wrote:
> > Hi Noel,
> >
> >
> > On Thu, Apr 4, 2013 at 6:08 AM, Noel
I got the latest release from the git repository, and now everything I do
prints this message (including OpenBabel tools):
==
*** Open Babel Error in RegisterOptionParam
The number of parameters needed by option "a" in API differs from an
earlier registration.
Is th
On Sat, May 11, 2013 at 10:50 AM, David van der Spoel
wrote:
> On 2013-05-11 19:30, Noel O'Boyle wrote:
> > While at the ACS a month ago I met some power users of Open Babel and
> > was surprised to hear that they are still using the babel executable
> > instead of obabel.
> >
> >>From this I assu
inks to Open Babel.
>
I use swig for a pure-C module with no problems, but I'm not having luck
with an almost-identical module that links to OpenBabel. In fact, there's
one function in my OpenBabel module that doesn't call OpenBabel at all, and
that function works.
Craig
This problem is driving me crazy. I have some functions written in C++
with a C wrapper that I need to make available from Perl. I wrote a swig
interface for them, and got it to compile and run. But OpenBabel can't
seem to initialize itself.
./test/swig_wrapper_test.pl
===
On Fri, Mar 29, 2013 at 7:33 AM, Reinis Danne wrote:
> On Wed, Mar 27, 2013 at 02:04:00PM -0700, Craig James wrote:
> > Reinis Danne wrote:
> >
> > > > I think it was the thread where I mentioned I'm working on
> > > > kekulization algorithm using gra
I found an inconsistency between N and P. If you read in each of the
SMILES [PH4+] and [NH4+], then remove the explicit H atoms from the
molecule, then
atom->ImplicitHydrogenCount()
returns 4 for N and 3 for P. To cure this, I added this rule to
atomtyp.txt, after all of the other P rules:
On Thu, Mar 28, 2013 at 6:47 AM, Chris Morley wrote:
> On 27/03/2013 17:35, Geoffrey Hutchison wrote:
> >> Maybe a proposed simplification of the valence system
> >> http://forums.openbabel.org/ImplicitH-failures-td2990439.html
> >> should be looked at again.
> >
> >
> > Copy/paste from Chris's e
On Wed, Mar 27, 2013 at 2:26 PM, David van der Spoel
wrote:
> On 2013-03-27 22:04, Craig James wrote:
> >
> >
> > Reinis Danne mailto:rei4...@gmail.com>>wrote:
> >
> > > I think it was the thread where I mentioned I'm working on
> >
Reinis Danne wrote:
> > I think it was the thread where I mentioned I'm working on
> > kekulization algorithm using graph theory (maximum matching). It
> > has been quite some time when I last looked at that code and it
> > is not yet usable.
>
>
I don't know if this overlaps with your work, but
On Wed, Mar 27, 2013 at 10:35 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > Maybe a proposed simplification of the valence system
> > http://forums.openbabel.org/ImplicitH-failures-td2990439.html
> > should be looked at again.
>
>
> Copy/paste from Chris's earlier message:
> > A s
for
> nitrogen. Although three actual Implicit Valences would cover the lot,
> we go around the houses catching all the different possibilities of
> bond orders, etc.
>
> So feel free to edit atomtyp.txt to patch it up for Boron. But better
> still, all in favor of replacing this impv
Anyone know what's going on with boron? The atomtyp.txt file looks right
to me. A double bond to oxygen seems to mess it up. I'm no chemist, but
everything I can find says this is just wrong.
$ echo "O=BO" | obabel -i smi -o smi
O=[BH]O
Note the extra H on the boron atom. Here's the same thi
just my two cents. Thanks again for helping me sort this out.
Craig
Thanks,
Craig
>
> - Noel
>
> On 21 March 2013 22:39, Craig James wrote:
> > Thanks, Noel! This is what I needed.
> >
> > I still don't understand why (for example) Aluminum is different from
>
Am I confused, or is this just wrong? These two SMILES should be the
identical molecule:
c1n1
c1[n]1
The first uses valence rules to deduce that there is no H on the nitrogen.
The second specifically says the same thing. Both should thus be the
identical molecule. However...
$ e
Hi Noel,
On Tue, Mar 19, 2013 at 3:16 PM, Noel O'Boyle wrote:
> I believe that the key value is the _impval property on an OBAtom,
> which is assigned by the atomtyper. Can you ask your program to print
> out the values after the EndModify() using atom->GetImplicitValence()?
>
It looks like y
Here's another very simple test program. It starts with [AlH3], delete the
hydrogens, then adds hydrogens back one by one. It will never print less
than three hydrogens, but will print correctly once you exceed the original
three hydrogens. A program is attached below; here is its output.
molecul
mValence() -> Num explicit bonds to non-H atoms
>
> To find the number of implicit Hs, GetImplicitValence() - GetValence()
>
> BOSum() -> The sum of the BOs of explicit bonds (otherwise known as
> ExplicitValence)
>
> To find the actual valence: BOSum() + GetImplicitHydro
ty on OBAtom)
> >> GetHvyAtomValence() -> Num explicit bonds to non-H atoms
> >>
> >> To find the number of implicit Hs, GetImplicitValence() - GetValence()
> >>
> >> BOSum() -> The sum of the BOs of explicit bonds (otherwise known as
> >>
Below is a test program, highly stripped down, that illustrates a problem I
can't figure out. The idea is to find ions that are neutral and show them
with a charge (don't worry about the chemistry behind this; this is highly
stripped down from the real code and just illustrates the inconsistency).
On Mon, Mar 4, 2013 at 1:08 PM, Richard West wrote:
> Just checking: I'm guessing the plan is to stick with (at least for now)
> the tickets tracker at sourceforge, or move to the issue tracker at github?
>
> And, less relevant to the GitHub Migration topic but still useful to know:
> is the best
Hi,
And now for something completely different ... I'm looking for an image of
a DNA strand that's quite long and that I can manipulate.
Is there an editor program and a template that I could use to create such a
thing? What I'm looking for is a DNA strand that on the macroscopic level
is also s
I downloaded the 2.3.2 tar.gz file from sourceforge. This looks like the
official release, right? (The web site doesn't have the 2.3.2 release yet.)
Is there an MD5 checksum for this? SourceForge seems to be pretty casual
about delivering source code over unencrypted networks.
Thanks,
Craig
On Wed, Jul 4, 2012 at 9:50 AM, Geoff Hutchison wrote:
> Chris,
>
> I've been backed up and have not had much time to merge patches into the
> 2-3-x branch yet. I'll do this over the next 2 days, but I think we'll have
> to push back the actual release until next week.
>
> Suggestions for release
On Sun, Jun 24, 2012 at 9:58 AM, Geoff Hutchison
wrote:
> > I originally had happyHTTP in the resolver format as you suggested,
> > giving good modularity.
>
> This is definitely what's going to happen for 2.3.2, along with some
> testing. I'm a bit hesitant on code which is clearly unmaintained.
On Sat, Jun 23, 2012 at 9:16 AM, Geoffrey Hutchison wrote:
> > I think there needs to be a 2.3.x release really soon. I'm waiting to
> see some resolution on Craig/Noel's discussions about stereochem issues.
>
> So I think we should make a target date for 2.3.2, since Craig seems happy
> with the
informative warnings. I'll test it either today or Monday.
Craig
>
> - Noel
>
> On 21 June 2012 16:13, Craig James wrote:
> > Hi Noel,
> >
> > I'm back from my vacation and caught up with the seemingly inevitable
> > backlog of stuff that build up.
Hi Geoff,
Are there any plans for an official bug-fix release?
Thanks,
Craig
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT m
Hi Noel,
I'm back from my vacation and caught up with the seemingly inevitable
backlog of stuff that build up... now back to reality!
On Sun, May 20, 2012 at 10:15 AM, Noel O'Boyle wrote:
> On 16 May 2012 16:28, Craig James wrote:
>
>> On Mon, May 14, 2012 at 3:46
th 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 wrote:
> > I've edited the SMILES writer so that it doesn't add hydrogens to
> > chiral cente
On Thu, Jun 7, 2012 at 8:29 AM, My Th wrote:
> Hi!
>
> I was looking at bug #3508648 and it turns out that it segfaults in
> expandKekulize() due to stack overflow. The routine in question uses
> recursive algorithm to assign bond orders for aromatic systems. For
> large molecules (1bxr has almos
On Thu, May 31, 2012 at 7:13 AM, Noel O'Boyle wrote:
> On 30 May 2012 16:29, Craig James wrote:
> > Hi Tim,
> >
> > When I reverted the SMILES canonicalizer (that is,
> > SMIBaseFormat::WriteMolecule()) back so that it doesn't copy the
> molecule, I
&g
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 your tautomer code briefly, but before I spend a great
deal of time f
On Tue, May 29, 2012 at 6:04 PM, Geoff Hutchison
wrote:
> > I started with a completely clean computer ... it didn't even have a g++
> compiler, cmake, or anything else (definitely not OpenBabel). This computer
> had never been used before.
>
> Out of curiosity, what version of g++ and cmake are y
te:
> > 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 wrote:
> >
> >> T , 2012-05-30 09:26 +0100, Noel O'Boyle rakstīja:
> >>>
On Tue, May 29, 2012 at 2:42 PM, My Th 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 system doesn't.
> >
> > I started wi
On Tue, May 29, 2012 at 11:42 AM, My Th wrote:
> > I don't know why my results are different than the build platform, but
> > I'm virtually certain that the test failures are not due to an error
> > or misconfiguration on my part.
>
> I made a fresh checkout just now and it works for me on Gentoo
I've confirmed absolutely on Ubuntu: Testing in the build directory works.
Testing with an installed OpenBabel system doesn't.
I started with a completely clean computer ... it didn't even have a g++
compiler, cmake, or anything else (definitely not OpenBabel). This computer
had never been used be
On Tue, May 29, 2012 at 9:52 AM, My Th wrote:
> O , 2012-05-29 09:24 -0700, Craig James rakstīja:
> > On Mon, May 28, 2012 at 3:08 AM, Noel O'Boyle
> wrote:
> >
> > > > Now I've checked the tautomer tests, and it also fails with the
> &
On Mon, May 28, 2012 at 3:08 AM, Noel O'Boyle wrote:
> > 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:
> > can
On Fri, May 25, 2012 at 2:20 AM, Noel O'Boyle wrote:
> It takes under 2 minutes to run the tests before committing...hint hint :-)
>
> Commit by cjames53 :: r4763
> /openbabel/trunk/src/formats/smilesformat.cpp: (link)
> - Causes graphsym and tautomer tests to fail.
>
Now I've checked the tautom
On Fri, May 25, 2012 at 2:20 AM, Noel O'Boyle wrote:
> It takes under 2 minutes to run the tests before committing...hint hint :-)
>
> Commit by cjames53 :: r4763
> /openbabel/trunk/src/formats/smilesformat.cpp: (link)
> - Causes graphsym and tautomer tests to fail.
>
It's the graphsym test itse
Hi Noel,
On Fri, May 25, 2012 at 2:20 AM, Noel O'Boyle wrote:
> It takes under 2 minutes to run the tests before committing...hint hint :-)
>
> Commit by cjames53 :: r4763
> /openbabel/trunk/src/formats/smilesformat.cpp: (link)
> - Causes graphsym and tautomer tests to fail.
>
Sorry about that
>
> If I'm not mistaken, these two SMILES should represent the same molecule,
but OB thinks they're different:
c1n1
c1[n]1
According to the SMILES spec, putting the nitrogen in brackets only says
that its charge is zero and H-count is zero, which are the defaults when
the nitrogen i
Here are my changes:
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/formats/smilesformat.cpp?r1=4758&r2=4763&;
Craig
On Thu, May 24, 2012 at 8:00 AM, Craig James wrote:
> On Thu, May 24, 2012 at 7:45 AM, Craig James wrote:
>
>> On Thu, May 24, 2
On Thu, May 24, 2012 at 7:45 AM, Craig James wrote:
> On Thu, May 24, 2012 at 6:03 AM, Noel O'Boyle wrote:
>
>> Looking at "blame" online, it seems that Tim made the change to allow
>> ferrocene structures to be normalised for the eMolecule
>>
hly 10,000 slowdown disappeared completely
on analyzing fullerenes.
Craig
>
> I haven't checked whether there are other modifications to the
> structure, but it would be easy to test with a before and after
> comparison.
>
> - Noel
>
> On 23 May 2012 23:50, Crai
More information on this question...
On Wed, May 23, 2012 at 3:05 PM, Craig James wrote:
> Hi,
>
> I've run into a case where one of my algorithms runs something like 10,000
> time slower in 2.3.x than it did in 2.2.x, and running valgrind with the
> "callgrind&quo
Hi,
I've run into a case where one of my algorithms runs something like 10,000
time slower in 2.3.x than it did in 2.2.x, and running valgrind with the
"callgrind" tool seems to indicate that aromaticity detection is the
problem.
Here's the problem: Normally when you generate a SMILES, it detects
> On 22 May 2012 21:53, My Th wrote:
> > Hi!
> >
> > Is the conclusion reached on this issue? And what would be the next
> > steps to take, if any.
> >
> > SVN history import into Git is pretty straightforward if dealing just
> > with one branch (there are already some old and outdated imports in
Hi,
Version 2.3.x is declaring lots of double bonds to not be cis or trans that
version 2.2.x thought were. In many cases 2.3.x is actually correct: the
cis/trans spec in the bond block didn't match the 2D coordinates or was
just plain wrong (for example, two "down" bonds on the same atom), so th
On Sun, May 20, 2012 at 10:19 AM, Noel O'Boyle wrote:
> Can you provide some small example code that triggers this?
>
I've been trying to find a simple example but haven't yet. I'll keep
working on it.
Craig
>
> - Noel
>
> On 16 May 2012 02:08, Craig Ja
On Mon, May 14, 2012 at 3:46 AM, Noel O'Boyle wrote:
> 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.
>
Here's how that conversation ended. Greg wrote:
>> S
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. The first stack trace reports the invalid
free, and the second stack trace shows the code that freed the memory
earlier.
Craig
==23964
On Mon, May 14, 2012 at 1:00 PM, David Lonie wrote:
> I think the most practical reason to switch is the cheap
> branching. Being able to work on several new features/bug fixes from the
> same checkout is a very handy feature, and one that I sorely miss when I
> have to work on an svn-hosted proj
On Mon, May 14, 2012 at 12:40 PM, David Lonie wrote:
> On Mon, May 14, 2012 at 3:34 PM, My Th wrote:
>>
>> > > By the way, is a general migration to git still off the table?
>> >
>> > I'm OK with this, but I think we'd need a more comprehensive vote.
>>
>> That is two, how about others? :)
>
>
>
On Mon, May 14, 2012 at 8:57 AM, Noel O'Boyle wrote:
> 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:
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 aren't present in 0D) or tet parities (which the spec explicitly
>> says to
This looks bad:
echo "C/C=C/C" | babel -i smi -o sdf | babel -i sdf -o can
CC=CC
Notice the cis/trans bonds are lost. In OB 2.2.x, it works correctly:
echo "C/C=C/C" | babel -i smi -o sdf | babel -i sdf -o can
C/C=C/C
The problem seems to be here in 2.3.x:
echo "C/C=C/C" | babe
On Thu, May 10, 2012 at 6:44 AM, Noel O'Boyle wrote:
> Can you confirm that this does not affect canonical labels for regular
> molecules?
It actually only affects molecules with two or more disconnected
fragments (e.g. "OCO.Br.Br"). The canonical labels are computed
separately for each fragment
On Wed, May 9, 2012 at 12:59 PM, Geoff Hutchison
wrote:
>
> > I'm currently working with the development branch, SVN revision 4744
> > (snapshot from about two weeks ago). If I run "make; make install; make
> > test", almost every test crashes with a segmentation violation. This makes
> > me ner
I'm currently working with the development branch, SVN revision 4744
(snapshot from about two weeks ago). If I run "make; make install; make
test", almost every test crashes with a segmentation violation. This makes
me nervous.
Should I be worried? I haven't tried to debug it yet to find the so
On Tue, May 8, 2012 at 11:18 AM, David Lonie wrote:
> On Tue, May 8, 2012 at 2:05 PM, Craig James wrote:
>
>> On Tue, May 8, 2012 at 10:04 AM, David Lonie wrote:
>>
>>> Hi all,
>>>
>>> I'm setting up a new windows build environment usi
On Tue, May 8, 2012 at 10:04 AM, David Lonie wrote:
> Hi all,
>
> I'm setting up a new windows build environment using Windows 7 and MSVC
> 2010 C++ express, and my application is unable to find some of the symbols
> from openbabel, namely etab and obErrorLog:
>
A while back we had this same prob
match the
libraries.
Craig
On Mon, May 7, 2012 at 11:05 AM, Craig James wrote:
> On Mon, May 7, 2012 at 10:09 AM, Geoffrey Hutchison wrote:
>
>>
>> On May 4, 2012, at 10:45 PM, Craig James wrote:
>>
>> > But it seems to be the atom iterator, not the ring i
On Mon, May 7, 2012 at 10:09 AM, Geoffrey Hutchison wrote:
>
> On May 4, 2012, at 10:45 PM, Craig James wrote:
>
> > But it seems to be the atom iterator, not the ring iterator, that's
> causing the problem.
>
> Huh. Here's comparable code in forcefield
find
the problem.
But it seems to be the atom iterator, not the ring iterator, that's causing
the problem.
Thanks,
Craig
>
>
> On Fri, 2012-05-04 at 19:30 -0400, Craig James wrote:
> > Can anyone tell me why this code crashes? It's copied almost verbatim
> > from th
Can anyone tell me why this code crashes? It's copied almost verbatim from
the OpenBabel OBRing API page.
Note: I wasn't sure if the "mol->GetSSSR()" call was needed before calling
mol->GetData("RingList"), so I added it to be sure. The man page wasn't
clear about this.
Thanks,
Craig
mol->Ge
I just checked in a simple but important change to canon.cpp. It's been a
long time since I worked on this stuff and the canon.cpp file is completely
rewritten, so if someone familiar with this file could check it, I'd
appreciate it. Here's the SVN comment:
"Fixed a bug in CalcCanonicalLabels():
I doubt anyone will be able to shed light on this, but... OpenBabel is
randomly hanging in the C++ deallocator. See the stack trace below.
I've run into weird problems like this before, and it was related to the
fact that I'm linking a C++ library (OpenBabel) into a C program (the
Postgres databa
On Tue, Apr 24, 2012 at 8:22 AM, Jörg Kurt Wegner
wrote:
> Third, I would highly recommend that we replace the tautomerization
> framework with an alternative solution, e.g. the SMIRKS ennumeriation
> from Markus Sitzman. The SMIRKS patterns are part of his publication
> Article (sin10)
> Sitzmann
;s just 30 lines
> typed in from Peter Ertl's paper.
>
> I guess it's not so important, but maybe going forward we can attach a
> CC0 license to files if they are reusable by others.
>
> - Noel
>
> On 3 March 2012 17:15, Craig James wrote:
> > Hi Noel,
> &g
Hi Noel,
Did I miss a previous discussion? Which data files are we talking about?
Craig
On Sat, Mar 3, 2012 at 4:43 AM, Noel O'Boyle wrote:
> 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 da
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