OBBond.IsAromatic(). See the docs.
I would not use Smarts patterns to type atoms or bonds, but rather do it in
code. The former is just too error prone, slow and less readable.
On Tue, 27 Jul 2021, 07:18 David van der Spoel,
wrote:
> On 2021-07-27 07:51, Noel O'Boyle wrote:
> &
Is there a particular problem you are trying to solve where underlying
kekule representation is causing a problem?
On Mon, 26 Jul 2021, 21:28 David Koes, wrote:
> In my opinion, if the only fractional value will be 1.5 then non-integer
> bond orders aren't worth the pain of breaking compatibili
Hi all,
I've just uploaded Windows binaries for the Python bindings to PyPI. This
took quite a while due to some issues with Swig.
Swig 4.0.1 is out, and looks pretty interesting (e.g. Doxygen comments can
be included in the Python bindings), but...it doesn't work for us. They've
overhauled the P
Would you consider a beta release first? I won't be able to get things
together by Friday.
- Noel
On Mon, 27 Apr 2020, 16:06 Geoffrey Hutchison,
wrote:
> I'd like to make a 3.0.1 release on Friday - it's sorely needed. Any last
> issues or patches to consider before the release?
>
> -Geoff
>
>
Looks great so far. EIGEN3 is in the msvc dependencies that you've
untarred. It should just be a matter of
-DEIGEN3_INCLUDE_DIR=MSVC_DEPS_DIR\include".
On Fri, 10 Apr 2020, 00:52 Geoffrey Hutchison,
wrote:
> Hi Noel,
>
> I've been working bit-by-bit to migrate OB's test builds from Travis /
> Ap
Looking at the link in that tweet you Liked, Geoff, it may be that we need
to transition to the Travis GitHub App, rather than whatever we were doing.
Or are we on that already?
- Noel
On Wed, 8 Apr 2020 at 09:45, Noel O'Boyle wrote:
> I've just checked a few PRs and it seems th
I've just checked a few PRs and it seems that the Travis CI is not being
run. The Appveyor build is running, but I don't think that runs the tests.
Regards,
- Noel
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A fairly easy first issue would be to fix the two warnings found when
compiling with a recent gcc. Note that a simple loop should be preferred
over expressions that involve recent C++ standards (due to portability).
Regards,
- Noel
On Thu, 13 Feb 2020 at 14:15, Naruki Yoshikawa
wrote:
> Hello H
I believe I've covered the issues you've raised, but let me know if not.
I'll also mention this on Twitter to see if anyone has anything to add.
https://github.com/openbabel/documentation/pull/15
On Tue, 11 Feb 2020 at 19:54, Noel O'Boyle wrote:
> Hi Stefano,
>
>
nt("Anti-clockwise winding")
> else: # elif config.winding==ob.OBStereoUnknownWinding: ?
> print("Undefined winding winding")
> --
>
> Also, I know the support for non-tetrahedral chirality is not complete,
> but I'm wondering
> if there a way to use the
metry implementation.
> >
> > The key challenge is that we'd want to save the expected stereo
> configuration around atoms
> > and bonds - and then when generating 3D coordinates, test to see if the
> generated
> > configurations match the expected ones.
>
geometry implementation.
> >
> > The key challenge is that we'd want to save the expected stereo
> configuration around atoms
> > and bonds - and then when generating 3D coordinates, test to see if the
> generated
> > configurations match the expected ones.
> >
> >
Hi there,
I've been very slowly pulling together some docs on using the API for
stereo. I remember someone on the list a few months back discussing
difficulties with this part of the library - if anyone has any particular
examples they'd like me to discuss, this would be a good time to mention
the
Here are some timings for "obabel -:C -osmi" for the first run of the day
(note that OB here is on a network drive so I would guess this will be
slower than for most other people):
real 0m1.981s
user 0m0.029s
sys 0m0.086s
and the second:
real 0m0.032s
user 0m0.020s
sys 0m0.010s
Personally, I do
If you delete all of the plugins you don't want, this will speed things up
for you.
Alternatively, if you make a static build (I forgot the precise
invocation), then the plugins are compiled in rather than loaded
dynamically.
I don't have time right now to go into why plugins are a great idea, bu
Should have used vim. :-)
On Tue, 26 Nov 2019 at 13:12, David van der Spoel
wrote:
> Den 2019-11-26 kl. 13:58, skrev Noel O'Boyle:
> > The "M CHG" line looks dubious. It states that there is a single
> > charge, a +5 charge on atom 1. What is the sour
The "M CHG" line looks dubious. It states that there is a single charge,
a +5 charge on atom 1. What is the source of this SDF file?
Regards,
- Noe
On Tue, 26 Nov 2019 at 12:12, David van der Spoel
wrote:
> Den 2019-11-26 kl. 13:06, skrev Noel O'Boyle:
> > Hi David,
Hi David,
Can you provide the input file?
Regards,
- Noel
On Tue, 26 Nov 2019 at 09:50, David van der Spoel
wrote:
> Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle:
> > An SDF file describes the number of hydrogens on each atom. Open Babel
> > is neither adding nor removin
An SDF file describes the number of hydrogens on each atom. Open Babel is
neither adding nor removing them. AddHydrogens() is just making them
explicit.
Regards,
- Noel
On Tue, 26 Nov 2019 at 06:50, David van der Spoel
wrote:
> Hi,
>
> I was trying to use obprop on an SDF file, but found out th
For the record...
http://archive.ambermd.org/201910/0141.html
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No worries. Just checking. There's no hurry.
On Wed, 23 Oct 2019, 16:31 Geoffrey Hutchison,
wrote:
> \Are we good to go? Or are you waiting on me for something? I think I've
> done all I can.
>
>
> I've just been busy, but I'll send out an announcement about the release
> today.
>
> -Geoff
>
___
Are we good to go? Or are you waiting on me for something? I think I've
done all I can.
On Tue, 15 Oct 2019, 21:43 Noel O'Boyle, wrote:
> Ok - I've managed to get the docs and API docs up on openbabel.github.io
> at:
> https://openbabel.github.io/docs/3.0/
Does your pdb file have hydrogens? If not, even more guessing. Gaussian
files have all the atoms at least.
On Fri, 18 Oct 2019, 19:54 David van der Spoel,
wrote:
> Den 2019-10-18 kl. 20:37, skrev Noel O'Boyle:
> > With pdb files we have to guess the bond orders. With sdf files
With pdb files we have to guess the bond orders. With sdf files, we don't.
There shouldn't be any other difference.
On Fri, 18 Oct 2019, 18:52 David van der Spoel,
wrote:
> Hi,
>
> it seems that the algorithm for determining bonds and atomtypes depends
> on the input file, is that correct?
> Whe
bove. This at least gives us the
defaults. I think that there might be some other way to customise it if we
want.
Last thing to do is update the links from the Mediawiki install page to
point to the new docs. But it's getting late
- Noel
On Thu, 10 Oct 2019 at 21:12, Noel O'
As separately emailed, I've had trouble getting the GitHub pages suite to
build and deploy, but I've uploaded the docs there and you can copy to
openbabel.org.
Since I can't currently depoly to GH pages, could you rebuild the API docs
and deploy to your site? Personally, I would make the following
I've attached the binaries to the draft release, and I think the Python
binaries are ready to go.
I was thinking about uploading the docs to the github pages site. You could
redirect from openbabel.org/docs when it's ready. I could do the same for
the API docs.
- Noel
On Sun, 6 Oct 2019 at 03:44
Let's do it.
Can you leave a week between the tagging and the announcement? It's not
just the Windows binaries but going around updating the download links,
release notes, etc. Hopefully our conda wizards will also have time to
build things in this timeframe too.
I note in passing that I'm in the
Centos is binary compatible AFAIK.
On Tue, 17 Sep 2019, 16:19 Patrick Lorton, wrote:
> I've not been able to google a solution around redhat docker images
> needing a subscription to install any packages, something which I'm not
> really sure how to procure for public use in a github open source
frey Hutchison <
>> geoff.hutchi...@gmail.com> wrote:
>>
>> To start out, I'll emphasize that OB has been a default package on
>> several intentionally slow-to-upgrade distros. I'm not surprised to access
>> new supercomputing resources to find Open Bab
A good place to put those scripts would be the repo I've just made:
https://github.com/openbabel/maintenance
Should I tag the source differently next Monday? Also, I think I messed up
the release digits in the Cmake file. I should have had .0a1 but instead
have .a1.
I'll upload the Windows binari
yor build or a
> Docker to make the Windows binaries. There are some scripts around for
> making "continuous" binaries available from Travis or AppVeyor, which
> seems like a good step forward.
>
> On Thu, Sep 12, 2019 at 10:13 AM Noel O'Boyle
> wrote:
> >
&
Hi Geoff,
Are you going to be able to look after the source release tomorrow? Or will
I? Either way, it would be good to have a write-up of the steps involved.
I've updated the release notes and am currently struggling through updating
my build toolchain on Windows. Will I have some binaries for
Hi all,
I've tagged the 3.0.0a1 release ("git checkout openbabel-3-0-0a1" I think
will work), and a GitHub release will appear on Friday, hopefully alongside
other releases such as Snaps, Python bindings, Windows executables, Docker
build scripts, etc. Or more likely, I'll find out that I have to
own RDKit and builds it on Ubuntu - in this case to be used
> with GPUSim, but you can see it'd be trivial to just run the tests at the
> end. This is how I guarantee my changes on GPUSim are working on Ubuntu
> (the most popular platform for it) even when I do all my dev on A
Hi all,
Geoff asked me to bring up the discussion of a release schedule for OB 3.0.
It's been so long since the last release, that it's become painful for us
to do a release, which is a bit of a vicious cycle as you can imagine.
So
I have some time to do this now (with help I hope!) so I'm go
I'm on the fence. Usually I'd say avoid extensions by default, but this
looks like a common extension that preserves information. But I can't
really say as I don't deal with PDB files. But if you do go ahead with
this, it's important that there is an option to turn it off in case it does
cause prob
If you use canonical SMILES instead of the InChI to evaluate changes in
stereo, do the results change? If you use canonical SMILES, you will also
be able to manually verify what's different.
- Noel
On Fri, 21 Jun 2019 at 09:05, Naruki Yoshikawa
wrote:
> Hi all,
>
> I've been developing a new di
Well, personally, I don't want that dependency. It would mean dropping
support for particular legacy OSes, where Open Babel has compiled without
trouble until now (similarly the CXX11 requrest). As I see it, users of
Open Babel will see no benefit from us using Boost, but will find it more
difficul
Are we going to do this for 3.0? I think we should.
Regards,
- Noel
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Hey Geoff et al,
The last thing I want to tidy up before 3.0 are the functions I added in
obfunctions.h. These are 3 atom and bond based functions that I didn't want
to just chuck into atom.h and bond.h.
What I'd really like to do is have atommanip.h (or atomfunctions.h,
atomops.h, whatever) that
>From my point of view, the only required changes before the next release
are those that break the API or change behaviour as they can't be done
thereafter. With this in mind, I'm going to send in a few pull requests for
changes which I think would be good tidy ups (e.g. functions marked as
depreca
Hi everyone,
I have a bit more free time now. Let's work towards a release.
Regards,
- Noel
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I presume it's a C++ "static method", what's called a "class method" in
Python. These are methods that don't require an instance of an object, but
that you can call directly. The confusing part is that (in this case) the
return value is an instance of the class.
This approach might seem a bit roun
Well done. I hope you found the experience useful. It was also good to meet
you at the ACS.
All the best for your future work.
Regards,
- Noel
On Sat, 25 Aug 2018 at 07:27, Naruki Yoshikawa
wrote:
> Hi everyone,
>
> In April, I introduced my Google Summer of Code project: "Fast, Efficient
> Fr
Hi Geoff,
It looks like the Clang build is failing on master. If you've a chance, can
you track down what specific merge/commit is causing this? Or am I wrong?
Regards,
- Noel
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May I suggest that we replace Unset functions for flags (e.g.
UnsetAromaticPerceived()), with a parameter to the Set functions (e.g.
SetAromaticPerceived(false))? This is already the case for some of the Set
functions. This would tidy the API a bit, and ensure that we actually have
the ability to b
; ./VectorpInternalCoord.cs(47,23): error CS0246: The type or namespace
> name `Action' could not be found. Are you missing `System' using directive?
>
> ./VectorpRing.cs(47,23): error CS0246: The type or namespace name `Action'
> could not be found. Are you missing `System&#x
Hi Mohammad,
Just to take a step back, could you describe how users of Open Babel will
benefit from this? That is, what they might use these charges for? I know
that Open Babel already has several charge models, but none are documented
currently, and so I have no clue what to do with them except c
I forgot to say that the background to all of this is that I was writing up
docs describing the handling of aromaticity in Open Babel, and when I got
to the section describing DeleteAtom() I found that the behaviour was not
how I thought.
- Noel
On 14 June 2018 at 07:03, Noel O'Boyle
Hi all,
I've sent in a pull request (
https://github.com/openbabel/openbabel/pull/1847) regarding to DeleteAtom()
and aromaticity, and Geoff asked me to bring it up here.
Currently, when you delete an atom (to be exact, it's actually
Begin/EndModify that I'm changing), the flag that indicates tha
Sigh. Oh InChI. At a recent meeting, 'we' tried to encourage InChI to move
to Github and an open development model, but the bogeyman of people
modifying the code and still calling it InChI was brought up. As Roger
pointed out, you don't need the InChI code to do this, you can just make up
an InChI
ese SMILES fragments, read them in
> again and write out again.
> > But I think Noel has a new way of generating canonical SMILES from
> fragments. I’d suggest posting to the list and asking. Either way would
> consolidate all these strings into c1c1
>
> Do you have any sugg
It was on Github. Here you go:
https://github.com/openbabel/openbabel/pull/1712
Are you sure you don't just want the canonical labels? I'm happy to
review...
On 17 May 2018 at 11:47, Geoffrey Hutchison
wrote:
> Hi Noel,
>
> I'm working with Naruki, the student with GSoC developing the
> fragmen
Let me know if you need anything from me.
On Fri, 20 Apr 2018, 16:11 Geoffrey Hutchison,
wrote:
> It's been about 18 months since the release of 2.4.1. While there's a lot
> of progress (thanks mostly to Noel) for 3.0 at the end of the summer, I'd
> like to push for a 2.4.2 release ASAP.
>
> The
amp; Systems Biology
> University of Pittsburgh
>
>
> On Apr 26, 2018, at 2:43 AM, Noel O'Boyle wrote:
>
> Okay, I think it's close to completion. Again, comments welcome...
>
> https://gist.github.com/baoilleach/d9f02fb906e70277f6b4721d63d68b59
> <https://na01.safe
s stdin to the commandline
> specified as the second argument).
>
> Definitely want to know how to add input/output files and properly
> reference them from all three test scenarios.
>
> David Koes
>
> Assistant Professor
> Computational & Systems Biology
> University
Hi Naruki,
Welcome to the list. I wish you all the best - this would be a great
improvement to Open Babel.
Regards,
- Noel
On 25 April 2018 at 12:18, Naruki Yoshikawa
wrote:
> Hi everyone,
>
> I am going to work on the project "Fast, Efficient Fragment-Based
> Coordinate Generation"
> https://
missing or could be explained better?
- Noel
On 25 April 2018 at 07:17, Noel O'Boyle wrote:
> On the topic of documentation, here's what I've got so far. Anything
> missing?
>
> On 17 April 2018 at 06:58, David van der Spoel
> wrote:
>
>> Den 2018-04-
On the topic of documentation, here's what I've got so far. Anything
missing?
On 17 April 2018 at 06:58, David van der Spoel wrote:
> Den 2018-04-17 kl. 07:51, skrev Noel O'Boyle:
>
>> To avoid digressing, absolutely we would like to do this and have the
>> tec
To avoid digressing, absolutely we would like to do this and have the
technical means to enforce...once we reduce the warnings. I did a certain
amount already this year. Once a particular type of warning is eliminated
we can add it as a requirement using gcc's treat warnings as errors. But
we're no
times looking at the test directory, I said “well, I’m not using the python
>> bindings, so I’ll ignore those files and try to figure out the c++ files
>> and how they run tests”, when the reality is that the python files provide
>> the easy route to testing the command line progra
re those files and try to figure out the c++ files
> and how they run tests”, when the reality is that the python files provide
> the easy route to testing the command line programs.
>
> -David
>
>
> > On Apr 3, 2018, at 4:42 AM, Noel O'Boyle wrote:
> >
> >
Hi all,
Very few PRs come with test cases. Basically, we just don't know if any of
them do what they say, and even if they do, they probably will bit rot at a
future date due to other PRs. The irony is that the person who wrote the
code clearly tested it (one would assume) - but just didn't check
Should be fixed now.
On 17 March 2018 at 21:31, Mohammad Mehdi Ghahremanpour <
ghahramanpou...@gmail.com> wrote:
> Fellow developers,
>
> I just synced my fork with master and I got this compilation error:
>
>
> [ 72%] Built target pubchem
> *Scanning dependencies of target xmlformat*
> *openbabe
My proposal is open for comments. See:
https://github.com/openbabel/enhancement-proposals/pull/8
Regards,
Noel
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There's bits and pieces on different pages that are worth keeping but I
don't know that the pages themselves should form part of a new website.In
other words, after removing clearly unneeded pages (e.g. the formats) I'd
put everything down into a legacy subdirectory and just create a simple
clear w
(e.g., the == in
> GetAtomicNum() == 1).
>
> You could even shorten the name to “Is”:
> atom->Is(OBElement::Hydrogen)
>
> David Koes
>
> Assistant Professor
> Computational & Systems Biology
> University of Pittsburgh
>
>
> On Jan 12, 2018, at 9:01 AM, Noel O
Hi David,
We don't break backwards compatability lightly. The last time was 12 years
ago. In that time, there has been some accumulation of cruft, and in
addition there are some necessary changes in order to fix underlying
problems.
Regarding the specific functions you mention, the IsElement() fu
Hi Geoff,
I've been looking into whether Travis provides some means to indicate
performance changes, but it seems not, and I kind of understand why:
https://github.com/travis-ci/travis-ci/issues/352 (2011)
https://github.com/travis-ci/travis-ci/issues/3313 (2015)
Given that that's the case, is it
Sounds good.
On 24 October 2017 at 21:05, Geoffrey Hutchison
wrote:
> Hi everyone,
>
> I’d like to modernize the Open Babel webpages, including migrating away
> from MediaWiki to Markdown / Jekyll.
>
> The idea behind the MediaWiki site was to enable anyone to edit.
> Unfortunately, unlike Wikip
Ok - I'll make it so, if no-one else gets there first...
On 9 October 2017 at 14:23, Geoffrey Hutchison
wrote:
> > Is it okay if I increment the version number on master? That is, to
> 2.4.2 (or something else if that's the usual procedure, e.g. 2.4.2dev).
>
> It’s definitely time to increment t
Hey Geoff,
Is it okay if I increment the version number on master? That is, to 2.4.2
(or something else if that's the usual procedure, e.g. 2.4.2dev).
I've just gotten snap builds working a bit better now, and I'd like to make
dev versions available. This will be cleared marked as 2.4.2dev or
som
Hi Geoff,
I've been looking into enabling support for OBReaction from Python, and
started with excavating what was previously tried.
Apparently, I added support back in 2013 via
https://github.com/openbabel/openbabel/pull/21. The catch with Swig is not
only are all OBMols turned into shared_ptrs,
(This question is probably better suited to openbabel-discuss rather than
devel)
Just type "MW formula" into the box "Append properties or descriptors to
title". A list of available properties is in the menu under Plugins,
Descriptors.
On 16 August 2017 at 07:23, RicardoMBorges via OpenBabel-Deve
FYI, I filed an issue with PyBEL on the name conflict:
https://github.com/pybel/pybel/issues/217
Resolved as "won't fix" (my words).
Regards,
- Noel
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eng
I think his edits were on master, so...after resetting they might have
disappeared. Still should be upstream though.
On 7 July 2017 at 15:11, Mohammad Mehdi Ghahremanpour
wrote:
>
> On Jul 7, 2017, at 4:00 PM, Geoffrey Hutchison
> wrote:
>
> Before doing that, my branch was ahead by 6 commits an
rect.
>
> Thanks,
> Mohammad
>
> On Jul 7, 2017, at 3:26 PM, Noel O'Boyle wrote:
>
> I beg your pardon, here is the link:
> https://github.com/openbabel/openbabel/pull/337
>
> On 7 July 2017 at 14:25, Noel O'Boyle wrote:
>
>
I beg your pardon, here is the link:
https://github.com/openbabel/openbabel/pull/337
On 7 July 2017 at 14:25, Noel O'Boyle wrote:
> Hi Mohammad,
>
> Here is your pull request:
> https://github.com/openbabel/openbabel/pull/337/files/9fdfc1120fff9fd3009df4c
Hi Mohammad,
Here is your pull request:
https://github.com/openbabel/openbabel/pull/337/files/9fdfc1120fff9fd3009df4cfe8d789c92a49c1e1..beba494f1c977dca1af1279eab267d65c0f3261e
I think that you have not rebased correctly. The pull request contains
a huge number of commits that are unrelated to th
Hi Geoff,
I've just converted the isotope table in isotope.txt to a switch
statement in the code (elements.cpp in
https://github.com/baoilleach/openbabel/commit/91a320713f498e78db1b3e4579a1a87478f0c55a).
I have some more work to do with adding comments and so forth, but
what I'm wondering is, ther
, cf(98), es(99), fm(100),
> md(101), no(102), lr(103), rf(104), db(105),
> sg(106), bh(107), hs(108), mt(109), ds(110),
> rg(111)
> }
>
>
> Matt
>
>
> On 29 June 2017 at 08:41:31, Noel O'Boyle (baoille...@gmail.com) wrote:
>
> Hi Matt,
>
> I
Hi Matt,
I'm in the middle of
https://github.com/openbabel/enhancement-proposals/pull/4 and have
come to the JSON formats.
When parsing the PubChem JSON you try first whether it's an integer
and then later if it's a string. I think it's always an integer and
plan to remove the string code - is th
Hi there,
At the start of the year (or was it last year?), I said to Geoff that
I felt that the single major problem with OB was its handling of
implicit hydrogens. And he called my bluff. :-)
Well, "the fix" has now been merged. Everything should be faster but
also more correct. As this is a maj
/conda-openbabel/build/1.0.23/job/hvv95j1fagio4ike
>>
>>
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>> 2017-06-09 15:19 GMT+02:00 Maciek Wójcikowski :
>>>
>>> I'm on it as we speak.
>>>
e issue with tests later on.
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-09 14:23 GMT+02:00 Noel O'Boyle :
>>
>> I'm keen to get my code merged, so I'm going to press you on this.
>> I&#x
I'm keen to get my code merged, so I'm going to press you on this.
I've spent several months getting these tests to 100% passing. I'm
happy to send a screenshot showing this on my Windows machine.
- Noel
On 6 June 2017 at 20:52, Noel O'Boyle wrote:
> Th
me time by the end of the week.
>
> PS.
> https://ci.appveyor.com/project/baoilleach/openbabel/build/1.0.481 this
> build says 100% tests passed. Am I looking at the wrong one?
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
&g
Hey Geoff,
I'm going to turn off tests for the Appveyor build due to the problems
with PR#1572. I don't think they are real - do you remember a similiar
issue with a PR of David Koes, where I had exactly the same problem
(except here it's multiple tests)? Something's funny with the VMs that
Appvey
No - we do not have AM1, nor any semi-empirical method.
On 24 May 2017 at 13:09, Yalda wrote:
> goodafternoon i have 485 target from binding database by 3d sdf format best
> forcefield to get minimum energy is AM1 in semi empirical method are there
> AM1 in the forcefield of openbabel? thanks
> _
Hi all,
Geoff has prompted me to look into sorting out the "pip install pybel"
versus "pip install openbabel" problem.
Talking to Matt Swain he pointed out that our install procedure is a
bit non-standard in the first place. So I'm suggesting changing things
to having a folder (i.e. Python packag
ith that,
Geoff :-)
- Noel
On 14 April 2017 at 11:22, Noel O'Boyle wrote:
> If you're interested in what I hope will be the future of OB, you can
> try out my work on changing the handling of implicit hydrogens and
> implementing a new kekulization algorithm:
> https:/
Hi Nitish,
Welcome and best of luck. Hope you enjoy your project, and I look
forward to seeing your progress.
- Noel O'Boyle
On 8 May 2017 at 14:06, Nitish Garg wrote:
> Hi everyone,
>
> I am working on the project "Computational Chemistry Web repository" during
>
If you're interested in what I hope will be the future of OB, you can
try out my work on changing the handling of implicit hydrogens and
implementing a new kekulization algorithm:
https://github.com/baoilleach/openbabel/tree/workingimph
This is partly to let people know that there's work in progre
Hi there,
Geoff has established a "Babel Enhancement Proposal" (or BEP) system
for proposing and discussing changes to the API. This is to be done on
Github via a new repo.
To check out my first proposal, see:
https://github.com/baoilleach/enhancement-proposals/blob/master/remove_kekule_and_aro
A week or two ago, Geoff migrated bugs (/etc?) from SF over to Github.
After some fiddling, just now I figured out how to put the SF bug/etc
trackers into read-only mode. If you go there yourself as a developer,
you may still see the "Create" button but regular users won't.
If you are on this lis
Hi Andrey,
This is very useful although we find that ABI compliance checker has
false positives. What would be super useful is Github integration on
pull requests. Even if this was not something you yourself had the
resources to support, if you had a recipe for projects to set up
Github hooks ours
May I suggest that we change openbabel-dev to only allow posting by
members? That is, that posts by non-members are rejected (with a
message) without review. This would reduce the admin burden on spam
filtering. There is a list of existing non-members with posting rights
on the mailman interface, a
or so patterns to be tested, so
> I though doing the perception once and storing it would have been a good
> idea. On the other hand, I don't think performance is an issue for this
> kind of functions.
>
> I have no idea how to implement this with a switch statement without
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