Re: [OpenBabel-Devel] Non-integer bond orders for resonant groups

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 wr

[OpenBabel-Devel] Python bindings for 3.1.1

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

Re: [OpenBabel-Devel] Last call for 3.0.1 release

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 > >

Re: [OpenBabel-Devel] Migrating to GitHub build actions

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 / >

Re: [OpenBabel-Devel] Travis CI no longer running on PRs

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 that the Tra

[OpenBabel-Devel] Travis CI no longer running on PRs

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 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net

Re: [OpenBabel-Devel] Willing to contribute to Openbabel

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

Re: [OpenBabel-Devel] Docs on handling of stereo

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, > > When you call GetCon

Re: [OpenBabel-Devel] Docs on handling of stereo

ise 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 OBStereo.Type with the fa

Re: [OpenBabel-Devel] Docs on handling of stereo

at 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. > > > > I think we can probably go through the code and examine

Re: [OpenBabel-Devel] Docs on handling of stereo

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. > > > > I think we can probably go through the code and examine

[OpenBabel-Devel] Docs on handling of stereo

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

Re: [OpenBabel-Devel] Why are there plugins?

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

Re: [OpenBabel-Devel] Why are there plugins?

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,

Re: [OpenBabel-Devel] Hydrogen management bug

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 source of

Re: [OpenBabel-Devel] Hydrogen management bug

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, >

Re: [OpenBabel-Devel] Hydrogen management bug

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 removing the

Re: [OpenBabel-Devel] [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber from Elvis Martis on 2019-10-10 (Amber Archive Oct 2019)

For the record... http://archive.ambermd.org/201910/0141.html ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel

Re: [OpenBabel-Devel] ANNOUNCE: Open Babel 3.0.0 Released

And a big thanks to Geoff for pulling it all together. Hip hip ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel

Re: [OpenBabel-Devel] 3.0 release?

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 >

Re: [OpenBabel-Devel] 3.0 release?

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/index.html >

Re: [OpenBabel-Devel] Algorithm for FF atomtypes

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, we

Re: [OpenBabel-Devel] Algorithm for FF atomtypes

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? >

Re: [OpenBabel-Devel] 3.0 release?

. 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'Boyle wrote

Re: [OpenBabel-Devel] 3.0 release?

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

Re: [OpenBabel-Devel] 3.0 release?

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

Re: [OpenBabel-Devel] 3.0 release?

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

Re: [OpenBabel-Devel] Docker files...

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

Re: [OpenBabel-Devel] maeparser depends on boost iostreams, can openbabel use it?

gt; 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 Babel 2.3.2 or something >>

Re: [OpenBabel-Devel] 3.0.0alpha 1

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

Re: [OpenBabel-Devel] Source release

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: > > > > H

[OpenBabel-Devel] Source release

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

[OpenBabel-Devel] Open Babel 3.0.0a1 tagged

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

Re: [OpenBabel-Devel] Release Schedule

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 Arch. > > Pat > > On Fri

[OpenBabel-Devel] Release Schedule

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

Re: [OpenBabel-Devel] PDB files with multiple bonds via CONECT

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

Re: [OpenBabel-Devel] Stereochemistry check using InChIKey

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

Re: [OpenBabel-Devel] maeparser depends on boost iostreams, can openbabel use it?

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

[OpenBabel-Devel] Removal of babel

Are we going to do this for 3.0? I think we should. Regards, - Noel ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel

[OpenBabel-Devel] Atom and bond manipulation

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)

Re: [OpenBabel-Devel] Towards a release

>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

[OpenBabel-Devel] Towards a release

Hi everyone, I have a bit more free time now. Let's work towards a release. Regards, - Noel ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel

Re: [OpenBabel-Devel] OBOp

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

Re: [OpenBabel-Devel] GSoC project completion

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 >

[OpenBabel-Devel] Failing master

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 -- Check out the vibrant tech community on

[OpenBabel-Devel] Proposal to remove "Unset" functions for flags

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

Re: [OpenBabel-Devel] Implementation of s-type Slater orbitals in open babel

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

Re: [OpenBabel-Devel] Invalidation of aromaticity flags

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 wrote

[OpenBabel-Devel] Invalidation of aromaticity flags

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

Re: [OpenBabel-Devel] Getting SMILES Atom Order data

; My suggestion would be to take these 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 c1

Re: [OpenBabel-Devel] Getting SMILES Atom Order data

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

Re: [OpenBabel-Devel] Need for a stop-gap 2.4.2 release.

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

Re: [OpenBabel-Devel] Proposal to require test cases

; Computational & Systems Biology > University of Pittsburgh > > > On Apr 26, 2018, at 2:43 AM, Noel O'Boyle <baoille...@gmail.com> wrote: > > Okay, I think it's close to completion. Again, comments welcome... > > https://gist.github.com/baoilleach/d9f02fb906e70277f6b4721d6

Re: [OpenBabel-Devel] Proposal to require test cases

its first argument as 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 &

Re: [OpenBabel-Devel] GSoC project introduction - Fast, Efficient Fragment-Based Coordinate Generation

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 >

Re: [OpenBabel-Devel] Proposal to require test cases

or could be explained better? - Noel On 25 April 2018 at 07:17, Noel O'Boyle <baoille...@gmail.com> 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 <sp...@xray.bmc.uu.se> > wrote:

Re: [OpenBabel-Devel] Proposal to require test cases

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 <sp...@xray.bmc.uu.se> 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

Re: [OpenBabel-Devel] Proposal to require test cases

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

Re: [OpenBabel-Devel] Proposal to require test cases

might be helpful. I know my first few >> 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 >&g

Re: [OpenBabel-Devel] Proposal to require test cases

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 programs. > > -David > > > > On Apr 3, 2018, at 4:42 AM, Noel O'Boyle

[OpenBabel-Devel] Proposal to require test cases

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

Re: [OpenBabel-Devel] compilation error of developing version

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* >

[OpenBabel-Devel] Proposal: Store reactions as annotated molecules

My proposal is open for comments. See: https://github.com/openbabel/enhancement-proposals/pull/8 Regards, Noel -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org!

Re: [OpenBabel-Devel] First pass at converting Open Babel wiki to Jekyll

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

Re: [OpenBabel-Devel] Release 3.0

cedence (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

Re: [OpenBabel-Devel] Release 3.0

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()

[OpenBabel-Devel] Performance tests

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

Re: [OpenBabel-Devel] Migrating from MediaWiki

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. >

Re: [OpenBabel-Devel] Version number on master

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

[OpenBabel-Devel] Version number on master

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

[OpenBabel-Devel] Support for OBReaction in Python

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

Re: [OpenBabel-Devel] Append molecular formula and molecular weight to SMILES format list

(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-Devel] Pybel versus PyBEL

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 -- Check out the vibrant tech community on one of the world's most

Re: [OpenBabel-Devel] pull request for an old patch

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: > >

Re: [OpenBabel-Devel] pull request for an old patch

can I fix the rebasing if it was incorrect. > > Thanks, > Mohammad > > On Jul 7, 2017, at 3:26 PM, Noel O'Boyle <baoille...@gmail.com> 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'B

Re: [OpenBabel-Devel] pull request for an old patch

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 <baoille...@gmail.com> wrote: > Hi Mohammad, > > Here is your pull request: > https://github.com/openbabel/openbabel/pull/337/files/9fdfc1120fff9fd3009df4

Re: [OpenBabel-Devel] pull request for an old patch

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

[OpenBabel-Devel] Isotope table

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,

[OpenBabel-Devel] JSON parsing of elements

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

[OpenBabel-Devel] Explicit "implicit hydrogen" count and kekulisation now merged

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

Re: [OpenBabel-Devel] Appveyor tests

mac...@wojcikowski.pl>: >>> >>> I'm on it as we speak. >>> >>> >>> Pozdrawiam, | Best regards, >>> Maciek Wójcikowski >>> mac...@wojcikowski.pl >>> >>> 2017-06-09 15:09 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>

Re: [OpenBabel-Devel] Appveyor tests

nd figure out what is the issue with tests later on. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > 2017-06-09 14:23 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>: >> >> I'm keen to get my code merged, so I'm going to press you

Re: [OpenBabel-Devel] Appveyor tests

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 <baoille...@gmail.com> wrote: > The link is

[OpenBabel-Devel] Appveyor tests

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

Re: [OpenBabel-Devel] FYI, Implicit hydrogens and kekulization branch

:-) - Noel On 14 April 2017 at 11:22, Noel O'Boyle <baoille...@gmail.com> 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: >

Re: [OpenBabel-Devel] GSoC project introduction - C.C. web repository

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 <nitish.garg.6...@gmail.com> wrote: > Hi everyone, > > I am working on the project "Computational Chemistry We

[OpenBabel-Devel] BEP: Proposal for removal of Kekule and Aromatic Bond Orders

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:

[OpenBabel-Devel] Moving trackers from SF to GitHub

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

Re: [OpenBabel-Devel] API/ABI changes review for OpenBabel

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

[OpenBabel-Devel] Mailing list change proposal

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,

Re: [OpenBabel-Devel] Convenience functions

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 > having to do the bond

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

The discussion over at opensmiles was that both forms are reasonable and Geoff prefers the current behavior, so I'll stick to that. On Thursday, 2 March 2017, Andrew Dalke wrote: > On Mar 2, 2017, at 21:31, Andrew Dalke >

Re: [OpenBabel-Devel] Convenience functions

ile and match them with the requested atom. > > S > > > > > On 03/02/2017 02:22 AM, Noel O'Boyle wrote: >> >> Hi Stefano, >> >> Sounds good. But the guidelines are not unfortunately the existing >> guide. I'm currently in the process of rewriting

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

To avoid multiple threads, let's move this over to the opensmiles list. On 2 March 2017 at 20:31, Andrew Dalke wrote: > On Mar 2, 2017, at 20:34, Craig James wrote: >> Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

n 2 March 2017 at 19:34, Craig James <cja...@emolecules.com> wrote: > Hi Noel, > > On Thu, Mar 2, 2017 at 10:11 AM, Noel O'Boyle <baoille...@gmail.com> wrote: >> >> In the course of sorting out the handling of implicit Hs, I've found >> that the current S

[OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

Hi there, 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](C)(C)(C)(C)C or "FIF" as "F[I]F". This is unusual behaviour

Re: [OpenBabel-Devel] Convenience functions

Typo: "But the guidelines are not unfortunately the existing code. " On 2 March 2017 at 10:22, Noel O'Boyle <baoille...@gmail.com> wrote: > Hi Stefano, > > Sounds good. But the guidelines are not unfortunately the existing > guide. I'm currently in the process o

Re: [OpenBabel-Devel] Convenience functions

ack > other developers suggestions. > > This would be a great chance for us to understand how to contribute code > that would integrate better and match the guidelines you guys follow. > > Thanks (for the patience), > > S > > > > > > On 02/26/2017 02:

Re: [OpenBabel-Devel] Proposal to overhaul/replace OBElementTable

These days I've got a Python script that generates switch statements. On 25 Feb 2017 11:06 p.m., "Geoffrey Hutchison" wrote: > > 2. The GetAtomicNum() will be a compiled prefix tree using switch > > statements. Right now, if you ask what is the atomic number of

[OpenBabel-Devel] Convenience functions

Hi there, As some of you know, I would like to remove all convenience functions from classes in Open Babel. I would like to explain why. It's hard to exactly define a convenience function, but it's an addition to the API that is implemented entirely using existing API calls and that makes it

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