[OpenBabel-Devel] Proposal to overhaul/replace OBElementTable

Hi there, The OBElementTable has some problems, and I propose a replacement. Conversion of element numbers to symbols and vice versa is one of the operations that should be optimal in a cheminf toolkit but is not currently. Here's what I propose: 1. No global etab is necessary, just a collection

[OpenBabel-Devel] Proposal to remove all duplicated std::string versus const char* methods

Hi there, As part of an API cleanup, I propose the removal of all std::string accepting methods that have duplicate const char* methods. Here's an example from OBElementTable: int GetAtomicNum(const char *, int ); int GetAtomicNum(std::string name, int ); (I note in passing

Re: [OpenBabel-Devel] Migrating bugs, features from SourceForge to GitHub

I agree - I'm the same. +1 - Noel On 21 February 2017 at 20:35, Geoffrey Hutchison wrote: > I must admit that I'm not following bug reports and feature requests on > SourceForge - partly because of spam and low signal to noise. > > That said, there are some useful

Re: [OpenBabel-Devel] Race conditions

was probably a red herring, an artifact of my use of the debugger where I may have jumped between threads. A few problems still remain, like in chains.cpp, but the main path _seems_ sorted. - Noel On 20 February 2017 at 12:52, Noel O'Boyle <baoille...@gmail.com> wrote: > On 19 February 2017

Re: [OpenBabel-Devel] Race conditions

On 19 February 2017 at 21:01, Geoffrey Hutchison wrote: >> Does anyone know exactly what problem the locale stuff is fixing? And >> a follow-on, is there another way to fix it? > > The problem is that we parse things like decimals for coordinates (0.) > which exist

Re: [OpenBabel-Devel] Race conditions

I). After all of the changes on the pull request, it can now take quite a while before segfaulting (mostly in locale, but worryingly once in NewAtom). Progress of sorts, I guess :-) I think I'm done for the moment with this. - Noel On 19 February 2017 at 10:47, Noel O'Boyle <baoille...@gmail.co

Re: [OpenBabel-Devel] Race conditions

February 2017 at 10:21, Noel O'Boyle <baoille...@gmail.com> wrote: > I've made progress, but my current problem is that it's not possible > to match the same SmartsPattern on different threads (as required, for > example, by the typers, where sets of smarts patterns are ini

Re: [OpenBabel-Devel] Race conditions

this will need an API change. - Noel On 12 February 2017 at 20:18, Noel O'Boyle <baoille...@gmail.com> wrote: > ...googling through the mailing list, I see that David Lonie mentions > that OBErrorLog has problems, and Tim that all formats are singletons. > I need to think some more ab

Re: [OpenBabel-Devel] Race conditions

...googling through the mailing list, I see that David Lonie mentions that OBErrorLog has problems, and Tim that all formats are singletons. I need to think some more about this latter. - Noel On 12 February 2017 at 16:45, Noel O'Boyle <baoille...@gmail.com> wrote: > Classes or

Re: [OpenBabel-Devel] Race conditions

. I haven't really looked at OBErrorLog, and my time is up right now. Have I missed any classes that you know of? David, do you have any test code that reads an SDF multithreadedly, that could be used to force segfaults? Regards, - Noel On 11 February 2017 at 21:08, Noel O'Boyle <baoi

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

Would it be okay to do that as part of a separate pull request? i.e. if there are no other concerns, could you merge it as is. The easiest way to do the pruning is to comment out relevant code one at a time, and seeing whether the results change (for the worse). This will take some time, but it

Re: [OpenBabel-Devel] Race conditions

Here's of what I was thinking: https://github.com/baoilleach/openbabel/commit/697b92180f9f61f738ef3e5c04d30340b9f8ee8e If it looks okay, I can make a similar change to other classes that have the same problem (assuming one size fits all). - Noel On 8 February 2017 at 09:32, Noel O'Boyle

Re: [OpenBabel-Devel] Race conditions

f Pittsburgh > > >> On Feb 7, 2017, at 5:20 AM, Noel O'Boyle <baoille...@gmail.com> wrote: >> >> Hi there, >> >> Wouldn't a better solution to the race conditions that David Koes is >> experiencing with global state be to remove the global state? For t

[OpenBabel-Devel] Race conditions

Hi there, Wouldn't a better solution to the race conditions that David Koes is experiencing with global state be to remove the global state? For the cases he mentioned, e.g. the OBAromTyper, the global state relating to a single molecule can easily be moved to a OBAromTyperPrivate class

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

w extra that may or may not be as intended. However, I won't do this unless you agree. Regards, - Noel On 30 January 2017 at 22:07, Noel O'Boyle <baoille...@gmail.com> wrote: > Maybe am overthinking. If it doesn't change the final output (as > regards aromatic SMILES) on ChEMBL, m

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

Maybe am overthinking. If it doesn't change the final output (as regards aromatic SMILES) on ChEMBL, maybe it's not worth worrying about now. - Noel On 30 January 2017 at 18:31, Noel O'Boyle <baoille...@gmail.com> wrote: > Great. One question I've run into is what was the intention

Re: [OpenBabel-Devel] Replacement of aromatic.txt SMARTS patterns with switch statement

gt; should retain aromaticity. It's possible, perhaps to set some level of "if >> it was initially flagged as an aromatic atom, be more lenient" rules in the >> code. >> >> I'd like to continue the concept of an annual release, so in the meantime, >

Re: [OpenBabel-Devel] Compiling OpenBabel with gcc and g++

Have you tried diffing the build output from the Mac vs Linux? My guess is that you're missing some optional dependencies...optional, but required for the tests. Regards, - Noel On 19 January 2017 at 14:42, Mohammad Mehdi Ghahremanpour wrote: > Hello, > > I have

Re: [OpenBabel-Devel] FASTA File

Also, you may have obabel installed on your system, so make sure to use "./obabel" if it's in the current folder, and "which obabel" to determine the path. - Noel On 14 November 2016 at 04:06, Geoffrey Hutchison wrote: >> Doing this had no effect on running "obabel"

[OpenBabel-Devel] Fwd: InChI Software version 1.05

@stanford.edu>, Martin Braendle <braen...@chem.ethz.ch>, Martin Post <julia.mar...@xs4all.nl>, Michael Conley <mcon...@leadscope.com>, Mitch Miller <mitch.mil...@thinkscience.us>, Muthukumarasamy Karthikeyan <karthi...@gmail.com>, Nicole Jung <nicole.j...@ki

[OpenBabel-Devel] Fwd: Re: Python bindings version

Forwarding to list for the record... . -- Forwarded message -- From: "Noel O'Boyle" <baoille...@gmail.com> Date: 22 Sep 2016 8:56 p.m. Subject: Re: Python bindings version To: "Maciek Wójcikowski" <mac...@wojcikowski.pl> Cc: "Matt Swain

Re: [OpenBabel-Devel] problem with requesting for git pull

Hi Mohammad, The pull request never reached us, and I don't see any branches at your repo that could be merged. I'm not sure what's happening, as usual with git. :-) My advice would be to start over. Here's how I would do it. Note that I never commit to the master branch and all the work is done

Re: [OpenBabel-Devel] OB API/ABI changes

; > Dept. of Integrative Structural > and Computational Biology, MB-112F > The Scripps Research Institute > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > fax: +1 (858)784-2860 > email: fo...@scripps.edu

[OpenBabel-Devel] Conda Windows

Hi Maciej, Regarding your work on setting up a Windows conda build, it might be good to discuss with Björn on getting this into bioconda. Bioconda already has the Linux builds. - Noel -- Attend Shape: An AT Tech Expo

[OpenBabel-Devel] Treat warnings as errors

Hi all, Over the last year, several developers have spent time fixing warnings reported by various tools. This sort of maintenance is best done by the original developer at the point of commiting. Warnings are fairly easy to fix and knowing about them improves programming skills. An easy way to

Re: [OpenBabel-Devel] OB API/ABI changes

Hi Stefano, Your comment about guidelines is of course true. I've been thinking about this. My feeling is that only needed functions should be in the API. So it's not that a function is not useful, or that someone might find it useful. This is not a concrete guideline of course, but it's

Re: [OpenBabel-Devel] Release notes - anything missing?

r should it stay alive for some reason? > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > 2016-06-12 18:51 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>: >> >> The sort order is a quirk of mine. But how else wo

[OpenBabel-Devel] Release notes - anything missing?

Hi there, I've been helping with the release notes for the forthcoming release: https://github.com/openbabel/documentation/blob/master/ReleaseNotes/ob240.rst If there's anything missing or wrong, please let me know. Also, many of the new features described are missing documentation. If you

Re: [OpenBabel-Devel] OB API/ABI changes

is that you have the match of each atom to each virtual atom of the pattern. For a function of OBAtom, it's just boolean true or false. - Noel On 2 June 2016 at 07:37, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 02/06/16 08:33, Noel O'Boyle wrote: >> Hi Stefano, >&g

Re: [OpenBabel-Devel] Many test exception on Mac OSX with -DCMAKE_BUILD_TYPE=Debug

Missing Eigen. On 8 February 2016 at 13:28, David van der Spoel wrote: > Hi, > > if I compiled OB with -DCMAKE_BUILD_TYPE=Debug on my mac (OSX Mavericks, > gcc 4.9) many tests fail with > 4/150 Test #4: test_align_4 .***Exception: Other > 6.57 sec

Re: [OpenBabel-Devel] Minimum version of MSVC for Open Babel master?

, feel free to check it in. - Noel On 6 February 2016 at 20:35, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Sat, Feb 6, 2016 at 3:17 PM, Noel O'Boyle <baoille...@gmail.com> wrote: >> >> The msvc build requires an additional repo. See github msvc-

Re: [OpenBabel-Devel] Minimum version of MSVC for Open Babel master?

s part of C99. I can upgrade the compiler (and have a few >> newer ones present, but they will need some work on dependencies that won't >> build). >> >> Probably should have searched longer, I see, > > commit 8e5bf94ef9348e5d83f9a04bd26fa7424392f0c1 > Au

Re: [OpenBabel-Devel] Gen2D screws up stereo?

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 On 7 October 2015 at 20:22, Craig James wrote: > Can anyone shed some light on this? If I use Gen2D and then try to write > out an

Re: [OpenBabel-Devel] Problem with Win7 and MinGW - no Plugins loaded

As background a bit more info would be useful. What were the versions of everything, how did you do the compilation, and did you run make install? On 21 August 2015 at 15:02, Daggi dagmar.l...@cec.mpg.de wrote: Hi everybody, We tried to make a new build of openbabel for windows 7 using MinGW,

Re: [OpenBabel-Devel] git version of OB broken?

Can you provide a test case? On 12 July 2015 at 13:32, David van der Spoel sp...@xray.bmc.uu.se wrote: Hi, I compiled a fresh OB clone but get SEGV on a number of programs, including babel. % babel -ig98 decane-g4.log -osdf koko.sdf Segmentation fault and % valgrind !! valgrind babel

Re: [OpenBabel-Devel] Fwd: [openbabel] OBConversion improvements (#191)

Biology University of Pittsburgh On 06/16/2015 06:21 AM, Noel O'Boyle wrote: I think we need to embrace a certain amount of backwards incompatability over a few releases in order to get the toolkit where it needs to be, so I've no particular problem with that. It would be nice to have

Re: [OpenBabel-Devel] Fwd: [openbabel] OBConversion improvements (#191)

I think we need to embrace a certain amount of backwards incompatability over a few releases in order to get the toolkit where it needs to be, so I've no particular problem with that. It would be nice to have the build failures fixed so I can test on Windows though... On 15 June 2015 at 20:45,

Re: [OpenBabel-Devel] MOE extensions to SMARTS

Email the authors. On 8 May 2015 at 13:50, Matt Harvey m.j.har...@acellera.com wrote: Hi, Hi, I've been looking at implementing the SMARTS-based decision tree scheme for pKa prediction outlined in http://pubs.acs.org/doi/pdf/10.1021/ci8001815 It should be pretty straightforward, except

Re: [OpenBabel-Devel] Windows 3rd party libs/dlls

Looks to be working fine. I've signed up for the git lfs, so I should hear when it comes available. One other thing. There's a windows-msvc folder also which Marcus created to separate out the windows-vc2008 includes. I presume this should be left as part of the main repo. If so, I was thinking

Re: [OpenBabel-Devel] Windows 3rd party libs/dlls

. Marcus On Mon, May 4, 2015 at 6:55 AM, Noel O'Boyle baoille...@gmail.com wrote: Looks to be working fine. I've signed up for the git lfs, so I should hear when it comes available. One other thing. There's a windows-msvc folder also which Marcus created to separate out the windows-vc2008

[OpenBabel-Devel] Windows 3rd party libs/dlls

Hi there, I propose moving the MSVC-specific 3rd party libs, dlls and include files to a separate git submodule. Or perhaps just a separate repo (to avoid needless downloading for Linux/Mac users). One motivating factor is that I see in the future the need to check in multiple versions of C++

[OpenBabel-Devel] Appveyor

I saw that Greg of RDKit mentioned Appveyor, basically a Travis for Windows. I spent 5 minutes just creating the account and so forth. I see that now it appears on Github (I didn't realise this) and just shows it as failing. Please ignore this for the moment, until I get it set up properly.

Re: [OpenBabel-Devel] Strange behavior when finding forcefields (Python)

It's true. To trigger plugin detection you need to make an obconversion object. This is a gotcha. Pybel does this on import. - Noel On 13 April 2015 at 23:12, Stefano Forli fo...@scripps.edu wrote: Hi all, I was debugging my Python code and I found a behavior that doesn't make much sense to

Re: [OpenBabel-Devel] 1H-tetrazole and 2H-tetrazole

This is more an email for the discuss list, rather than developers. But the answer is that this is a feature of the InChI, not a problem. It normalises some tautomers. The \h1H,(H,2,3,4,5) means that the atoms 2, 3, 4 and 5 (the numbering is specific to InChI) share one H (as far as I remember).

Re: [OpenBabel-Devel] I installed open babel 2.3.90, but I still can't import pybel

Sounds like it did work. After you do make install, just add the location of wherever pybel.py was installed to your PYTHONPATH and away you go. - Noel On 13 March 2015 at 18:56, David Hall li...@cowsandmilk.net wrote: What version of CMake are you using? -David

Re: [OpenBabel-Devel] Thermochemistry

Could you use -- for options where the keyword is more than one letter, and - only for those with a single letter? - Noel On 5 February 2015 at 14:34, David van der Spoel sp...@xray.bmc.uu.se wrote: I now made a program obthermo that works like this: % obthermo methane-g3-298.log obthermo -

Re: [OpenBabel-Devel] Google Summer of Code

Hi Geoff, Could you post the relevant timelines and I'll give a shoutout on the blog. Regards - Noel On 24 January 2015 at 02:49, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: Hi, Open Chemistry is offering to serve as a Google Summer of Code umbrella organization for multiple open

Re: [OpenBabel-Devel] IMPVAL

Sounds about right. It is used just for the first atom. Note that this is a general implicit valence model. Really each of the various file formats that support implicit valence has its own implicit valence model which should instead be used. This hasn't been implemented yet, except I think for

Re: [OpenBabel-Devel] Missing OpenBabel Plugins

Did you run make install? On 15 January 2015 at 16:01, Eva Lacy e...@lacy.ie wrote: Hi, I'm trying to compile and run OpenBabel for the first time, and I managed to get as far as running the obabel executable when I noticed it didn't support any format. Then I noticed that when I typed

Re: [OpenBabel-Devel] High memory usage when converting to PNG

Apart from providing a small standalone piece of code as Craig says, the only other thing to check is whether the problem still exists with the current dev code. Regards, - Noel On 2 December 2014 at 15:26, Ernst-Georg Schmid ernst-georg.sch...@bayer.com wrote: Hello, The first thing I'd

Re: [OpenBabel-Devel] Big CIF file handling

Can you check the code into a branch? Do you mean 5% faster at ConnectTheDots, or 5% faster over the whole reading in? - Noel On 10 February 2014 02:40, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I got the hash-based algorithm up and running (commit here). I ran it on a folder of

Re: [OpenBabel-Devel] Big CIF file handling

for the bond inference algorithm. Do you know where to look for this? Thanks, Pat On Mon, Feb 3, 2014 at 3:17 PM, Noel O'Boyle baoille...@gmail.com wrote: FYI, Roger added a connect the dots to RDKit a few months back for a PDB parser. You can see his discussion of various algorithms at the end

Re: [OpenBabel-Devel] Big CIF file handling

FYI, Roger added a connect the dots to RDKit a few months back for a PDB parser. You can see his discussion of various algorithms at the end of http://www.slideshare.net/NextMoveSoftware/rdkit-gems. We could repurpose this code considering the licence. - Noel On 3 February 2014 19:58, Patrick

Re: [OpenBabel-Devel] Connecting Molecular Fragments from Separate OBMol Structures (C++)

Here at NM, various tricks are sometimes used to store the identity for these sorts of things; e.g. setting the isotope number, adding atom classes or atom data. We could make an API addition to return the identity of the new atoms after calling .Add functions if you pass in a suitable vector. -

Re: [OpenBabel-Devel] Templates not exported under MSVC

today or tomorrow, and doublecheck it doesn't cause any problems elsewhere - Noel On 25 November 2013 13:36, Noel O'Boyle baoille...@gmail.com wrote: The problem is the AnnotationData...Actually just leave this with me for a day or two - I want to check if just expanding the template

Re: [OpenBabel-Devel] Templates not exported under MSVC

CustomBool within the format itself, like the example in the Generic Data docs? http://openbabel.org/dev-api/generic_data.shtml Matt On 23 Nov 2013, at 18:35, Noel O'Boyle baoille...@gmail.com wrote: The json formats won't link under MSVC as the templates as the OBPairTemplates

Re: [OpenBabel-Devel] Travis CI

The InChI code was not working. This has been fixed (by others). Now there should only be one test failing (and I will work on this now). Does your dashboard automatically build? I can't see any new test results. - Noel On 20 November 2013 16:14, Noel O'Boyle baoille...@gmail.com wrote: Ignore

Re: [OpenBabel-Devel] Travis CI

Ignore my last question - obviously the answer is on the dashboard. Doh! - Noel On 20 November 2013 09:36, Noel O'Boyle baoille...@gmail.com wrote: Awesome. I am currently in the process of reviving our CDash builds but the more automated build systems the better. I've been looking at those

Re: [OpenBabel-Devel] considering new SWIG binding for R

It might be obvious, but once you get things going, it would be super useful to create an R script which we or you could run to verify that the bindings were working as you expect for all of the Classes of interest. If you have trouble getting started, email the list again and I can take a look.

Re: [OpenBabel-Devel] Tenure Thanks

Whoo, hooo - that's great news! I'm delighted for you, and glad you have been recognised for your enormous contributions here and over at Avogadro. - Noel On 30 October 2013 20:10, Geoffrey Hutchison geo...@pitt.edu wrote: Dear everyone, My department voted recently to recommend me for tenure

Re: [OpenBabel-Devel] CMake Python Changes

Doesn't the use of DESTDIR cover this very case? - Noel On 24 October 2013 15:18, Reinis Danne rei4...@gmail.com wrote: On Tue, Oct 22, 2013 at 11:52:11AM -0400, David Hall wrote: Let me know if you have any questions or see any problems with these changes. Hi! PYTHON_INSTDIR should be

Re: [OpenBabel-Devel] Confab

The current development version has it. If you are familiar with git and github, you can get the code there. Otherwise you will just have to wait until the next release, which could be in a few months or so. - Noel On 20 August 2013 01:13, Ling Chan slch...@yahoo.com wrote: Dear Noel or Geoff,

Re: [OpenBabel-Devel] Disabled chirality in SMARTS?

I found the change (rather easily in the end - it's the last commit to parsmart.h). The magic phrase Potential ABI/API change prevented it being merged to the release branch. Revision: a439d0fc1350a1c50e970f2467a0e837ec80a181 Author: Noel O'Boyle baoille...@gmail.com Date: 10/11/2011 09:20:42

Re: [OpenBabel-Devel] MSVC, no prebuilt binaries and inttypes.h

enough of this to contribute much, but all the components used to build with the Express versions of VS 2008, 2010, 2012 and 2013 must be freely available and distributable. One prebuilt binary that we would be better without is vcredist_x86.exe. Chris I On 24/07/2013 17:39, Noel O'Boyle wrote

Re: [OpenBabel-Devel] MSVC, no prebuilt binaries and inttypes.h

Would renaming windows-vc2008 to msvc solve the problem? - Noel On 24 July 2013 15:57, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi, We build Open Babel on Windows without prebuilt binaries, and have tracked down an issue with the C99 headers and MSVC. The headers in

Re: [OpenBabel-Devel] Testing...

ENABLE_TESTS=ON I think? Then make test will work. - Noel On 23 July 2013 21:48, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: 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

Re: [OpenBabel-Devel] Confab

Sorry for the delay - I've reverted the change to IsSetupNeeded and merged it all to trunk. (And in future I'll make branches in a forked repo rather than one at the main repo.) On the P.S., I've never been a big fan of comparison articles - but we definitely need a doc chapter on this. And on

Re: [OpenBabel-Devel] highlight substructures with pybel

We added --highlight to provide this functionality. This is an operation, and is used as follows: import pybel mol = pybel.readstring(smi, CC(=O)Cl) highlighter = pybel._operations[highlight] highlighter.Do(mol.OBMol, C(=O) green) mol.write(svg, tmp.svg, opt={u:None, C:None}, overwrite=True)

Re: [OpenBabel-Devel] InChI from obabel differs from direct C++ code

I understand where the expected output is coming from, but where's the 'wrong' output coming from? You have pmol_conv_ich-SetInAndOutFormats(inchi, inchi); This does mean you are reading one of those InChIs and roundtripping it? Or are you reading the SMILES somewhere else and using this

Re: [OpenBabel-Devel] InChI from obabel differs from direct C++ code

This is for marking the molecule as 2D (i.e. having 2D coordinates associated with it). After reading a SMILES it should be marked as 0D. - Noel On 18 June 2013 19:48, Craig James cja...@emolecules.com wrote: (forgot to cc list the first time...) On Tue, Jun 18, 2013 at 10:34 AM, Noel

Re: [OpenBabel-Devel] Perl bindings

If you're using the development source, you will need to create the bindings with SWIG. For once (!) this *is* in the docs :-) http://openbabel.org/docs/2.3.1/Installation/install.html#advanced-build-options - Noel On 12 June 2013 02:21, Craig James cja...@emolecules.com wrote: Trying to get

Re: [OpenBabel-Devel] Persistent OBConversion error message

It's harmless. Look in the repo for a recently added or edited format. Someone added a RegisterOptionParam. Deleting this will make the problem go away. Registering these option parameters was necessary for babel in certain circumstances. - Noel On 11 June 2013 21:38, Craig James

Re: [OpenBabel-Devel] Better(?) test runner

I've just merged this to the mainline. Seems to work same as before (there's one failing ffgaff test due to my changing of the LSSR some time ago - I should sort this out). Let me know of any teething problems. For the record, the -g options for the forcefield (etc) test file generation are now

Re: [OpenBabel-Devel] Confab

I don't disagree about having a calcrmsd, but the executable provided as part of confab is not an all-purpose RMSD calculator. It's pretty specific for the Confab output, hence the 'rename' to confabreport format. I would argue for a separate calcrmsd executable that covered the common use cases

[OpenBabel-Devel] Better(?) test runner

I've always found the 50 or so executables that Open Babel currently creates as part of the test build to be annoying. They slow the build, hog screen space on the MSVC IDE, and yet are still not fine-grained enough to indicate which test inside the executable actually failed. CMake provides a

[OpenBabel-Devel] Partial charges

If you copy a molecule it triggers partial charge perception on the original one. This doesn't seem right. It's triggered by OBAtom::Duplicate: _ele = src-GetAtomicNum(); _isotope = src-GetIsotope(); ... _pcharge = src-GetPartialCharge(); There seem to be different partial

[OpenBabel-Devel] Confab

Hi Geoff, The Confab branch is ready for merging, or at least consideration for merging, to the master. I would appreciate if you could check it out and let me know if you want any clarification. I've left the confab and calcrmsd executables in there, but I plan to remove them as they are

Re: [OpenBabel-Devel] 'oping for help with confab

- Noel On 27 April 2013 15:12, Chris Morley c.mor...@gaseq.co.uk wrote: On 27/04/2013 13:58, Noel O'Boyle wrote: I'm trying to turn the confab executable into an op as I would prefer not to maintain the executable. Essentially, the op generates conformers for each input molecule

Re: [OpenBabel-Devel] 'oping for help with confab

Or maybe I'm trying to fit a square peg into a round hole, and I should just go with my existing (and working) executable... - Noel On 27 April 2013 13:58, Noel O'Boyle baoille...@gmail.com wrote: Hi Chris, I'm trying to turn the confab executable into an op as I would prefer not to maintain

Re: [OpenBabel-Devel] types.txt

It's always good to link changes in the code to specific bugs that need fixing. It may be useful to see whether you identify such cases here before you spend time on this. If you decide to go ahead, I would suggest that you add some test cases to ensure that existing correct behaviour is retained.

Re: [OpenBabel-Devel] types.txt

-26 11:17, Noel O'Boyle wrote: It's always good to link changes in the code to specific bugs that need fixing. It may be useful to see whether you identify such cases here before you spend time on this. If you decide to go ahead, I would suggest that you add some test cases to ensure

Re: [OpenBabel-Devel] Bug in obabel on Mac when input and output formats match

Does it improve if you leave out the --log and if you use -O myfile.cml instead? - Noel On 8 April 2013 20:28, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi, We are using obabel to perform geometry optimizations etc on the command line, and we are hitting a bug that seems to only

Re: [OpenBabel-Devel] Bug in obabel on Mac when input and output formats match

-O ethanol.cml On 9 April 2013 00:20, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-04-09 03:28, Marcus D. Hanwell wrote: Hi, We are using obabel to perform geometry optimizations etc on the command line, and we are hitting a bug that seems to only present itself on the Mac. If

Re: [OpenBabel-Devel] Can't initialize OB internals from swig-generated module

Long shot: Are there any files in your current directory with the same names as files in Open Babel's data directory? This is a nice way to confuse Open Babel. Have you altered any files in Open Babel's data directory? Just a note: with Open Babel we moved away from using Makefile.PL as it just

Re: [OpenBabel-Devel] Can't initialize OB internals from swig-generated module

I'm all out. Have you looked at the output 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 cja...@emolecules.com wrote: Hi Noel, On Thu, Apr 4, 2013 at 6:08 AM, Noel O'Boyle

Re: [OpenBabel-Devel] using openbabel in R

plugin is its own shared library and then they get loaded at run time with the dlopen function (on linux at least). I have verified that this code is still being executed when called from within R, but it doesn't work for some reason. Kevin On 03/21/2013 05:51 AM, Noel O'Boyle wrote

Re: [OpenBabel-Devel] Wrong

It might be a good idea to sit down while you read this. You seem to have forgotten that Implicit Valence is not implicit valence, but rather the number of bonds to an atom. atomtyp.txt says 3 bonds to a boron. The =O and the OH is two bonds, so there's one missing. That's the reason for the two

Re: [OpenBabel-Devel] using openbabel in R

This isn't exactly answering your question, but have you considered creating the R Swig wrapper. This may just simply work out of the box (or indeed not!) with little effort. - Noel On 20 March 2013 16:13, Kevin Horan kevinho...@globalrecordings.net wrote: I would like to make use of open

Re: [OpenBabel-Devel] Hydrogen/charge inconsistency?

PM, Noel O'Boyle baoille...@gmail.com 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 your analysis is spot

Re: [OpenBabel-Devel] Hydrogen/charge inconsistency?

I haven't looked into the details of your code (but I will if no-one else does), but regarding the relationship between different things, you may find the following notes I have made useful: In the Open Babel world, the valence methods of an atom refer to the number of bonds, rather than the sum

Re: [OpenBabel-Devel] Hydrogen/charge inconsistency?

it sank in). Similarly, this information is used at the point of writing. - Noel On 19 March 2013 22:16, Noel O'Boyle baoille...@gmail.com 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

[OpenBabel-Devel] OB at Fall ACS Indianapolis

Hi all, FYI, Tony Williams and Robert Lancashire are organising a session (CINF013) on Exchangeable Molecular and Analytical Data Formats and Their Importance in Facilitating Data Exchange and got in touch to see whether anyone from OB is interested. I'm afraid I can't make it myself (I'll be at

Re: [OpenBabel-Devel] OB at Fall ACS Indianapolis

for most of us. Geoff On Mar 13, 2013, at 11:32 AM, Noel O'Boyle baoille...@gmail.com wrote: Hi all, FYI, Tony Williams and Robert Lancashire are organising a session (CINF013) on Exchangeable Molecular and Analytical Data Formats and Their Importance in Facilitating Data Exchange and got

[OpenBabel-Devel] What's new in OB?

Hey all, I'm thinking about giving a CINF flash talk at the Spring ACS on What's new and cooking in OB. It's somewhat rough, but here are the items I have so far. I've gone through the commit logs, but there seems to be a bias towards features I've added (!) so I'd appreciate if you could let me

Re: [OpenBabel-Devel] segmentation fault

Somethings wrong with the SMILES string. Daylight won't accept it for example: http://www.daylight.com/daycgi/depict?5b43405d3132335b4340405d34285b4340485d285b4e5d2843433543433529434333294329436333633163284f5b4340485d3243283d4f29434334296328636333294f294f We should fix the segmentation fault

Re: [OpenBabel-Devel] GitHub Migration

Hi Chris, It seems that the core devs have direct commit access to the repo. This means that you can essentially keep working as before. 1. Create an a/c at github.com and send the name to Geoff to add to the Open Babel project (note: only applies to core devs I guess) 2. Install TortoiseGit

Re: [OpenBabel-Devel] Can we contribute code to contributed/trunk/java?

Also it would be great to get a page or so of text, images, whatever, describing it and its use which I can add to the HTML documentation. In the past, contributed code has been somewhat hidden, but there are some great things in there, and documenting them in the official docs will bring them to

Re: [OpenBabel-Devel] openbabel substurcture

If using Eclipse, you can ask it to add the necessary imports. (If not using Eclipse, good luck writing Java :-) In this case, I'm guessing something like import org.openbabel.vectorvint or so...? - Noel On 12 February 2013 09:09, mounika mouni07...@gmail.com wrote: In Substructure search i am

Re: [OpenBabel-Devel] Perceive bonds with obabel

See http://baoilleach.blogspot.co.uk/2010/04/plug-cclib-into-avogadro.html 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

Re: [OpenBabel-Devel] Perceive bonds with obabel

Apologies. The question was about obabel, not the API... On 12 February 2013 16:52, Noel O'Boyle baoille...@gmail.com wrote: See http://baoilleach.blogspot.co.uk/2010/04/plug-cclib-into-avogadro.html On 12 February 2013 16:26, David Lonie david.lo...@kitware.com wrote: Hi list

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