Re: [OpenBabel-Devel] Debugging tests

It would help a lot to know more about the patch. Yes, it seems as if the coordinates are different. This may be less relevant (e.g., you change a force field, so the optimization will differ). Best, -Geoff On Feb 14, 2024 at 3:35:14 PM, David van der Spoel < david.vandersp...@icm.uu.se>

[OpenBabel-Devel] Open Babel website

Unfortunately, as part of a routine hosting update (e.g., my provider changed DNS) the openbabel.org website is currently down. It’s not clear from the logs why the site remains down. I’m going to take the opportunity to cleanup a new website based on Noel O’Boyle’s excellent docs:

[OpenBabel-Devel] Setting a security policy for Open Babel?

GitHub has been adding various security-related features (e.g., security auditing). One thing they've added is for a "security policy" - as in, how people should report security issues. Since we handle user-supplied / possibly questionable data and are a dependency for many other packages, I

[OpenBabel-Devel] script bindings / Use of EXTERN in headers

As part of the 3.0.1 release process, I spun up a new build bot on Github to generate /all/ the script bindings. - At the moment, the R binding is broken - open to suggestions on how to fix / build it - The Ruby binding is broken because EXTERN evokes a macro in a Ruby header to issue warnings

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. What do you have in mind? I think considering how late 3.0.1 is, it's better to get something out soon, even if we need to make a 3.0.2 or something later this spring. Now that we can make

[OpenBabel-Devel] Last call for 3.0.1 release

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

[OpenBabel-Devel] Migrating to GitHub build actions

Hi Noel, I've been working bit-by-bit to migrate OB's test builds from Travis / Appveyor to the new GitHub action infrastructure. (Microsoft, which now owns GH is evidently providing tons of cloud resources.) Good news: - Linux (Ubuntu) builds for standard and SWIG builds - Mac build I have

Re: [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. Yes, I've noticed this across a few projects (OB, Avogadro, etc.). IMHO, I may try to migrate directly to GitHub actions to replace Travis. If

[OpenBabel-Devel] Hardening Open Babel (i.e. fuzzing)

I'm taking some of my work-from-home time to firm up some bug fixes. As part of that, I'm also working to get automated 'fuzz' testing going for Open Babel. If you haven't heard about fuzz testing, it involves feeding various data into programs and libraries to get them to crash. This may take

Re: [OpenBabel-Devel] Fixing distance geometry stereo issue

> 3) Handling of unpsecified stereochemistry in SMILES-SDF roundtrip test > > Using the SDF file format for the rountrip tests is also problematic. > Although we correctly write out unspecified atom stereo parities, these are > ignored (by default) when reading … > > Does this sound

[OpenBabel-Devel] If someone had time on their hands (now) …

As many of you may know, Open Babel is participating in Google Summer of Code 2020. The last two years, we've been lucky to have Naruki working on the fragment-based builder in 3.0 as well as improvements in the not-quite-finished distance geometry builder. If you know of students who might be

Re: [OpenBabel-Devel] Mixed compilation does not compile novel plugin

> Does anyone have any idea why the plugin is not working on the mixed compiled > executable? > If you're not using the normal shared library / plugin support, you'll need to hack src/plugins.cpp to add your format. You'll see a long list… Hope that helps, -Geoff

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

> I came across an Openbabel GSOC project idea (Develop a validation and > standardization filter) at Openchemistry.org and it piqued my interest. > I'm well aware that the organizations haven't been announced yet, > nevertheless, I'm looking to contribute to Openbabel to get a start in >

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

Yes, Naruki and I were running into confusion when using these classes for the distance 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

Re: [OpenBabel-Devel] Problem with reading the Gaussian G4 calculations

> [BirdMac:~] % obabel -ig09 Liquids/MOLECULES/G4/water/water-g4.log.gz -osdf > -O koko.sdf > Segmentation fault I mean in this case, you'd want to run inside a debugger and see where the crash occurs. > [csb:~] % ~/GG/openbabel-dev/install/bin/obabel -ig09 >

Re: [OpenBabel-Devel] fatal error: 'maeparser/Writer.hpp' file not found

> I just synced my open babel fork with the master branch but could not compile > it. Clearly the maeparser didn't compile. Do you have Boost installed? -Geoff ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net

[OpenBabel-Devel] ANNOUNCE: Open Babel 3.0.0 Released

I'm pleased to announce the release of Open Babel 3.0.0 [finally]: This release represents a major update and is strongly recommended for all users. It also removes deprecated components and breaks the API in a few places. For information on migrating from the previous version, please see:

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. I've just been busy, but I'll send out an announcement about the release today. -Geoff___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net

Re: [OpenBabel-Devel] Algorithm for FF atomtypes

I'd have to hunt through the code more carefully, but in formats like Gaussian, we know that all atoms (including hydrogens) are explicit. Unfortunately, that's not true from PDB — in the vast majority of cases, hydrogens are omitted and implicit. So, for example in src/formats/pdbformat.cpp

Re: [OpenBabel-Devel] Algorithm for FF atomtypes

put everything up, including the training and test sets (i.e., you can add problematic molecules to improve the training). Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @g

Re: [OpenBabel-Devel] 3.0 release?

> 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. Sure. Let's target Oct. 14th for

Re: [OpenBabel-Devel] Visual studio version

openbabel> Beyond that, we are about to make a 3.0 release and there will be Windows binaries made available as part of that. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchi

[OpenBabel-Devel] 3.0 release?

Well, it's the start of October, so we missed our self-imposed deadline to get 3.0 out the door by the end of September. I think I have all the source packaging issues sorted out. OTOH, I don't currently have a way to make Windows binaries. Should I tag a 3.0 release so we get it out the door

Re: [OpenBabel-Devel] [Open Babel] Default force field option for --gen3d

> Depending on the scenario, I would consider either vacuo (1) or water (80) to > be good > choices, but 4 is a 'close enough approximation' of 1. There are a variety of papers suggesting that the effective dielectric constant inside a peptide is ~4.0. Most organic solvents are ~2-2.3 epsilon.

[OpenBabel-Devel] Default force field option for --gen3d

While it's possible to change the force field with the -gen3d option, most people don't. I think for 3.0 it might be nice to: - Use MMFF94s (i.e., the one with planar aromatic nitrogens) - Use a default dielectric constant of ~4.0 In my testing #1 helps a bit - and #2 at least doesn't hurt when

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 > Yep - I was just rushing out the door, so a gist was faster. > Should I tag the source differently next Monday? Also, I think I messed up

[OpenBabel-Devel] 3.0.0alpha 1

Yesterday, I dusted off the "make a source release" script on my desktop.. to find that it's been long enough that my new desktop doesn't have all the various compilers to check PHP, C#, etc. I also discovered that GitHub is annoying about naming files matching their auto-generated .tar.gz and

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

Since I don't use Linux, I'm a bit less clear on versions, but I'd suggest - Ubuntu LTS (18.04) - RHEL LTS 7 maybe? - Debian 10 I mean, that would cover common DEB and RPM packages - IMHO let's start from there and people can add others as desired. Thanks, -Geoff --- Prof. Geoffrey Hutchison

Re: [OpenBabel-Devel] Source release

Yes, I can make a source release tomorrow. One way or another, I'd like to have either the AppVeyor 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

Re: [OpenBabel-Devel] C++11 requirement for 3.0 release (and going forward)?

Thanks, that's helpful info from package maintainers. > Actually, the above devtoolsets are available for RHEL/CentOS 6, too. > So, if you still care about that old distro, you don't have to rely > on its base gcc-4.4.7 version. One problem that I've run into personally has been computing

[OpenBabel-Devel] C++11 requirement for 3.0 release (and going forward)?

There are a few patches and pull requests asking for C++11 support in Open Babel. My main question is when we "pull the plug" on older compilers. Pro - drop older compilers for 3.0 since we're dropping a bunch of backwards compatibility Con - we're changing a lot of other stuff, let older

Re: [OpenBabel-Devel] Release Schedule

> With this in mind, I'm going to suggest that we feature freeze and focus on > release blockers. We shouldn't be dogmatic (e.g. I note that I have already > agreed to review/merge David Koes mega PR) but we should try to avoid making > the documentation out-of-date during the release

Re: [OpenBabel-Devel] Release Schedule

> Hi Noel - I'd be happy to put together some Docker recipes for the most > important platforms and all their versions OpenBabel is supposed to support. > If that's done then anyone with docker installed on their machine could just > run single commands to confirm that OpenBabel builds and

[OpenBabel-Devel] Bond Order perception (was PDB files with multiple bonds via CONECT)

> I would love to have accurate bond orders in .sdf files (and also location of > charged groups) but do not know what the status is. I mention these things > since last time I checked (4 years ago) determining border was not very > accurate (10% error rate). There are a few interesting

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

David Koes has contributed a pull request that fixes a bunch of file handling errors via round-trip testing. One thing he's implemented is to bring back writing PDB files with multiple bond orders via repeated CONECT records. Before I consider the rest of the patch, I want to know opinions on

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

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 similarly old. As a result, I do think backwards compatibility for compilers is

Re: [OpenBabel-Devel] Towards a release

> I have a bit more free time now. Let's work towards a release. First off, Noel deserves a lot of thanks for pushing a lot of changes for 3.0 and keeping things going. In other words, let's get a list of any remaining critical bugs  and push towards a defined release date for 3.0? (Speaking

Re: [OpenBabel-Devel] Can not find force field

> Hi, we are trying to implement the babel force field code into gromacs but > face a weird problem. In summary, we copied the relevant lines from > obenergy.cpp: > … > However this does not help when using the above statement in gromacs. > Anything we have forgotten? My guess, without having

Re: [OpenBabel-Devel] OBOp

Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ -- Check out the vibrant tech community on one

Re: [OpenBabel-Devel] From string to stringstream

> std::string b = a.toUtf8().constData(); If you want to read data from a string, you need to use the ReadString() method: http://openbabel.org/api/2.3/classOpenBabel_1_1OBConversion.shtml#a93558e9c89cda2e1a4f9fb2cadc5c8d1 Hope that helps, -Geoff

Re: [OpenBabel-Devel] OBabel in QtCreator

> is it possible to use libraries in Qt creator, If so, how can I integrate > it? This sounds like a question for the Qt forum, not an Open Babel forum. But a quick search for "Qt Creator cmake" turns up some likely suggestions: http://doc.qt.io/qtcreator/creator-project-cmake.html

Re: [OpenBabel-Devel] Failing master

> 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? If you look in the build history, it starts with your first/last commit:

Re: [OpenBabel-Devel] Getting rid of all warnings

> I mentioned in an earlier thread it would be good to get rid of all warnings > in order to make it easier to find real issues. I started with a little patch > https://github.com/openbabel/openbabel/pull/1862, I guess this is the > preferred way of proceeding? It is, although I'm opposed on

Re: [OpenBabel-Devel] does OpenBabel support HIPEigen?

> Anyone tried compiling OpenBabel with it yet? Interesting. I'm not sure how much it would help at the moment. The main thing I'd imagine would be for force fields, and that code currently doesn't use Eigen much at all. Now if someone's interested in helping with *that* work, please let me

Re: [OpenBabel-Devel] Modest Proposal - Gen3D won't do conformer searching

> In addition it would be nice if the 3D generation would not crash every once > in a while (at least it does in Avogadro). I guess due to numerical issues. If you have an example that causes a crash, please report it otherwise we can't fix it. We fixed several bugs this spring thanks in part

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

> 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 > calculate the values and write them out. That's probably a matter for me to improve the documentation. Generally people assign charges for force

[OpenBabel-Devel] Modest Proposal - Gen3D won't do conformer searching

Hi, One of the GSoC projects this summer is an improved fragment-based coordinate generation method. While that's going, I've been reading a lot of papers on 3D coordinate generation. As near as I can tell, no other program attempts to do a conformer search as part of the 3D generation.

Re: [OpenBabel-Devel] InChI Software version 1.05

> Not sure how relevant this is to OpenBabel, but I assume we modify InChi > in order to integrate it? No, we do not modify the InChI code in any way in the integration. > Did somebody bring this up with the Inchi Trust? I would guess 'no.' I don't think IUPAC or the InChI Trust really

[OpenBabel-Devel] Getting SMILES Atom Order data

Hi Noel, I'm working with Naruki, the student with GSoC developing the fragment-based coordinate generation. He's updating my old fragmentation code, which used the SMILES Atom Order data to canonicalize fragments. I can't find your comments on this, and I don't remember whether it was in the

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

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. There are some clearly easy bug fixes that can be back-ported to the 2.4.x series. If you have particular

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

> How about making warning-free code a must? > Whenever I compile OB I get tons of warnings of potentially serious character. Patches that reduce/fix warnings are always accepted. :-) Julien Nabet (serval2412) has contributed *many* such patches. Keep in mind many (most?) of the warnings are

Re: [OpenBabel-Devel] Different ADF Outputs

> ADF is designed so that it comes with separate executables. The two that I am > currently interested in are band > (https://www.scm.com/product/band_periodicdft/ > ) and dftb > (https://www.scm.com/product/dftb/

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 I think one key

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

I'm currently in the process of converting the MediaWiki site to a Jekyll site (e.g., like https://avogadro.cc/) - Pages can still be edited through GitHub - We can easily merge in the rewritten documentation https://open-babel.readthedocs.io/en/latest/ What I'd like to ask is "what parts of

Re: [OpenBabel-Devel] Release 3.0

> Is there any work planned for that? At the moment, no. As you know, it's certainly do-able, but I think the main question is "what's the use case." (I'm getting more focused in my old age, I guess.) > A while back I looked at the code trying to fix a few problems (chirality of > protonated

Re: [OpenBabel-Devel] Release 3.0

> I’m mostly just grumpy because these changes broke my build. Have you > considered going through a deprecated phase? While I appreciate the grumpiness, you don't have to break a build - the "master" branch is naturally going to have changes. I'd like to think Noel (and I) were pretty

Re: [OpenBabel-Devel] Release 3.0

If you don't mind, I'm putting your message onto the developer list. I initiated an OB-3.0 release plan on GitHub because I think the changes you've made so far are significant and backwards-incompatible. I think that's really worth signaling. (As in, if you have code that uses OB-2.x APIs,

[OpenBabel-Devel] OBStereo

Hi Noel, As you know, I'm working on a distance geometry builder for Open Babel, like in RDKit. The bonus would be stereo-correct coordinate generation and likely faster than the current OBBuilder. I sat down and wrote a unit test, but there's something totally weird. Here's the PR:

[OpenBabel-Devel] 24PullRequests and "simple issues"

GitHub is publicizing an effort for "holiday giving" to open source projects: https://24pullrequests.com/contributing I like the idea and would like to push it a bit for Open Babel. So my question is whether there are some volunteers to mark issues as "beginner" or "easy" (e.g., documentation

[OpenBabel-Devel] Migrating from MediaWiki

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 Wikipedia, we don’t have the same level of anti-spam resilience. So we had to move

Re: [OpenBabel-Devel] Version number on master

> 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 the version number, but we’d want 2.4.90 or something to indicate that it has dev versions for 2.5. -Geoff

Re: [OpenBabel-Devel] Ring conformations from builder

> I think the all-axial groups are the result of trying to configure as many > bonds as trans as possible. Yes, exactly. So there needs to be a special case for ring bonds. > By looking at the current code, it seems implementing the new DG method > wouldn't be incompatible with the perception

Re: [OpenBabel-Devel] Ring conformations from builder

> I've tried looking into it to propose a possible solution, but I couldn't pin > exactly where this happens in the code. ... > I suspect the problem might be in builder.cpp, where the math for the bond > angles is computed, but where exactly I have no idea. It's most likely here in

Re: [OpenBabel-Devel] Reading multiple charge types from Gaussian output

> What I need is to read and store all the charge types. > My concern is that if I add this feature, how it will affect other parts of > the code or other tools, other places that the partial charges are used to > calculate energy, for example. Partial charges are not used to calculate

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

It's worth pointing to the GitHub Flow docs in the future: https://guides.github.com/introduction/flow/ https://help.github.com/articles/github-flow/

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

> Before doing that, my branch was ahead by 6 commits and was behind by several > commits, while after rebasing it is written that my branch is ahead by 6 > commits. > > How can I fix the rebasing if it was incorrect. Yeah, the problem as Noel indicated is that to do the review now, we have

Re: [OpenBabel-Devel] Isotope table

> I have some more work to do with adding comments and so forth, but > what I'm wondering is, there's also a file isotope-small.txt. Am I > right in saying that this is legacy and I can ignore (and delete) it? The "small" isotope table was compiled into the data header - it included the most

Re: [OpenBabel-Devel] Output of charge to sdf file or inchi

> I am reading a lot of Gaussian output files and added the following line to > src/formats/gaussformat.cpp: >mol.SetTotalCharge(total_charge); I'd make sure this isn't run before the EndModify call. But I'm confused, because the code already does this: >

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

> Now I need to tidy things up a bit, rebase and send a pull request. > Oh, and someone's going to have to review it. Good luck with that, > Geoff :-) Sounds great. I look forward to seeing it. :-) Cheers, -Geoff --

Re: [OpenBabel-Devel] Mailing list change proposal

> On the other hand, I don't know openbabel-dev works, but if every single > message needs to > be approved, it sounds like more work to me. No. Members can submit just fine. Any other messages are held for moderation. I believe SourceForge has some level of spam filtering too. As I mentioned

Re: [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. I don't think this is a good idea. I don't want to find out if the spammers have figured out how to sign up for mailing lists. If

Re: [OpenBabel-Devel] Convenience functions

> About the PDB atom name, unfortunately I don't fully understand the > performance issue implied in my suggestion, but from an interface point of > view, it seems more intuitive to access an atom property from OBAtom instead > of going back to the OBResidue (and pass the OBAtom). The OBAtom

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

> 2. The GetAtomicNum() will be a compiled prefix tree using switch > statements. Right now, if you ask what is the atomic number of Fermium > (element 100), it will do 100 string comparisons. Fair enough - does it make sense to hand-write the switch statements, though? > 4. We can add an enum

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

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 bug reports and feature suggestions. Should I attempt a migration? - Yes, it's good to consolidate, even if there's a pile of

Re: [OpenBabel-Devel] Race conditions

> 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 in the C locale. So we need to make sure the parsing code works in C locale not any other

Re: [OpenBabel-Devel] API break (was Race conditions)

> I remember Chris saying that he felt that surprisingly few changes were > necessary to make this happen. He may be right. Sounds great. If you work on a branch, we can all take a look. If you need help - send out a post. :-) -Geoff

Re: [OpenBabel-Devel] API break (was Race conditions)

I would be just fine making 2017 the target for 3.0 and some level of API breaks and cleanups. There are already a pile of methods marked “deprecated” in the code. I don’t think it’s worth changing atom indexing - but anything else should be on the table. -Geoff > This is an API breakage,

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

> Personally, I'd also like to remove any "patterns" that aren't > triggered by (aromatic atoms in) molecules in any of these databases, > on the basis that it's better to have a set of patterns that we know > are correct (and all covered by test cases) I’d be fine with some pruning. I’ve been

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

I think it's a great idea. Chris Morley had recommended similar concepts in terms of implicit valence. Yes, many of the stranger SMARTS patterns here are for "dodgy" SMILES that should retain aromaticity. It's possible, perhaps to set some level of "if it was initially flagged as an aromatic

Re: [OpenBabel-Devel] Proline Bond Lists

Can you send me the PDB file? Thanks, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ -- Check out

Re: [OpenBabel-Devel] Proline Bond Lists

> Sorry, small error in the loop variable labels. Here is the correct version: I think my bigger question is "how are you getting here?" That is, are you reading a PDB file and the bonds aren't created correctly? Or are you reading in an XYZ file and perhaps bond perception and residue

Re: [OpenBabel-Devel] FASTA File

> Doing this had no effect on running "obabel" or "babel" even though I was > using fasta format as the input format (i.e. ./babel -ifa a.fa -opdb a.pdb) > after recompiling. I ask because I want to change the behavior of how fasta > interprets strings (for instance, making it sensitive to

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

> What I find weird is that the 2.4 library version is 4.0.0 while the > 2.3.2 library version was 4.0.2, i.e. higher. I thought I replied to this, but my e-mail program is indicating no reply. This was a mistake. I'm not sure why the "master" branch didn't update the library version, so I left

[OpenBabel-Devel] ANNOUNCE: Open Babel 2.4.0 Released

I'm pleased to announce that Open Babel 2.4.0 has finally been released. This release represents a major update and should be a stable upgrade, strongly recommended for all users. We intend to move to an annual major release every September, with bug fix releases as needed. A sample of major

Re: [OpenBabel-Devel] OBABEL crashes Re: Another bug: -oreport reports incorrect hydrogen number

> I found another bug: While I appreciate the multiple bug reports, e-mail isn’t a good way to file bugs. My e-mail inbox is a mess. The bug tracker is here: https://github.com/openbabel/openbabel/issues If you can take a minute to post them, we’d greatly appreciate it. Otherwise, it’s likely

Re: [OpenBabel-Devel] Implicit copy constructor

> How about fixing these warnings to have a compilation without any warning? Sure. If you submit a patch that fixes warnings, it will be reviewed and likely accepted. Several people have submitted patches for warning fixes and cpp-check fixes. Thanks and best regards, -Geoff

Re: [OpenBabel-Devel] [Open Babel] GAFF2 in babel?

> I don't know whether people would like to implement this new GAFF2 into > BABEL... Sure, although as David van der Spoel mentioned, there was a considerable effort in updating the parameters and typing recently. Personally, I'd push to see if the GAFF2 developers can set up a

Re: [OpenBabel-Devel] Windows + Data directory.

> We can check "obabel -:c1c1 -omol2 >/dev/null" == "1 molecule converted", > or to be more specific the following should be empty: > obabel -:c1c1 -omol2 2>&1 >/dev/null | grep "Cannot open *.txt defaulting > to compiled data." This test seems like it would only work on Linux/UNIX

Re: [OpenBabel-Devel] Windows + Data directory.

> I also had a problem with Data on linux, when I want to compile openbabel > library statically. Don't you think, that it will be a good idea to link the > library By default, the library compiles versions of the data statically. These can be found in data/*.h and used if no data files are

Re: [OpenBabel-Devel] Conda Windows

> If we go for openbabel channel on anaconda.org we > should set it up, I already registered an openbabel organization on anaconda.org. I'm happy to add people/owners as needed. -Geoff -- Attend

Re: [OpenBabel-Devel] Windows + Data directory.

It's easy to fix the _subdir bug. The key question is how we can add testing (e.g., with AppVeyor) to make sure this doesn't regress again. Should we have some sort of test for, e.g., accessing element.txt and returning FAIL if it defaults to compiled data? Thanks, -Geoff > BABEL_DATADIR is

Re: [OpenBabel-Devel] fillUC sets space group to P1?

> I'm just curious. Does anyone know why we are setting the space group to P1 > here in fillUC? I think the intent had been that a full transformation occur. But no, obviously the PDB file doesn't represent P1. Feel free to fix it. Thanks, -Geoff

Re: [OpenBabel-Devel] Treat warnings as errors

> Hopefully we can put some pragmas in the InChI code or do some other > hack (e.g. google says "-isystem") to suppress warnings from those. Since all the InChI code is C, but ours is C++, it’s a matter of setting CXXFLAGS differently than CFLAGS. I already do this for warnings. -Geoff

Re: [OpenBabel-Devel] Pybel error

Please don't send e-mail directly to me. There are many users of Open Babel and Pybel that can help you out. Fundamentally, pybel.py and _openbabel.so, etc. - the Python bindings for Open Babel are not found by the python interpreter. Running "locate pybel.py" might help. I suspect that

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

> I'd like to deprecate babel, but it's up to Geoff whether that's an official > position. Sounds like a good idea. We can deprecate now, and in 2.5 or 2.6, remove it entirely. -Geoff -- What NetFlow Analyzer can do

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

> SMARTS pattern 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. Moreover, there's already OBAtom::MatchesSMARTS()

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

> http://baoilleach.webfactional.com/site_media/ob_api_check/compat_report_21052016.html > It makes a few mistakes here and there but is accurate in general. It's a bit weird about adding optional parameters, e.g. bool Build(OBMol ); becomes bool Build(OBMol , bool stereoWarnings = true);

[OpenBabel-Devel] Hard, Slow, or Tricky Kekule structures

Hi, I have some students working on an efficient (parallel) implementation of Kekule assignment through the perfect weighted match algorithm. https://github.com/ghutchis/parallel-matching Consequently, I'm looking for some nasty aromatic / Kekule structures: 1) Really large (e.g., graphene,

Re: [OpenBabel-Devel] [Open Babel] 1-substituted adamantane InChIKeys

> There are four right? > [john@hal ~]$ obabel -:'CC(C)(C)C(=O)C12CC3CC(CC(C3)C1)C2' --gen3d -omol | > obabel -imol -osmi > CC(C)(C)C(=O)[C@]12C[C@H]3C[C@H](C[C@H](C3)C1)C2 The problem is that these carbons are not, technically chiral - the molecule is symmetric.

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

> I solved the problem of the missing Eigen (eigen3 @3.2.5 is installed), but > still cannot compile openbabel with OpenMP on Mac OS. While I can understand your interest in compiling with OpenMP, there is at the moment, no Apple-supported compiler for OpenMP on Mac. I can compile with GCC on

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