[Avogadro-devel] Moving Translations / i18n to Weblate

For a long time, we've hosted translations on Launchpad (https://translations.launchpad.net/avogadro) - this has been wonderful, since we've gotten dozens of translation and localization contributions. Launchpad is not ideal. It's designed around gettext PO files, and imports translation

[Avogadro-devel] GitHub action buildbot

I spent more time than I probably should getting a GitHub action build matrix going: https://github.com/ghutchis/avogadrolibs/actions/runs/74990496 At the moment, it only builds Ubuntu and Mac versions and uses CPack to save the binaries. I had trouble getting the Windows builds working. >

[Avogadro-devel] Avogadro2 Translations (and Launchpad)

I'd like to really push to get Avogadro2 shipped and 'out the door' - with the new plugin system, it will be much easier for people to contribute scripts, interfaces to other programs, etc. One part of that is making sure we have translations going. We've previously used Launchpad as our

[Avogadro-devel] Building avogadrolibs "core" only

Hi Marcus, I'm working along on the force field code - and wondering if there's documentation on building the "core" parts of avogadrolibs. I have the sense that you do something like this for the Python interfaces - that you build everything except the Qt GUI? This seems like it would be a

[Avogadro-devel] Adding cartoons / ribbons for Avo2

Dear Gaurav and Jonathan, First off, thanks both for coming and giving great talks at the User Group Meeting a few weeks ago, and for Jonathan's pile of patches and pull requests. It's great to see how Avo2 is helping out, and I think there's going to be continuing interest in "gamifying"

Re: [Avogadro-devel] Working as a programmer on Avagadro

Dave, I'm cc'ing the avogadro-devel mailing list as well as Patrick Avery and Marcus on this. I'm quite sure you don't need to build Qt for Windows before compiling OpenChemistry on Windows, but I don't use Visual Studio. (I install a binary version on Mac, which saves loads of time.)

[Avogadro-devel] Using "clazy" and other static analysis with Travis CI?

Once upon a time, KDE offered Krazy - a static analysis tool for KDE/Qt. There's now clazy a tool that uses clang: https://github.com/KDE/clazy/ https://www.kdab.com/uncovering-32-qt-best-practices-compile-time-clazy/ This looks like a *very* useful tool for static analysis for avogadrolibs. I'm

[Avogadro-devel] Community Survey

If you follow @AvogadroChem on Twitter or the new http://discuss.avogadro.cc forum, you'll know that we posted a survey for community feedback. As we reach for Avogadro 2 and 1 million downloads, we’d like to get more input from the broader community. How do you install Avogadro, what you use

Re: [Avogadro-devel] GSoC: Avogadro 2 - Biological Data Visualization

Dear Dale, Thanks for your e-mail and I’m glad to hear from you. You may already have the background to understand different representations (e.g., cartoons, ribbons, etc.) so I apologize if some of the comments below are generic. I wrote this up for others interested in the project. It’s

[Avogadro-devel] v2 Workflow Plugins

I posted a bunch of thoughts for discussion on the forum: https://discuss.avogadro.cc/t/improving-avogadro-v2-workflow-plugins/2645 My goal is that by the end of April, we'll have a full workflow/command API 'handshake' worked out. If people would like to help, I can see a few tasks that would

Re: [Avogadro-devel] (GSoC 2018) MD Proposal

Thanks for the reminder. :-) > Including support for Quantum Espresso with Avogadro is not quite an > idealistic thing to do at the moment, as it will have the same problem as > faced by VASP, i.e. apart from the positions of the various atomic species, > one also needs to provide a couple of

Re: [Avogadro-devel] Google Summer of Code 2018 - GPU Accelerated Calculation of Molecular Surfaces and QM Data

-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/ > On Mar 8, 2018, at 10:52 AM, Yang, Tony <zeyu.yan...@imperial.ac.uk> wrote: > > Dear Geofrrey, >

[Avogadro-devel] Migrating to Discuss.Avogadro.cc

Hi, While I'll continue to respond to these e-mail lists for a while, I'd like to encourage migration to http://discuss.avogadro.cc/ the new Discourse forum for Avogadro. Discourse allows you to get e-mail summaries (like digests for these lists) and reply to topics via e-mail. It also allows

[Avogadro-devel] Avogadro Applying for Google Summer of Code

As we've done for the last few years, Avogadro is working with Open Chemistry to apply for the Google Summer of Code 2018. If you're interested in participating or particularly interested in *mentoring* please let me know. If you have ideas for projects, those are great too. :-) Thanks,

[Avogadro-devel] Realistic Release Roadmaps

It's been entirely too quiet on the list. So let's make some noise. I'd like to discuss how we get Avogadro 2.0 "out the door." The last release was actually a year ago… The roadmap is here: http://wiki.openchemistry.org/Avogadro_Roadmap Most importantly, I'd like to come up with the key bits

Re: [Avogadro-devel] How to change color of atoms

Hi Jianhui, I'm very sorry - I just saw your message. At the moment, the only way to change the default color is with editing the source code. If you'd like some tips on that, please let me know. Thanks and best regards, -Geoff > On Oct 31, 2017, at 10:51 PM, Jianhui Lan

[Avogadro-devel] Fwd: PubChem QC in Avogadro

in Avogadro > Date: July 24, 2017 at 10:57:14 PM EDT > To: geoff.hutchi...@gmail.com > Cc: t-shimaz...@riken.jp, pc...@ml.riken.jp > > Dear Prof. Geoffrey Hutchison, > > We have launched "Public Computational Chemistry Database Project" > http://pccdb.org/ in 2

Re: [Avogadro-devel] Mac build automatically installed in /Applications

> I'd like to just turn the bundle application off, and make a regular unix > app, even on the mac. Any ideas how to do this? I tried setting -D > MACOSX_BUNDLE=OFF in the cmake configuration script, but it still installed > everything into /Applications. Here's my config script: That's going

Re: [Avogadro-devel] Mac build automatically installed in /Applications

> I tried to build my conda recipe for avogadro on my mac laptop, and was > surprised to see the code installing under /Applications rather than in the > conda environment subdirectory where I had expected it. The default is to install in /Applications because that's where Mac apps go. It's

Re: [Avogadro-devel] Conda builds?

> I had been trying to compile v1.1.1 with eigen3. Just switched to the github > version and it passed the cmake step and is now compiling. Fingers crossed! > > Argh. Hopes dashed. > [ 4%] Generating moc_pythonengine_p.cxx >

[Avogadro-devel] Want to Support Avogadro?

Dear Avogadro community, A while ago, I circulated a survey about financial support for Avogadro. The results were very positive - lots of people were willing and interested in contributing to fund Avogadro development and promotion. I talked a bit with Marcus and investigated several options.

[Avogadro-devel] GLSL rendering of implicit functions

I’ve been talking with Ugo Varetto, the former developer of Molekel - he published an article on real-time volume rendering of quantum data. Unfortunately, that code isn’t available, but he was willing to share recent GLSL work on isosurface and volumetric rendering of arbitrary functions:

[Avogadro-devel] Issue Templates

As I was finishing up the new avogadro.cc webpage, I came across GitHub issue templates: https://help.github.com/articles/creating-an-issue-template-for-your-repository/ I think this would be a *huge* help. Here's my current draft - thoughts? - [ ] I believe this to be a bug with Avogadro -

[Avogadro-devel] Avogadro wiki spammed

t to *help*, please let me know. :-) 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/ --

Re: [Avogadro-devel] Regarding GSOC-2017

or partially automate pybind11 along the lines of SWIG. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ > On Jan 21, 2017, at 1:54 PM, Vrushank Upadhyay <uv

Re: [Avogadro-devel] [Avogadro-Discuss] Issue with Eigen3/avogadro1.1

> #error Eigen2-support is only available up to version 3.2. Please go to > "http://eigen.tuxfamily.org/index.php?title=Eigen2; We're well aware. (https://github.com/cryos/avogadro/issues/842 ) Debian has a patch in their repository for

[Avogadro-devel] CJSON in Open Babel

Hi Marcus, As we continue to develop the workflow idea, one obvious help would be to integrate CJSON into Open Babel. I'm willing to do some of the work, since there's already other JSON formats (src/formats/json). I'm curious about multiple coordinate sets and/or conformers. Right now, there

Re: [Avogadro-devel] Workflow Scripts (for Avo2)

> Have you looked at pymatgen? It has a lot of useful features for crystal > structures and some also for molecules as well. Great idea. The pieces aren't fully in place, but there will be a system for workflow plugins to require dependencies. Do you have any first use cases, e.g., "insert

Re: [Avogadro-devel] Selection tool progress

> is much nicer than how we did it before, and it seems like it would be > simple to add to CJSON. I think it's a good idea to add selection to CJSON for a few reasons. One, the concept of "named selections" was in Avo1 but never really used. For example, an enhanced QM (or other) generator

[Avogadro-devel] Roadmap for 1.91?

Hi Marcus, You mentioned previously wanting to get out a new release fairly soon (1.91). Do you have a target date? Dec. 1st? Should we be clear about the roadmap for the release as well as post-1.91 release plans? Thanks, -Geoff

Re: [Avogadro-devel] Avogadro2 Tool Priorities

The patch (https://github.com/OpenChemistry/avogadrolibs/pull/118 ) simply adds priorities and changes the order the tools appear in the toolbar. It doesn't change which tool is default. Avo2 desperately needs a settings dialog, and

Re: [Avogadro-devel] Plugin Repositories & Archives

> CMake just internally includes libarchive, zlib, and libbzip2 here: > https://github.com/Kitware/CMake/tree/master/Utilities > OK. In short, my worries about including libarchive are unfounded. (Sorry, the last time I worked on

Re: [Avogadro-devel] Moving to C++11/14, ramping up devleopment

> Great goal. I think we should lay out some plans for that, e.g., > http://wiki.openchemistry.org/Avogadro_Roadmap I was reading up on the new GitHub projects feature: https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-tools-forums-and-features

Re: [Avogadro-devel] Moving to C++11/14, ramping up devleopment

> I want something everyone feels is usable by Christmas (or > insert your winter celebration towards the end of December). Great goal. I think we should lay out some plans for that, e.g., http://wiki.openchemistry.org/Avogadro_Roadmap I think the most pressing thing would be fragment / residue

[Avogadro-devel] What Service to Use for Community Support

A few weeks ago, I posted a very informal survey about community financial support for Avogadro. The results were very positive, particularly considering that I didn't really "push" the survey very hard (e.g., on the Avogadro webpage, other community forums). I have talked a bit with the

[Avogadro-devel] Chemical JSON Spec

Hi Marcus, I know as part of the GSOC project there were some questions about a more formal spec for CJSON. Considering that I'd like to start adding pieces into Open Babel (and maybe RDKit?) it would be really helpful if there was a more formal write-up. Does one currently exist, e.g. as

Re: [Avogadro-devel] Avo2 - Paste & Python Dialogs

>> - I'm going to take the InputGeneratorWidget out of avogadrolibs / molequeue >> and put it into qtgui/ as InterfaceWidget. It will handle both input >> generators and the new action scripts (i.e., parsing the JSON from the >> scripts) - I will probably add small subclasses to handle the two

Re: [Avogadro-devel] Make Package for Avogadro

> Geoff has some custom scripts he runs that are not in the build > system, I wasn't able to generate a DMG last time I tried in Avogadro > 1, but as Geoff always made the DMG I didn't look into it much more > deeply. On Mac, with v1 I simply run “make install” and then have a script that copies

Re: [Avogadro-devel] CMake Error building MoleQueue on OSX 10.9.5

> I've installed Qt (5.6.0) and Cmake (3.3.1) using anaconda, and followed the > instructions here: That may be the problem. I've had trouble with anaconda (or homebrew) versions of the Qt packages. I'd highly recommend Mac users go for the binary distribution:

Re: [Avogadro-devel] Progress this Week

> I haven't even tried VS 2015, I thought you had a student who had > managed to get it building with 2015 Ethan got Avogadro v1.x building, but is now starting in on Avo2. > I was working on 2013 but was hoping to see some of what that student had > done. I think we need to > get 2015 working,

[Avogadro-devel] Fwd: Progress this Week

I have an undergrad student, who will be working on some features in Avogadro v2. Has there been success at VS2015 compilation? Thanks, -Geoff > I was only able to put in about two hours this week working on building > Avogadro 2. Since I am attending PennApps this weekend, I won't be able to

[Avogadro-devel] Extending Avo2 "Input Generators" to "Modify" scripts

I’ve been talking with Paul Boone, an experienced Python programmer on staff here at Pitt (and soon to be PhD student) about the Python interface to Avo2. Short message - we think it's easy to add script support for a *lot* of use cases without much work. - Scripts could pop up an options

Re: [Avogadro-devel] Rendering Options

> Sorry, missed this mail. It is view configuration, … display types for View > Configuration, clicking on I see that tab, but there is never anything in it. The UI in Avo1 was nice in that it was clear “click here for options” - perhaps the Display Types needs a button in each row like that?

[Avogadro-devel] Avogadrolibs Roadmap

Hi Marcus, As things get rolling more on Avo2, I wanted to ask about some general design / API things. I think we have some people to make progress on a “full” release, but some of the design decisions aren’t always clear. Also, as discussed on the tracker about undo/redo

Re: [Avogadro-devel] Pre-releases for Avogadro 1.2

Please make sure to CC the list. Are you saying that gaff.dat is not in the install directory? (I don't know - I don't use Windows.) The binary was provided by Patrick Avery. I believe VS 2010 was used for this build. -Geoff > On Jun 11, 2016, at 4:57 AM, iwao aoyama

Re: [Avogadro-devel] Avo2 - Downloading from GitHub

> I wonder if we might either use the GitHub APIs We can definitely use the GitHub API via HTTP. The catch is this ties us to GitHub a bit more, while using Git directly makes it easier to point at multiple repositories. It's pretty easy to walk the JSON from the API, e.g.

Re: [Avogadro-devel] Avo2 - Downloading from GitHub

> GNU Octave can download and compile its C++ packages automatically. > Perhaps it can serve as an example? My concern is this requires a C++ compiler from the end-user. On Mac and Windows in particular, that’s not very common. Moreover, while we've offered nice C++ APIs for Avo1, I think the

[Avogadro-devel] Fwd: A final 1.2 Windows binary?

I'm stumped. I had network fetch problems on Mac, but the issue was redirects from HTTP -> HTTPS. That's fixed. I'm not sure where the problem would be for Windows.. > From: Patrick Avery > > Well, I ran a few tests. From what I can tell, the network features haven't >

[Avogadro-devel] Avo2 - Downloading from GitHub

One of my dreams for Avogadro was to facilitate a wide pool of plugins - much like Eclipse or Atom.. (OK, probably smaller scale since this isn’t as wide-spread a tool.) The problem, of course, was that compiled C++ is hard to distribute in a cross-platform way. Right now, Avo2 has support for

Re: [Avogadro-devel] Pre-releases for Avogadro 1.2

> Sorry it took a while, I had less time on the weekend than I thought I would > have. No sweat. I just wanted to make sure I knew the timescale (i.e., that I wanted to get a release out and worst case, we'd have to do a 1.2.1 release to get packaging fixed). >

Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

> So I was just taking another look, and I think all you need assuming > you have the QtGui::Molecule, and the Atom object you want to access: > > RWAtom rwAtom = molecule->undoMolecule()->atom(atom.index()); No, no. It's the reverse. I want the Atom from an RWAtom.. -Geoff

[Avogadro-devel] avogadro-super custom targets?

Hi Marcus, There was a request for an “uninstall” target for openbabel. So I added one. Now, the avogadro-super build fails because there are duplicate custom targets.. Any suggestions to resolve this? Thanks, -Geoff

Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

> I thought that ideally HydrogenTools would operate on the RWMolecule, > but RWMolecule is now a lightweight class. There is not currently a > way to get the Atom from an RWAtom, but the code would be very simple > so if we want to add it we can. Just a follow-up.. Can you point me in the

[Avogadro-devel] Avo2 - no POVRay menu item?

Hi Marcus, We're trying to port some of the VMRL export code to Avogadro 2 - so I thought we should start with the POV-Ray export plugin: qtplugins/povray/ But it doesn't appear in the interface, at least on Mac?! Any ideas? -Geoff

Re: [Avogadro-devel] Avogadro 2 release number simplification/jump

> I assume it won't get to there, but it makes sense to plan for it. .. > GNOME for example starts with X.90 from their release candidates I > think. I agree 100% with starting from 1.90, which I think indicates "not quite 2.0" nicely. I once made a 1.100 release for Open Babel, I don't think

[Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

Hi Marcus, I'm trying to fix up the draw tool so that it does automatic hydrogen adjustment on the atoms in the edit, etc. (The new catch is that it will "snap to" standard bond lengths and ideally angles as well.) But I keep coming back to the pain of the hydrogentools code operating on Atom

Re: [Avogadro-devel] GitHub issue import test

> How many have contact details/any recent activity? So long as they > have a tag we can filter on I think either one works. Many had no contact details at all. For others, there's the challenge of mapping SF user names to GH users. Looking at other projects who have used this approach, they

[Avogadro-devel] GitHub issue import test

I started a test run of importing the Avogadro SourceForge bugs and feature requests to GitHub issues: https://github.com/ghutchis/sfimporttest/issues * It's very difficult to script importing the milestone versions - but it should be easy to make some batch changes (e.g., find the v_1_0 label

Re: [Avogadro-devel] Executing systematic search in source

I think the big question would be what the "difficulty" is. At a quick glance, the code looks OK, although I'm not 100% sure how the systematic search handles constraints. What are you trying to do with the constraints - freeze some atoms? -Geoff > I'm in the process of making my own extension

Re: [Avogadro-devel] [Google Summer Of Code 2016] Project Interest

Some level of chemistry would be extremely useful. The project you mention likely requires less chemistry knowledge, since embedding a Python scripting interpreter in the code requires more coding competence than chemistry background. However, a competitive proposal would likely require some

Re: [Avogadro-devel] Proposal for GSoC

> My research is about photoemission simulations and think it would be useful > to add some features about surfaces in Avogadro. This would require some more > implementation about symmetry in order to create slabs from primitive and > conventional cells. > The symmetry part could also be used

Re: [Avogadro-devel] Hello GSoC-2016

> I'm interested in the project "Python script bindings in Avogadro > 2". I see that there is already a boost-python branch for > avogadrolibs. Are you already settled on boost-python or are > other solutions still considered? Other solutions are definitely open. Indeed, that’s the key question

[Avogadro-devel] Avogadro in Google Summer of Code

Avogadro (and OpenChemistry) has been accepted into the Google Summer of Code for 2016: https://summerofcode.withgoogle.com/organizations/6290185763422208/ http://wiki.openchemistry.org/GSoC_Ideas_2016 If you are a student and interested in doing open chemistry software development this summer

[Avogadro-devel] Windows Build for v1.2

Hi Marcus, My undergrad this term is working on a Windows build (using VS 2015). He's had some problems with variable length array declarations and with linking. I'd like to get a v1.2 build finalized - do you still have the CDash build bot for Windows on v1.x master? Assuming we can get

[Avogadro-devel] Discourse Forum

I have set up an online Discourse forum: http://discuss.avogadro.cc/ * I have migrated past messages to the mailing lists and done general cleanup (e.g., merging people with multiple e-mail addresses). * It should allow OpenID sign-on from Google and GitHub, among others. Ping me if there are

[Avogadro-devel] Discourse and Translations

-and-launchpad-a-comparison-of-features * Transifex: Fedora, Tor, VLC * Pootle: LXDE, LibreOffice I'd be open to other suggestions - particularly if they natively support Qt's .ts files (Launchpad still doesn't.) Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh

Re: [Avogadro-devel] problems with openbabel libraries

It seems like there’s a problem with the Eigen libraries. Perhaps eigen2-dev wasn’t installed? Hope that helps, -Geoff > On Dec 9, 2015, at 5:01 PM, Luciano Costa wrote: > > Hi dear developers, > > I would like to report here maybe what can be a kind of a bug related to >

Re: [Avogadro-devel] Avogadro-1.0 and Eigen2/3

> Also, Anton Gladky has since updated our Eigen3 patch to drop > EIGEN2_SUPPORT and port the 1.0 codebase to Eigen3: Great, that's very helpful. I'll take a look later today. -Geoff --

Re: [Avogadro-devel] Avogadro-1.0 and Eigen2/3

> Or will there be a stable Avogadro-1.2 at some point? As soon as a Gaussian vs. Orca normalization bug is fixed, I will be releasing 1.2.0: https://github.com/cryos/avogadro/pull/31 -Geoff --

Re: [Avogadro-devel] [Openchemistry-developers] avogadrolibs UHF calculation representation

I should comment about STO vs. GTO.. Since we're primarily interested in visualization, it may be worthwhile to simply convert all STO wave functions to GTO via STO-3G coefficients. I don't have the formulas handy, but this would solve a great many issues. For example GAMESS-US will use STO

Re: [Avogadro-devel] Japanese translation and ts (po) file

> std::locale::global(std::locale("japanese")); Can you try a slight patch which I think would be better (i.e., not everyone uses Japanese) to see if it fixes the problem with Kanji filenames on Windows for you? QString lang = QLocale::languageToString(QLocale::system().language());

[Avogadro-devel] New Avogadro Manual

taking screenshots and working through tutorials and step-by-step guides. --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu

[Avogadro-devel] AO with ball-and-stick VdW

I sent this to Marcus previously, but I'll send to the list: Saw this in my Google Scholar report.. They claim to have a very efficient AO technique that can do molecular dynamics.. It would be great to adopt some of the techniques in Avogadro v2. :-)

Re: [Avogadro-devel] Symmetry element rendering

First off, a quick introduction to others - Marcus has been working on the libmsym library, which is now being used in Avogadro V1.x for point group symmetry detection and symmetrization. He's been working on what looks like a cool integration for AvoV2... Was wondering if anyone has some

[Avogadro-devel] Push for Avogadro v1.2 - High Profile Bugs

1.2.0. Ideally, please make sure the bug is listed on SourceForge or GitHub and send me a link. 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

[Avogadro-devel] Travis CI for GitHub

packages that need to be installed for Avogadro v1 (e.g., qt4-dev, libopenbabel-dev, etc.) 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

[Avogadro-devel] SVG Export

I put up a “bounty” to support a ball-and-stick style SVG depiction using Open Babel. I think the results are fairly good and I think with only a bit of work could be adapted to Avogadro. I’m curious to get some feedback about the style. One difficulty might be the atom labels, but I’m open

Re: [Avogadro-devel] japanese translations

A solution I used in Windows XP was to create an i18n forder in Program Files\Avogadro\share\avogadro and copy avogadro_cs.qm and libavogadro_cs.qm generated on a Mac or Linux box in said folder. Yes, we realized that some of the Windows builds did not have the *.qm translations. In

Re: [Avogadro-devel] Japanese translation and ts (po) file

The original Avogadro apparently can not handle multibytes characters in a file name and a directory path name. I think it is necessary to add some source codes to handle Japanese characters. It might be same for Chinese version. How did you deal? My Chinese students didn't seem to

Re: [Avogadro-devel] Japanese translation and ts (po) file

I had updated the ts file with Qt linguist for my own usage. Can I contribute with Qt ts file (or converted GNU GetText po file), instead of inputting on the Launchpad ? Of course. Launchpad will actually take a PO upload, but if you'd rather just send it to me, I'll handle the merge.

[Avogadro-devel] Insert Fragment / Crystal Library

In Avogadro v1.x, we had a set of common molecular fragments and a crystal library. I used a custom Qt class to give an outline view of the subdirectories with a search form that responded to various names. The big drawback was that it wasn't easy (or in some cases possible) to add your own

Re: [Avogadro-devel] Getting Avo2 to release

Selection and residues, along with some rendering features seem most critical to me (we have stick but it has a rendering bug I need to dig into). I'd put selection slightly above residues because I think it's critical for copy/paste/clear and moving fragments. (Which I guess also means that

Re: [Avogadro-devel] Getting Avo2 to release

Thoughts? Concerns? Something I've missed? Oh, I forgot color schemes and custom colors. My feeling is that can fall to nice to have for v2.1? -Geoff -- ___ Avogadro-devel

[Avogadro-devel] Getting Avo2 to release

I've been trying to sift through Avogadro v2 and trying to determine what needs polish and what are missing features needed for a release. I'd like to outline things that I think are critical versus nice to have, but could wait for 2.1 Thoughts? Concerns? Something I've missed? -Geoff

Re: [Avogadro-devel] Avogadro2 Extensions Priorities

I don't think it is very hard to do it, but maybe we failed to add the right prorities. The intent was to order things with priority, and fallback to alphabetical. We could add a convenience to increment priority by 1 for each action if that is desired. Well, I tried setting the priority on

[Avogadro-devel] Avogadro2 Extensions Priorities

I'd like to ask about Avogadro2 extensions and priorities. In Avogadro 1, plugins were loaded in alphabetical order (sorted by the filesystem) and then the extension provided an ordered list of commands. This meant that the extension basically was responsible for building out a menu in-order.

Re: [Avogadro-devel] Editing, viewing, and making things more fluid again

Are you talking about how the user should do this with respect to mouse button-drag and modifier keys? If so, it would be interesting to this ... information above. Right now in Avogadro v2 (git master) you have to pick an edit or view widget with a button, then open the file, etc. Compared

Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

It looks Avogadro2 will be using Chemical JSON whenever possible to transfer data. Do you think this would be possible with cclib? http://wiki.openchemistry.org/Chemical_JSON Right now, there aren't really specifications for computational data (MO, basis, etc.) in Chemical JSON. So CML would

Re: [Avogadro-devel] Ambient Occlusion in Avogadro 2: update

As some may have seen already, Avogadro 2 has a Van der Waals spheres display type with Ambient Occlusion. However, this is not nicely integrated with the overall rendering code and this mail contains information on how I plan to integrate this. I'm currently moving so I plan to start

Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

I think Albert was talking about a glue layer for quantum io, not for regular input. Regular input is probably best handled through Open Babel, since that already handles bond perception, typing, etc. Right now, Avogadro v1 and v2 have separate code for reading basis set and MO information

Re: [Avogadro-devel] Migrating website to Jekyll

on the The Avogadro Paper link (http://dx.doi.org/10.1186/1758-2946-4-17 http://dx.doi.org/10.1186/1758-2946-4-17). Best wishes, Jens On 30 November 2014 at 18:09, Geoffrey Hutchison geoff.hutchi...@gmail.com mailto:geoff.hutchi...@gmail.com wrote: Short summary: I have a beta site at http

[Avogadro-devel] Google Summer of Code

really like to see Avogadro apply and get a student or three funded again. So I'm curious for general ideas / brainstorming, and people who might be willing to serve as mentors. Thanks, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email

Re: [Avogadro-devel] Google Summer of Code

Personally, I'd like to see more interoperability between the open-source chemistry apps, including avogadro, openbabel and cclib Indeed, I think one big push is for Avogadro v2 to use cclib to read QM file formats (e.g., MO coefficients, basis set, etc.) rather than implementing them all in

[Avogadro-devel] Migrating website to Jekyll

Short summary: I have a beta site at http://avogadro.github.io/ (not the permanent home) and want feedback I mentioned this previously, but I've made significant progress in extracting everything from MediaWiki and getting a functional Jekyll site going. I'm tired of maintaining MediaWiki, and

Re: [Avogadro-devel] Avogadro v2 Roadmap - GitHub Wiki

Do we want to port the cartoon rendering from 1.0? This can be done (by me) in a reasonable timeframe. Yes, I think that would be a great start. -Geoff -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT

Re: [Avogadro-devel] Avogadro v2 Roadmap - GitHub Wiki

Coming from a more biological angle, I think cartoon rendering should definitely be an early priority. Avogadro can now visualise much larger systems, but it needs the cartoon rendering to make it really useful to a biologist. Agreed. This is why residue support is also critical. The

Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

It's worth noting that if you want to keep the wiki functionality but move it into GitHub, Indeed, I think this would be a nice way to separate out *developer* documentation and user documentation. The *dev* documentation can be put into the GitHub repository wiki. Also, if you can get the

Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

OK, a first pass is here: https://github.com/AvogadroChem/AvogadroChem.github.io e.g. https://github.com/AvogadroChem/AvogadroChem.github.io/blob/master/features.md This includes all the images I could grab, although I'm sure there are errors. It's not a functioning site yet, but if someone has

[Avogadro-devel] Migrating Wiki to GitHub Pages

Hi everyone, Despite the low level of action, I’ve been spending a lot of time *thinking* about Avogadro and the future. There are quite a few exciting things, although it may take a while before they fully appear. One thing I can talk about is pushing for tutorials and manuals. The University

Re: [Avogadro-devel] Switching to GitHub pull requests for review/merge?

Geoff gave me a +10 off-list, I will work on clearing the Gerrit Sorry, I thought that was on-list. Here's the message: We've been using GitHub pull requests for Open Babel and I lurk on a few other projects (i.e., cclib) where it works really well. I think a big advantage is the public

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