Re: [Avogadro-devel] Version 1.1 Enhancements

On Tue, Apr 19, 2011 at 11:34 AM, Geoffrey Hutchison geo...@pitt.edu wrote: I started a webpage for the 1.1 release, listing new features. I know it's incomplete -- since we've been working on this ever since branching for 1.0, please add any new functionality to the page:

[Avogadro-devel] Avogadro 1.0.2 tagged

Hi, As promised, I created the 1.0.2 tag for Avogadro. I have uploaded source tarballs, and a Windows installer without Python support. I am not quite sure how we make the Mac drag and drop installer, and so didn't do that (although I have a build that works fine locally in an app. I was out for

Re: [Avogadro-devel] Avogadro 1.0.2, 1.0.3 on Monday and then onto the 1.1 series

On Sun, Apr 24, 2011 at 10:15 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: As I already announced, Avogadro 1.0.2 was tagged, and released with a new Windows package. Oh, before I forget, are there wiki pages for the releases? We'll also need to bump the file for the update-checker

Re: [Avogadro-devel] Building Avogadro on OpenBSD

On Tue, Sep 20, 2011 at 10:43 AM, David Lonie lonieda...@gmail.com wrote: Hi Anthony, Run make VERBOSE=1, and look at the gcc/g++ commands that are being executed to see what include dirs (-I/include/path) are being searched. HTH, Dave On Sun, Sep 18, 2011 at 12:54 PM, Anthony J. Bentley

Re: [Avogadro-devel] Insert Crystal feature vs. File-Import

On Mon, Nov 7, 2011 at 12:53 PM, David Lonie lonieda...@gmail.com wrote: On Mon, Nov 7, 2011 at 12:12 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I posted an insert crystal feature to give Avogadro a crystal library of common structures, much like the molecular fragment database. I'm now

Re: [Avogadro-devel] Avogadro OSX Port Question

On Mon, Nov 7, 2011 at 12:04 AM, Eric Jang ericjang2...@gmail.com wrote: Hello, I am wondering if anybody has gotten compilation of Avogadro to work using XCode? I would like to study the program by stepping through the code and learning how to do it using XCode would really help. To my

Re: [Avogadro-devel] Bug in Avogadros CMake-System?

On Wed, Nov 23, 2011 at 8:07 AM, Carsten Niehaus cnieh...@gmx.de wrote: Hey, I just got this request https://git.reviewboard.kde.org/r/103209/#review8407 I cannot say anything about it, it is beyond me :) Hi, I need to recover my password to access reviewboard...but the fix is a bad one.

Re: [Avogadro-devel] Crashing bug report -- MoleculeDocument?

On Fri, Dec 16, 2011 at 11:48 AM, David Lonie lonieda...@gmail.com wrote: Any thoughts or opinions? This would be a large scale change, and I'm not sure what version something like this should be slotted for. But as evidenced by the bug report, we are turning away a lot of potential users with

Re: [Avogadro-devel] Gerrit branches

On Wed, Dec 21, 2011 at 5:11 PM, David Lonie lonieda...@gmail.com wrote: On Wed, Dec 21, 2011 at 4:25 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: You can look at our test deployment here, http://reviewtest.source.kitware.com:81 This is also where we have been testing out

Re: [Avogadro-devel] zlib cmake error building avogadro-squared on ubuntu

Hi Jens, On Wed, Jan 4, 2012 at 9:31 AM, Jens linuck...@gmail.com wrote: Hey Marcus! Many thanks for that. I was using cmake 2.8.0. I downloaded the latest version (2.8.7) from the website and built it from source and it then worked fine. Maybe the required cmake version for

[Avogadro-devel] Gerrit updates and replication to other locations

Hi, I wanted to let you all know that Gerrit was upgraded recently, it appears that there were a few teething issues with the replication process after this update. These are now resolved, and all new changes should be replicated automatically. You should review code, and once it is approved and

Re: [Avogadro-devel] Gerrit updates and replication to other locations

On Sun, Jan 22, 2012 at 2:54 PM, Geoff Hutchison ge...@geoffhutchison.net wrote: submit topics, and that will create an appropriate merge commit, which will be pushed to replicated locations (normally within minutes). So does that mean that we should review a whole topic branch and then submit

Re: [Avogadro-devel] compile error on Debian testing...

On Sun, Feb 5, 2012 at 2:33 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Egon, On Sat, Feb 4, 2012 at 2:08 PM, Egon Willighagen egon.willigha...@gmail.com wrote: Hi all, I started of today looking into Gerrit for the CDK, and found that Avogadro was using it already... good

Re: [Avogadro-devel] Change in avogadro[master]: Compilation fixes for Python wrapping.

On Mon, Feb 6, 2012 at 7:38 AM, Egon Willighagen egon.willigha...@gmail.com wrote: HI devs, On Sun, Feb 5, 2012 at 9:02 PM, Marcus D. Hanwell (Code Review) rev...@kitware.com wrote: I'd like you to do a code review.  Please visit    http://review.source.kitware.com/4169 to review

Re: [Avogadro-devel] Gerrit / Google OpenID issues?

On Tue, Feb 7, 2012 at 3:57 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I'm trying to review / approve some patches on Gerrit and I'm having a weird issue signing in with my Google OpenID. I consistently get The server could not process your request. But there's no additional information.

[Avogadro-devel] Compile failures on the dashboard

Hi, I think it would be great to get a 1.1.0 release out sometime in the near future. I was looking at a couple of compilation failures on the dashboards, and have addressed some of them here, http://review.source.kitware.com/#/t/36/ Albert just submitted a patch I merged to address something

[Avogadro-devel] OpenQube, Avogadro and Eigen 3

Hi, I wanted to let the list know that I just uploaded a patch porting OpenQube to use Eigen 3. Avogadro maintains a snapshot of it, and can optionally build against the system installed version. In the new work we are doing we want to use Eigen 3, and that was the motivation for porting to the

Re: [Avogadro-devel] Compile failures on the dashboard

On Tue, Feb 14, 2012 at 9:08 AM, David Lonie lonieda...@gmail.com wrote: On Mon, Feb 13, 2012 at 4:16 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: I think it would be great to get a 1.1.0 release out sometime in the near future. I was looking at a couple of compilation failures

Re: [Avogadro-devel] Questions about Avogadro

On Sun, Feb 19, 2012 at 3:44 PM, Donald Ephraim Curtis dcur...@milkbox.net wrote: Hey guys, long time mailing the list. So the other day I built Avogadro from scratch, starting off by downloading the latest Eigen and OpenBabel from code repositories.  I built both successfully but had

Re: [Avogadro-devel] python boost unresolved overloaded function type

On Mon, Feb 27, 2012 at 2:23 PM, Gary Kedziora gkedzi...@gmail.com wrote: I have having trouble compiling ~/libavogadro/src/python/fragment.cpp.  The issue appears to be that the python boost template function arguments can not be resolved when there is a constant and non constant version.  

Re: [Avogadro-devel] Python SIP module

Hi Gary, On Thu, Mar 1, 2012 at 10:56 AM, Gary Kedziora gkedzi...@gmail.com wrote: On Tue, Feb 28, 2012 at 3:03 PM, Gary Kedziora gkedzi...@gmail.com wrote: Hi, cmake/modules/PythonDeps.cmake is having trouble finding SIP on my system.  The sip.h on my system is in a nonstandard place.  I

Re: [Avogadro-devel] How to turn off graphics?

On Tue, Mar 13, 2012 at 12:26 PM, David Lonie lonieda...@gmail.com wrote: Hi Divya, On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divne...@umail.iu.edu wrote: I need avogadro to perform minimization and some other operations on proteins. I'm not sure how you would perform any

Re: [Avogadro-devel] Problem with Gerrit

Hi Tim, On Sun, Mar 18, 2012 at 11:45 AM, Tim Vandermeersch tim.vandermeer...@gmail.com wrote: Hi, I pushed a patch to gerrit but it doesn't show up on the webpage. When I try to push it again it says there is no Change-Id so I think the patch was uploaded correctly. Any ideas what might

[Avogadro-devel] Avogadro 1.1.0 rc next week

Hi, Geoff and I were chatting on IRC - the 1.1.0 release is well overdue. I was going over patches this morning. I would like to ask anyone who has pending patches they would like in the 1.1.0_rc1 to get them submitted to Gerrit ASAP. I will make a tag early next week (depending on feedback) and

Re: [Avogadro-devel] Avogadro 1.1.0 rc next week

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: We were just talking about this. I will make a tag/tarball now and let's start testing this out. Any chance I can put in the minor changes David requested for the slab builder? Is that the topic on Gerrit? I

Re: [Avogadro-devel] Avogadro 1.1.0 rc next week

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: We were just talking about this. I will make a tag/tarball now and let's start testing this out. Any chance I can put

Re: [Avogadro-devel] Avogadro 1.1.0 rc next week

Marcus D. Hanwell, Ph.D. RD Engineer, Kitware Inc. (518) 881-4937 On Wed, May 2, 2012 at 12:17 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison ge

Re: [Avogadro-devel] Bugfix installing avogadro-squared

On Wed, May 16, 2012 at 5:28 AM, Anders Steen Christensen ande...@nano.ku.dk wrote: Hey boys Avogadro-squared wouldn't compile because the zlib tarball from zlib.net was no longer there. Here's a patch. Hi, Sorry I missed this, I will get that applied and update the submodules while I am at

Re: [Avogadro-devel] [ avogadro-Bugs-3530795 ] File-Import-Insert Crystal segfaults

On Wed, May 30, 2012 at 10:52 AM, Michael Banck mba...@gmx.net wrote: On Wed, May 30, 2012 at 10:40:31AM -0400, Geoffrey Hutchison wrote: I think both things are important -- disable the menu item when no files are available. My concern about the source tree is knowing where that is. I'm not

Re: [Avogadro-devel] Cottrell Scholar's Meeting

On Wed, Aug 8, 2012 at 3:08 PM, Geoffrey Hutchison geo...@pitt.edu wrote: Before I forget, a few weeks ago, I gave a demo at the Cottrell Scholar's meeting -- an award given to non-tenured university faculty with strength in research and education. Avogadro was mentioned quite prominently:

[Avogadro-devel] Avogadro paper published in provisional form

Hi, In case anyone missed it, I am very pleased to announce that the Avogadro paper was published in provisional form today, http://www.jcheminf.com/content/4/1/17 It was a long time in the making, thanks to everyone who contributed to the paper and to Avogadro. It is open access, so anyone can

Re: [Avogadro-devel] Avogadro 1.1.0 tagging

On Tue, Sep 4, 2012 at 11:49 AM, Geoff Hutchison ge...@geoffhutchison.net wrote: I think we are more than ready to release once we have the Mac package. This is the first in the beta series to stabilize for a 1.2.0 release. I would like to get some of the pending changes on Gerrit merged (and

Re: [Avogadro-devel] Avogadro 1.1.0 tagging

On Tue, Sep 4, 2012 at 1:10 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Tue, Sep 4, 2012 at 11:49 AM, Geoff Hutchison ge...@geoffhutchison.net wrote: I think we are more than ready to release once we have the Mac package. This is the first in the beta series to stabilize

[Avogadro-devel] Avogadro 1.1.0 Released

We are very proud to announce the availability of Avogadro 1.1.0. Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows,

Re: [Avogadro-devel] Upgrading SourceForge for Avogadro

On Wed, Sep 12, 2012 at 1:32 PM, Geoffrey Hutchison geo...@pitt.edu wrote: One thing we should consider with the release of 1.1.0 is to upgrade Avogadro to the new SourceForge version: https://sourceforge.net/p/upgrade?search=avogadro I think the improved tracker would be great for handling

Re: [Avogadro-devel] Avogadro Paper Accesses

On Fri, Sep 14, 2012 at 10:35 AM, Geoffrey Hutchison geo...@pitt.eduwrote: I'll admit I've been very intrigued by the # of accesses statistic from J. Cheminf. I wish more journals showed this -- it's a very interesting way of measuring impact of particular articles. Thanks to Noel O'Boyle's

Re: [Avogadro-devel] 300,000 Downloads

On Sun, Jan 27, 2013 at 1:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I was pulling up statistics on Avogadro for an NSF proposal, and saw that we finally broke the 300,000 download mark! In 2012, there were ~100,000 downloads alone.

Re: [Avogadro-devel] Regarding request for suggestion.

On Sun, Feb 24, 2013 at 11:41 PM, Sujit Tangadpalliwar sujit_tangadpalli...@persistent.co.in wrote: I am using your software Avogadro since a month as it having multiple functionality like visualization, molecule editor, optimization structure

Re: [Avogadro-devel] painter

On Fri, Mar 1, 2013 at 1:31 PM, Marc-André Dubois ma.dub...@me.com wrote: Hi everyone, I would like to draw a sphere in the molecule render area of avogadro. I simply tried to test this command: gl-painter()-drawSphere(center,13.0); where gl is my GLWidget, but I

[Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

Hi, We have talked about this offline, and at times on the list. As many of you already know we are working on a rewrite of Avogadro, and we are preparing to make an initial alpha release. It features many great new features, but does not yet have feature parity with Avogadro 1.x. Avogadro 2 is a

[Avogadro-devel] Avogadro relicensing agreement update

Hi, Just a quick update from the replies I have received as far as agreement to relicensing goes. Those who have replied positively (one or two off-list, hopefully they will follow up with on list soon), Marcus D. Hanwell Casper Steinmann David Lonie Geoffrey Hutchison Jens Thomas Matthew

Re: [Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

On Mon, Mar 18, 2013 at 11:30 AM, Benoit Jacob jacob.benoi...@gmail.com wrote: Dear Avogadro developers, Yes, I agree to have all the code that I contributed to Avogadro relicensed to the 3-clause BSD license. Also, I would suggest moving to Eigen 3 if you haven't already: it is now

Re: [Avogadro-devel] [Avogadro-Translations] Avogadro in Spanish for Windows

On Fri, Apr 5, 2013 at 2:47 PM, Louis Ricard louis.ric...@polytechnique.edu wrote: Hi all, This is a recurrent problem for Windows users: Windows does not know i18n and, consequently, only english menus are available. Since the Windows version is not compiled with internationalization

[Avogadro-devel] First Avogadro 2 beta release

Hi, I wanted to let people on these lists know that we just made our first beta release of Avogadro 2, along with MoleQueue and MongoChem. Please see the blog post here, http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html We have created binary installers for Windows and

Re: [Avogadro-devel] First Avogadro 2 beta release

On Fri, Apr 12, 2013 at 9:29 AM, David Lonie david.lo...@kitware.com wrote: Hi Jens, On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote: Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very

Re: [Avogadro-devel] Avogadro 1.1.0 Released

On Fri, Apr 26, 2013 at 11:13 AM, Michael Banck mba...@debian.org wrote: Hi, On Wed, Sep 12, 2012 at 02:07:21PM -0400, Marcus D. Hanwell wrote: We are very proud to announce the availability of Avogadro 1.1.0. [...] Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.0

Re: [Avogadro-devel] Packmol, Symmol and other Fortran through Webapps

On Fri, May 24, 2013 at 4:49 AM, Jens linuck...@gmail.com wrote: On 23 May 2013 18:15, Geoffrey Hutchison geo...@pitt.edu wrote: I've been silent on the lists, since I'm hard at work getting tenure (the package gets submitted in early August). But I had a brainstorm about some of the

[Avogadro-devel] CML, NWChem, FoX, Avogadro paper

Hi, I wanted to point out our paper (part of the same special issue as the Avogadro paper) was released recently. It discusses the use of CML produced by NWChem using FoX and visualized in Avogadro. www.jcheminf.com/content/5/1/25 We should hopefully see releases of NWChem soon that can output

Re: [Avogadro-devel] Unable to configure OS X installation directory away from /Applications/Avogadro.app...

On Mon, Sep 2, 2013 at 1:33 AM, Christian Herbig c.her...@me.com wrote: I sincerely hope this is a question that can easily be answered, but I cannot at all figure out how to change the final installation directory from /Applications/Avogadro.app to /Applications/MacPorts/Avogadro.app. I

Re: [Avogadro-devel] Eigen3 Support

Hi Geoff, On Mon, Sep 30, 2013 at 8:17 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I had a little time to fiddle this afternoon and I've push a patch to Gerrit that allows building against Eigen3 using the support mode. This means that Eigen3's API is not yet supported in Avogadro 1.1.x

[Avogadro-devel] Avogadro 2 0.7.0 Released

We are very proud to announce the availability of Avogadro 2 0.7.0. Avogadro 2 is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for

[Avogadro-devel] Avogadro 1.1.1 Released

We are very proud to announce the availability of Avogadro 1.1.1. Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows,

Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I can take a look at this, and will see if I can improve it. The report doesn't reference what version you are referring to, but I presume 1.1.1? We have both a 512x512 icon and an SVG version, so this

Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

On Mon, Dec 23, 2013 at 2:41 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I can take a look at this, and will see if I can improve it. The report doesn't reference what version you are referring

Re: [Avogadro-devel] Building Avogadro2 w/o MoleQueue on Arch Linux-64bit

On Sun, Dec 29, 2013 at 5:12 AM, Mark Lee m...@markelee.com wrote: Salutations! I have been trying to build Avogadro2 (to test it out) on my Arch Linux 64 bit system. However, while building avogadrolibs-0.7.2; I get the following error from CMake: snip Is there a way to disable the

Re: [Avogadro-devel] avogadro 1.1.1: Building with Eigen3 fails

On Tue, Dec 31, 2013 at 8:55 AM, Daniel Leidert daniel.leid...@wgdd.de wrote: Hi there, I'm speaking as part of the Debian package maintainers of avogadro. The latest release 1.1.1 fails to build with Eigen3. The reason is, that Eigen2 is still required, e.g. in

Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote: Also, I had to add an include path for Eigen to fix building, do I have to make a separate branch for that single commit? I'm not sure why that (adding an Eigen include path) would be necessary. That should be covered by

Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

On Tue, Feb 4, 2014 at 10:45 AM, Jure Varlec jure.var...@ki.si wrote: On Tuesday 04 of February 2014 09:56:01 Marcus D. Hanwell wrote: Are you building with Eigen 2 or 3? I just looked at master, and libavogadro/src/CMakeLists.txt adds it to the include directories, the same is not true

Re: [Avogadro-devel] Avogadro 1.1.x and Linux Distributions

On Fri, Aug 29, 2014 at 6:58 PM, Michael Banck mba...@debian.org wrote: Hi, On Fri, Aug 29, 2014 at 04:51:49PM -0400, Geoffrey Hutchison wrote: Any progress on this? The Debian freeze is approaching in a couple of months, so I it would be nice to include Avogadro-1.2.0 into the next

Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

Hi Geoff, Sorry, crazy travel schedule, so didn't get this finished as soon as I had hoped. I am working on some changes to make the conversion much simpler, and to alleviate the UI issue. As I said at the time - totally agree, and not pushing to keep the current UI. I think it was a necessary

Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

, bigger hard drive too). I will have some time to actually work on this in the coming days though, apologies on the delay - I hadn't factored in spending so much time on real life stuff... Marcus On Thu, Sep 4, 2014 at 9:31 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Geoff, Sorry

Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

On Mon, Sep 8, 2014 at 10:14 AM, Defusco III, Albert A defu...@pitt.edu wrote: Good morning, Let me add a bit to this discussion as well. I've been working on the crystallography extension in Avogadro2 and I find it exceeding difficult to use the CrystalTools while editing or creating

Re: [Avogadro-devel] Discourse / Forum Interface

On Tue, Oct 7, 2014 at 12:46 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I've been looking around at web forums, since I see a lot of current undergrads and grad students (i.e., users) don't use e-mail much (much less mailing lists). There are multiple packages and I'm open to

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

On Mon, Oct 6, 2014 at 10:34 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi, Would there be any objections to switching to GitHub pull requests for development? The Kitware instance of Gerrit will be upgraded at some point, removing the topic branch functionality. Gerrit feels

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

On Thu, Oct 16, 2014 at 4:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote: 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.

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

I turned on wiki and issues for the repo if that helps. The GitHub wikis are backed by git, and have editing facilities built in, so that might be the easiest (I haven't used the GitHub wikis much, but willing to give it a try). Marcus On Fri, Oct 17, 2014 at 1:47 PM, Patrick Fuller

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

On Thu, Dec 11, 2014 at 4:14 PM, Defusco III, Albert A defu...@pitt.edu wrote: Hi guys, Would good project be to re-wire Avogadro to use cclib instead of relying on the quantumio in Avogadro2? I'm very much in favor of adding visualization capabilities for QuantumEspresso and CP2K. You

Re: [Avogadro-devel] Google Summer of Code

On Mon, Dec 8, 2014 at 3:00 PM, Michael Banck mba...@gmx.net wrote: On Mon, Dec 08, 2014 at 10:53:50AM -0500, Geoffrey Hutchison wrote: The deadline for applying to be a mentoring organization for Google Summer of Code is fast approaching. I'm not sure precisely where to hang our hat (e.g.,

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

On Thu, Dec 11, 2014 at 11:36 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: 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

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

Albert, I think CML will continue to be very much a first class citizen too. JSON feels much easier to change/augment, and Python support for JSON is very good - it would be great to add it, but I don't think it is critical. We could add some simple Python glue too, the format is super-simple.

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

Hi, So I slacked off a lot over the Christmas break, but have been working on a few patches and thinking about the overall data architecture in the Avogadro 2 application. We spent quite a while thinking about the design, and I looked at a lot of what went well and not so well in Avogadro 1. I

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

On Tue, Jan 6, 2015 at 12:03 PM, Michael Banck mba...@gmx.net wrote: On Tue, Jan 06, 2015 at 11:05:15AM -0500, Marcus D. Hanwell wrote: What doesn't work at all well is the edit/view GL widget, and the tough/hard line between editing a molecule/viewing it. I am working on merging the two

Re: [Avogadro-devel] Google Summer of Code

Hi, To update the list, we were not selected this year. I got feedback from Google which was very positive and encouraged us to apply again next year. They only accepted 137 organizations this year (down from a high of 190 last year). We had some great ideas, and we will continue to work on links

Re: [Avogadro-devel] Getting Avo2 to release

On Thu, Jun 4, 2015 at 4:07 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: 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

Re: [Avogadro-devel] subclass QColumnView

On Wed, Jun 3, 2015 at 10:55 AM, Defusco III, Albert A defu...@pitt.edu wrote: Hi everyone, I am nearing completion of my space group dialog. You can see the current state on GitHub https://github.com/AlbertDeFusco/avogadrolibs/tree/spg-rw The next thing I need to do is remove the final

Re: [Avogadro-devel] Require C++11/dropping Boost fallback

On Wed, Jun 3, 2015 at 6:50 PM, Michael Banck mba...@debian.org wrote: On Wed, Jun 03, 2015 at 01:20:01PM -0400, Geoffrey Hutchison wrote: Debian stable (jessie) ahs GCC 4.8 and 4.9, but it got released very recently and many are still on oldstable (wheezy) with GCC 4.7. I guess your

Re: [Avogadro-devel] Volume Rendering

On Thu, Jun 11, 2015 at 1:12 PM, Barry Moore moore0...@gmail.com wrote: Dear All, I recently saw Volume Rendering in the Getting Avo2 to release email and wanted to start some discussion. I recently exposed the Gaussian Cube file type to render MOs (pull request was submitted, including an

Re: [Avogadro-devel] Getting Avo2 to release

On Wed, May 27, 2015 at 3:55 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: 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? I have some time this next couple of weeks to take a stab at

Re: [Avogadro-devel] Avogadro2 Extensions Priorities

On Thu, May 21, 2015 at 3:43 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: 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

Re: [Avogadro-devel] Symmetry element rendering

On Wed, Aug 19, 2015 at 11:26 AM, Marcus Johansson mcode...@gmail.com wrote: Hi Was wondering if anyone has some input on rendering symmetry elements in Avogadro v2. There is a need for “disc” (mirror plane) and “vector” (rotation axis) geometries as well as alpha in order to make things

Re: [Avogadro-devel] Build Avogadro in Windows from source. MinGW or MSVC?

On Mon, Nov 16, 2015 at 7:13 AM, Carlos Salgado wrote: > Dear all, > > I am trying to build the developer version of Avogadro in Windows, but I am > not sure if I have to use MSVC or MinGW, and the corresponding version of > Qt. I have build it in UNIX with

Re: [Avogadro-devel] New Avogadro Manual

On Mon, Aug 31, 2015 at 4:51 PM, Geoffrey Hutchison wrote: > Thanks to support from the University of Pittsburgh Department of Chemistry, > there is a new manual for Avogadro: > http://ghutchis.gitbooks.io/avogadro/ > > You can find the images and Markdown on GitHub,

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

Adding Avogadro developers list to CC, this is probably most appropriate there. On Mon, Sep 14, 2015 at 9:14 AM, Bryce Anderson wrote: > First of all I should state my motivations: what I want is proper plotting > of UHF wave functions including being able to select

Re: [Avogadro-devel] Discourse and Translations

On Fri, Jan 1, 2016 at 1:06 PM, Geoffrey Hutchison wrote: > Happy New Year! > > I'm looking into forum options (e.g., Discourse vs. Biostar). Seems like both > can import mbox archives, so I think a key question would be setting up the > Docker instance for Discourse,

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

On Thu, Jun 9, 2016 at 1:57 PM, Geoffrey Hutchison wrote: >> 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 >

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

On Thu, Jun 9, 2016 at 1:25 PM, Geoffrey Hutchison wrote: >> 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,

Re: [Avogadro-devel] avogadro-super custom targets?

Hi Geoff, On Wed, May 25, 2016 at 2:51 PM, Geoffrey Hutchison wrote: > 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

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

On Fri, May 27, 2016 at 11:22 AM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison > <geoff.hutchi...@gmail.com> wrote: >>> I thought that ideally HydrogenTools would operate on the RWMolecule, >>>

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

On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison wrote: >> 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

Re: [Avogadro-devel] Avogadrolibs Roadmap

On Wed, Jun 15, 2016 at 3:44 PM, Geoffrey Hutchison wrote: > > - Are there general or specific “loose threads” in the code? It seems like > there are some needs for batch undo/redo in RWMolecule, for example. I would like to investigate grouping commands, and naming

Re: [Avogadro-devel] Windows Build for v1.2

Hi Geoff, On Wed, Jan 13, 2016 at 2:21 PM, Geoffrey Hutchison wrote: > 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. Some of the topics merged

Re: [Avogadro-devel] Avogadro v2 Roadmap

On Wed, Mar 16, 2016 at 4:01 PM, Geoffrey Hutchison wrote: > Since there's more interest in pushing for an Avogadro v2 "full" release in > 2016 (e.g., fall?) I wanted to start a roadmap. > http://wiki.openchemistry.org/Avogadro_Roadmap > > The text came from some

Re: [Avogadro-devel] Hello GSoC-2016

On Mon, Mar 14, 2016 at 10:01 AM, Reinis Danne wrote: > Two questions came up (Python binding project). > > 1. Is it ok to relay on C++11 compiler? A search showed that > there was this discussion before and it was decided that it is ok > to rely on the presence of C++11

Re: [Avogadro-devel] Hello GSoC-2016

On Mon, Mar 7, 2016 at 9:58 AM, Geoffrey Hutchison wrote: >> 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

Re: [Avogadro-devel] GitHub issue import test

On Sun, Apr 24, 2016 at 10:27 AM, Geoffrey Hutchison wrote: > 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

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

On Thu, May 12, 2016 at 2:51 PM, Geoffrey Hutchison wrote: > 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?!

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

On Wed, May 11, 2016 at 3:49 PM, Michael Banck <mba...@debian.org> wrote: > On Wed, May 11, 2016 at 03:43:19PM -0400, Marcus D. Hanwell wrote: >> So I had one or two queries recently that made me realize I should >> have done a better job on less ambiguous version number

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

Hi, So I had one or two queries recently that made me realize I should have done a better job on less ambiguous version numbering for Avogadro 2 releases. I would like to make the next Avogadro 2 release 1.90, and then after that 1.91, 1.92, 1.93, etc until we feel good with sticking a 2.0

Re: [Avogadro-devel] "Active" Molecules Emit Interface Updates?

On Thu, May 5, 2016 at 2:13 PM, Barry Moore wrote: > All, > > I have been thinking about upgrades to the surfaces interface in Avogadro 2, > but it brought me back to the "Molecules" widget (bottom left). Currently, > it doesn't really do much but I think this would be a

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

On Tue, Aug 2, 2016 at 5:52 PM, Geoffrey Hutchison wrote: > 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

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